From 5159afa2341ecf09cba77a96e5b3a54a8eb49cc8 Mon Sep 17 00:00:00 2001
From: Remi PLANEL <rplanel@pasteur.fr>
Date: Mon, 20 Nov 2023 16:15:15 +0100
Subject: [PATCH] Add mermaid experimental validation
---
.gitignore | 2 +-
.gitlab-ci.yml | 5 +-
Dockerfile | 12 +-
components/content/ListSystems.vue | 7 +-
components/content/Mermaid.vue | 40 +
content/3.defense-systems/abia.md | 31 +-
content/3.defense-systems/abib.md | 27 +-
content/3.defense-systems/abic.md | 66 +-
content/3.defense-systems/abid.md | 30 +-
content/3.defense-systems/abie.md | 28 +-
content/3.defense-systems/abig.md | 30 +-
content/3.defense-systems/abih.md | 29 +-
content/3.defense-systems/abii.md | 29 +-
content/3.defense-systems/abij.md | 28 +-
content/3.defense-systems/abik.md | 30 +-
content/3.defense-systems/abil.md | 29 +-
content/3.defense-systems/abin.md | 29 +-
content/3.defense-systems/abio.md | 29 +-
content/3.defense-systems/abip2.md | 39 +-
content/3.defense-systems/abiq.md | 29 +-
content/3.defense-systems/abir.md | 29 +-
content/3.defense-systems/abit.md | 29 +-
content/3.defense-systems/abiu.md | 30 +-
content/3.defense-systems/abiv.md | 36 +-
content/3.defense-systems/abiz.md | 37 +-
content/3.defense-systems/aditi.md | 30 +-
content/3.defense-systems/avs.md | 238 ++++-
content/3.defense-systems/azaca.md | 41 +-
content/3.defense-systems/borvo.md | 31 +-
content/3.defense-systems/brex.md | 63 +-
content/3.defense-systems/bsta.md | 71 +-
content/3.defense-systems/bunzi.md | 29 +-
.../3.defense-systems/butters_gp30_gp31.md | 24 +
content/3.defense-systems/butters_gp57r.md | 31 +
content/3.defense-systems/caprel.md | 50 +-
content/3.defense-systems/cbass.md | 67 +-
content/3.defense-systems/charlie_gp32.md | 24 +
content/3.defense-systems/dartg.md | 30 +-
content/3.defense-systems/dazbog.md | 42 +-
content/3.defense-systems/dctpdeaminase.md | 83 +-
content/3.defense-systems/detocs.md | 49 +-
content/3.defense-systems/dgtpase.md | 77 +-
content/3.defense-systems/disarm.md | 67 +-
content/3.defense-systems/dnd.md | 28 +-
content/3.defense-systems/dodola.md | 28 +-
content/3.defense-systems/drt.md | 127 ++-
content/3.defense-systems/druantia.md | 55 +-
content/3.defense-systems/dsr.md | 62 +-
content/3.defense-systems/eleos.md | 30 +-
content/3.defense-systems/fs_giy_yig.md | 33 +
content/3.defense-systems/fs_hepn_tm.md | 26 +
content/3.defense-systems/fs_hp.md | 32 +
content/3.defense-systems/fs_hp_sdh_sah.md | 24 +
content/3.defense-systems/fs_hsdr_like.md | 39 +
content/3.defense-systems/fs_sma.md | 41 +
content/3.defense-systems/gabija.md | 52 +-
content/3.defense-systems/gao_ape.md | 33 +-
content/3.defense-systems/gao_her.md | 46 +-
content/3.defense-systems/gao_hhe.md | 31 +-
content/3.defense-systems/gao_iet.md | 31 +-
content/3.defense-systems/gao_mza.md | 34 +-
content/3.defense-systems/gao_ppl.md | 31 +-
content/3.defense-systems/gao_qat.md | 30 +-
content/3.defense-systems/gao_rl.md | 31 +-
content/3.defense-systems/gao_tery.md | 31 +-
content/3.defense-systems/gao_tmn.md | 31 +-
content/3.defense-systems/gao_upx.md | 29 +-
content/3.defense-systems/gaps1.md | 25 +
content/3.defense-systems/gaps2.md | 25 +
content/3.defense-systems/gaps4.md | 27 +
content/3.defense-systems/gaps6.md | 27 +
content/3.defense-systems/gasdermin.md | 31 +-
content/3.defense-systems/hachiman.md | 47 +-
content/3.defense-systems/hna.md | 36 +
content/3.defense-systems/isg15-like.md | 94 +-
content/3.defense-systems/jukab.md | 24 +
content/3.defense-systems/kiwa.md | 29 +-
content/3.defense-systems/lamassu-fam.md | 129 ++-
content/3.defense-systems/lit.md | 28 +-
content/3.defense-systems/mads.md | 27 +
content/3.defense-systems/mazef.md | 24 +
content/3.defense-systems/menshen.md | 41 +-
content/3.defense-systems/mmb_gp29_gp30.md | 26 +
content/3.defense-systems/mok_hok_sok.md | 29 +-
content/3.defense-systems/mokosh.md | 52 +-
content/3.defense-systems/mqsrac.md | 25 +
content/3.defense-systems/nhi.md | 76 +-
content/3.defense-systems/nixi.md | 28 +-
content/3.defense-systems/nlr.md | 132 ++-
content/3.defense-systems/old_exonuclease.md | 31 +-
content/3.defense-systems/olokun.md | 29 +-
content/3.defense-systems/pago.md | 117 ++-
content/3.defense-systems/panchino_gp28.md | 28 +
content/3.defense-systems/paris.md | 48 +-
content/3.defense-systems/pd-lambda-1.md | 28 +-
content/3.defense-systems/pd-lambda-2.md | 33 +-
content/3.defense-systems/pd-lambda-3.md | 29 +-
content/3.defense-systems/pd-lambda-4.md | 31 +-
content/3.defense-systems/pd-lambda-5.md | 36 +-
content/3.defense-systems/pd-lambda-6.md | 29 +-
content/3.defense-systems/pd-t4-1.md | 30 +-
content/3.defense-systems/pd-t4-10.md | 32 +-
content/3.defense-systems/pd-t4-2.md | 31 +-
content/3.defense-systems/pd-t4-3.md | 30 +-
content/3.defense-systems/pd-t4-4.md | 31 +-
content/3.defense-systems/pd-t4-5.md | 31 +-
content/3.defense-systems/pd-t4-6.md | 30 +-
content/3.defense-systems/pd-t4-7.md | 30 +-
content/3.defense-systems/pd-t4-8.md | 32 +-
content/3.defense-systems/pd-t4-9.md | 31 +-
content/3.defense-systems/pd-t7-1.md | 28 +-
content/3.defense-systems/pd-t7-2.md | 36 +-
content/3.defense-systems/pd-t7-3.md | 34 +-
content/3.defense-systems/pd-t7-4.md | 31 +-
content/3.defense-systems/pd-t7-5.md | 30 +-
content/3.defense-systems/phrann_gp29_gp30.md | 24 +
content/3.defense-systems/pif.md | 28 +-
content/3.defense-systems/prrc.md | 31 +-
content/3.defense-systems/psyrta.md | 30 +-
content/3.defense-systems/pycsar.md | 40 +-
content/3.defense-systems/radar.md | 64 +-
content/3.defense-systems/retron.md | 289 +++++-
content/3.defense-systems/rexab.md | 29 +-
content/3.defense-systems/rloc.md | 27 +-
content/3.defense-systems/rnlab.md | 27 +-
content/3.defense-systems/rosmerta.md | 29 +-
content/3.defense-systems/rst_3hp.md | 29 +-
content/3.defense-systems/rst_duf4238.md | 28 +-
content/3.defense-systems/rst_gop_beta_cll.md | 30 +-
.../3.defense-systems/rst_helicaseduf2290.md | 28 +-
.../3.defense-systems/rst_hydrolase-3tm.md | 28 +-
.../3.defense-systems/rst_rt-nitrilase-tm.md | 28 +-
content/3.defense-systems/rst_tir-nlr.md | 33 +-
content/3.defense-systems/sanata.md | 28 +-
content/3.defense-systems/sefir.md | 28 +-
content/3.defense-systems/septu.md | 39 +-
content/3.defense-systems/shango.md | 30 +-
content/3.defense-systems/shedu.md | 31 +-
content/3.defense-systems/shosta.md | 42 +-
content/3.defense-systems/sofic.md | 28 +-
content/3.defense-systems/spbk.md | 28 +-
content/3.defense-systems/sspbcde.md | 83 +-
content/3.defense-systems/stk2.md | 41 +-
content/3.defense-systems/thoeris.md | 67 +-
content/3.defense-systems/tiamat.md | 29 +-
content/3.defense-systems/uzume.md | 30 +-
content/3.defense-systems/viperin.md | 199 +++-
content/3.defense-systems/zorya.md | 60 +-
package-lock.json | 954 ++++++++++--------
package.json | 1 +
plugins/mermaid.client.js | 11 +
public/pfam-a-hmm.csv | 15 +
server/plugins/content.ts | 2 -
153 files changed, 5825 insertions(+), 1323 deletions(-)
create mode 100644 components/content/Mermaid.vue
create mode 100644 plugins/mermaid.client.js
create mode 100644 public/pfam-a-hmm.csv
diff --git a/.gitignore b/.gitignore
index ac76cdee..0592ec30 100755
--- a/.gitignore
+++ b/.gitignore
@@ -14,4 +14,4 @@ scripts/Pfam-A.hmm.dat
meili_data
#refseq_res.csv
*.pyc
-pfam-a-hmm.csv
\ No newline at end of file
+# pfam-a-hmm.csv
\ No newline at end of file
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index dff2766e..164d39f6 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -265,8 +265,8 @@ get-pfam:
artifacts:
paths:
- public/pfam-a-hmm.csv
- rules:
- - if: $CI_COMMIT_BRANCH == "main"
+ # rules:
+ # - if: $CI_COMMIT_BRANCH == "main"
@@ -297,6 +297,7 @@ build:dev:wiki:
extends: .build
needs:
- set-meili-env:dev
+ - get-pfam
variables:
BASE_URL: /wiki/
rules:
diff --git a/Dockerfile b/Dockerfile
index a6ba33aa..52f865fa 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,5 +1,5 @@
### Stage Install ###
-FROM node:19.5-bullseye-slim as install
+FROM node:21.1-bookworm-slim as install
@@ -11,7 +11,7 @@ RUN npm install
### STAGE: Dev
-FROM node:19.5-bullseye-slim as dev
+FROM node:21.1-bookworm-slim as dev
ARG BASE_URL=/
ARG MEILI_HOST=http://localhost:7700
ARG MEILI_API_KEY=api_key
@@ -29,7 +29,7 @@ CMD ["npm", "run", "dev"]
### STAGE: Build ###
-FROM node:19.5-bullseye-slim as build
+FROM node:21.1-bookworm-slim as build
WORKDIR /usr/src/app
COPY --from=install /usr/src/app ./
@@ -37,7 +37,7 @@ COPY . /usr/src/app
RUN npm run build
### STAGE: serve ###
-FROM node:19.5-bullseye-slim as serve
+FROM node:21.1-bookworm-slim as serve
WORKDIR /usr/src/app
COPY --from=build /usr/src/app/.output ./
@@ -46,12 +46,12 @@ CMD [ "node", "server/index.mjs"]
### STAGE: Generate ###
-FROM node:19.5-bullseye-slim as generate
+FROM node:21.1-bookworm-slim as generate
ARG BASE_URL=/
ARG MEILI_HOST=http://localhost:7700
ARG MEILI_API_KEY
-
+ENV NODE_OPTIONS=--max_old_space_size=8192
ENV NUXT_APP_BASE_URL=${BASE_URL}
ENV NUXT_PUBLIC_MEILI_HOST=${MEILI_HOST}
ENV NUXT_PUBLIC_MEILI_API_KEY=${MEILI_API_KEY}
diff --git a/components/content/ListSystems.vue b/components/content/ListSystems.vue
index f54b92ba..ed19ba4b 100644
--- a/components/content/ListSystems.vue
+++ b/components/content/ListSystems.vue
@@ -33,11 +33,12 @@ function filterOnlyCapsText(value, query, item) {
return false;
}
const { initPfam } = usePfamStore();
-
-initPfam();
+onMounted(() => {
+ initPfam();
+})
</script>
<template>
- <v-card >
+ <v-card>
<v-toolbar density="compact">
<v-toolbar-title>Defense Systems</v-toolbar-title>
diff --git a/components/content/Mermaid.vue b/components/content/Mermaid.vue
new file mode 100644
index 00000000..c747d1f5
--- /dev/null
+++ b/components/content/Mermaid.vue
@@ -0,0 +1,40 @@
+<!-- this code is from
+ https://gitlab.com/dokos/documentation/-/blob/132cce8c6e2126d8dba8ad09b7c7dd6d08a7c461/components/content/Mermaid.vue
+ -->
+
+<template>
+ <pre ref="el" :style="{ display: rendered ? 'block' : 'none' }">
+ <slot />
+ </pre>
+</template>
+
+<script setup lang="ts">
+const slot = useSlots()
+const el = ref(null)
+const rendered = ref(false)
+
+async function render() {
+ if (!el.value) {
+ return
+ }
+ if (el.value.querySelector('svg')) {
+ // Already rendered
+ return
+ }
+
+ // Iterate children to remove comments
+ for (const child of el.value.childNodes) {
+ if (child.nodeType === Node.COMMENT_NODE) {
+ el.value.removeChild(child)
+ }
+ }
+ const { default: mermaid } = await import("mermaid")
+ el.value.classList.add('mermaid')
+ rendered.value = true
+ await mermaid.run({ nodes: [el.value] })
+}
+
+onMounted(() => {
+ render()
+})
+</script>
\ No newline at end of file
diff --git a/content/3.defense-systems/abia.md b/content/3.defense-systems/abia.md
index 82ca5651..d6f9d100 100644
--- a/content/3.defense-systems/abia.md
+++ b/content/3.defense-systems/abia.md
@@ -72,9 +72,28 @@ dataUrl: /abia/AbiA_small,AbiA_small__AbiA_small,0,DF-plddts_89.82347.pdb
## Experimental validation
-AbiA systems were experimentally validated using:
-
-A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2, P335 (Chopin et al., 2005)
-
-
-
+<mermaid>
+graph LR;
+ Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
+ Origin_0[lactococcal plasmid
+<a href='https://ncbi.nlm.nih.gov/protein/AAA65072.1'>AAA65072.1</a>] --> Expressed_0[lactococci]
+ Expressed_0[lactococci] ----> 936 & c2 & P335
+ subgraph Title1[Reference]
+ Chopin_2005
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ 936
+ c2
+ P335
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
diff --git a/content/3.defense-systems/abib.md b/content/3.defense-systems/abib.md
index 3c0de6fd..a9e98322 100644
--- a/content/3.defense-systems/abib.md
+++ b/content/3.defense-systems/abib.md
@@ -45,9 +45,28 @@ dataUrl: /abib/AbiB__AbiB-plddts_74.5545.pdb
::
## Experimental validation
-
-AbiB systems were experimentally validated using:
-
-A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936 (Chopin et al., 2005)
+<mermaid>
+graph LR;
+ Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
+ Origin_0[lactococcal plasmid
+<a href='https://ncbi.nlm.nih.gov/protein/AAA25158.1'>AAA25158.1</a>] --> Expressed_0[lactococci]
+ Expressed_0[lactococci] ----> 936
+ subgraph Title1[Reference]
+ Chopin_2005
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ 936
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
diff --git a/content/3.defense-systems/abic.md b/content/3.defense-systems/abic.md
index 3e70eaa0..4a337a1f 100644
--- a/content/3.defense-systems/abic.md
+++ b/content/3.defense-systems/abic.md
@@ -43,17 +43,61 @@ dataUrl: /abic/AbiC__AbiC-plddts_83.80335.pdb
::
## Experimental validation
-
-AbiC systems were experimentally validated using:
-
-A system from *Klebsiella pneumoniae's PICI (KpCIFDAARGOS_1313)* in *Escherichia coli* has an anti-phage effect against T5, Lambda, HK97, HK544, HK578, T7 (Fillol-Salom et al., 2022)
-
-A system from *Klebsiella pneumoniae's PICI (KpCIFDAARGOS_1313)* in *Salmonella enterica* has an anti-phage effect against P22, BTP1, ES18 (Fillol-Salom et al., 2022)
-
-A system from *Klebsiella pneumoniae's PICI (KpCIFDAARGOS_1313)* in *Klebsiella pneumoniae* has an anti-phage effect against Pokey, Raw, Eggy (Fillol-Salom et al., 2022)
-
-A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, P335 (Chopin et al., 2005)
-
+<mermaid>
+graph LR;
+ Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
+ Origin_0[Klebsiella pneumoniae's PICI KpCIFDAARGOS_1313
+<a href='https://ncbi.nlm.nih.gov/protein/QRS09118.1'>QRS09118.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T5 & Lambda & HK97 & HK544 & HK578 & T7
+ Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
+ Origin_0[Klebsiella pneumoniae's PICI KpCIFDAARGOS_1313
+<a href='https://ncbi.nlm.nih.gov/protein/QRS09118.1'>QRS09118.1</a>] --> Expressed_1[Salmonella enterica]
+ Expressed_1[Salmonella enterica] ----> P22 & BTP1 & ES18
+ Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
+ Origin_0[Klebsiella pneumoniae's PICI KpCIFDAARGOS_1313
+<a href='https://ncbi.nlm.nih.gov/protein/QRS09118.1'>QRS09118.1</a>] --> Expressed_2[Klebsiella pneumoniae]
+ Expressed_2[Klebsiella pneumoniae] ----> Pokey & Raw & Eggy
+ Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_1
+ Origin_1[lactococcal plasmid
+<a href='https://ncbi.nlm.nih.gov/protein/AAA53569.1'>AAA53569.1</a>] --> Expressed_3[lactococci]
+ Expressed_3[lactococci] ----> 936 & P335
+ subgraph Title1[Reference]
+ Fillol-Salom_2022
+ Chopin_2005
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_0
+ Origin_0
+ Origin_1
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_1
+ Expressed_2
+ Expressed_3
+end
+ subgraph Title4[Phage infected]
+ T5
+ Lambda
+ HK97
+ HK544
+ HK578
+ T7
+ P22
+ BTP1
+ ES18
+ Pokey
+ Raw
+ Eggy
+ 936
+ P335
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/abid.md b/content/3.defense-systems/abid.md
index e2a37864..155c4c99 100644
--- a/content/3.defense-systems/abid.md
+++ b/content/3.defense-systems/abid.md
@@ -43,11 +43,31 @@ dataUrl: /abid/AbiD__AbiD-plddts_91.87407.pdb
::
## Experimental validation
-
-AbiD systems were experimentally validated using:
-
-A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2, P335 (Chopin et al., 2005)
-
+<mermaid>
+graph LR;
+ Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
+ Origin_0[lactococcal plasmid
+<a href='https://ncbi.nlm.nih.gov/protein/AAA63619.1'>AAA63619.1</a>] --> Expressed_0[lactococci]
+ Expressed_0[lactococci] ----> 936 & c2 & P335
+ subgraph Title1[Reference]
+ Chopin_2005
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ 936
+ c2
+ P335
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/abie.md b/content/3.defense-systems/abie.md
index f2b7575e..b1921a6d 100644
--- a/content/3.defense-systems/abie.md
+++ b/content/3.defense-systems/abie.md
@@ -62,11 +62,29 @@ dataUrl: /abie/AbiE,AbiE__AbiEii,0,V-plddts_90.73768.pdb
::
## Experimental validation
-
-AbiE systems were experimentally validated using:
-
-A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936 (Chopin et al., 2005)
-
+<mermaid>
+graph LR;
+ Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
+ Origin_0[lactococcal plasmid
+<a href='https://ncbi.nlm.nih.gov/protein/AAB52382.1'>AAB52382.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/AAB52383.1'>AAB52383.1</a>] --> Expressed_0[lactococci]
+ Expressed_0[lactococci] ----> 936
+ subgraph Title1[Reference]
+ Chopin_2005
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ 936
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/abig.md b/content/3.defense-systems/abig.md
index f3958bf6..0bdc0f08 100644
--- a/content/3.defense-systems/abig.md
+++ b/content/3.defense-systems/abig.md
@@ -50,11 +50,31 @@ dataUrl: /abig/AbiG,AbiG__AbiGii,0,V-plddts_88.01846.pdb
::
## Experimental validation
-
-AbiG systems were experimentally validated using:
-
-A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2, P335 (Chopin et al., 2005)
-
+<mermaid>
+graph LR;
+ Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
+ Origin_0[lactococcal plasmid
+<a href='https://ncbi.nlm.nih.gov/protein/AAB38312.1'>AAB38312.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/AAB38313.1'>AAB38313.1</a>] --> Expressed_0[lactococci]
+ Expressed_0[lactococci] ----> 936 & c2 & P335
+ subgraph Title1[Reference]
+ Chopin_2005
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ 936
+ c2
+ P335
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/abih.md b/content/3.defense-systems/abih.md
index a5957d00..e0f74b88 100644
--- a/content/3.defense-systems/abih.md
+++ b/content/3.defense-systems/abih.md
@@ -45,11 +45,30 @@ dataUrl: /abih/AbiH__AbiH-plddts_91.3485.pdb
::
## Experimental validation
-
-AbiH systems were experimentally validated using:
-
-A system from *lactococci* in *lactococci* has an anti-phage effect against 936, c2 (Chopin et al., 2005)
-
+<mermaid>
+graph LR;
+ Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
+ Origin_0[lactococci
+<a href='https://ncbi.nlm.nih.gov/protein/CAA66252.1'>CAA66252.1</a>] --> Expressed_0[lactococci]
+ Expressed_0[lactococci] ----> 936 & c2
+ subgraph Title1[Reference]
+ Chopin_2005
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ 936
+ c2
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/abii.md b/content/3.defense-systems/abii.md
index 1e1d819a..950813ce 100644
--- a/content/3.defense-systems/abii.md
+++ b/content/3.defense-systems/abii.md
@@ -44,11 +44,30 @@ dataUrl: /abii/AbiI__AbiI-plddts_90.31131.pdb
::
## Experimental validation
-
-AbiI systems were experimentally validated using:
-
-A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2 (Chopin et al., 2005)
-
+<mermaid>
+graph LR;
+ Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
+ Origin_0[lactococcal plasmid
+<a href='https://ncbi.nlm.nih.gov/protein/AAB66882.1'>AAB66882.1</a>] --> Expressed_0[lactococci]
+ Expressed_0[lactococci] ----> 936 & c2
+ subgraph Title1[Reference]
+ Chopin_2005
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ 936
+ c2
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/abij.md b/content/3.defense-systems/abij.md
index 1e5f58de..2346d58c 100644
--- a/content/3.defense-systems/abij.md
+++ b/content/3.defense-systems/abij.md
@@ -45,11 +45,29 @@ dataUrl: /abij/AbiJ__AbiJ-plddts_85.12535.pdb
::
## Experimental validation
-
-AbiJ systems were experimentally validated using:
-
-A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936 (Chopin et al., 2005)
-
+<mermaid>
+graph LR;
+ Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
+ Origin_0[lactococcal plasmid
+<a href='https://ncbi.nlm.nih.gov/protein/AAA99069.1'>AAA99069.1</a>] --> Expressed_0[lactococci]
+ Expressed_0[lactococci] ----> 936
+ subgraph Title1[Reference]
+ Chopin_2005
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ 936
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/abik.md b/content/3.defense-systems/abik.md
index 9bb989a3..8c20ae2c 100644
--- a/content/3.defense-systems/abik.md
+++ b/content/3.defense-systems/abik.md
@@ -45,11 +45,31 @@ dataUrl: /abik/AbiK__AbiK-plddts_91.42521.pdb
::
## Experimental validation
-
-AbiK systems were experimentally validated using:
-
-A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2, P335 (Chopin et al., 2005)
-
+<mermaid>
+graph LR;
+ Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
+ Origin_0[lactococcal plasmid
+<a href='https://ncbi.nlm.nih.gov/protein/AAB53491.2'>AAB53491.2</a>] --> Expressed_0[lactococci]
+ Expressed_0[lactococci] ----> 936 & c2 & P335
+ subgraph Title1[Reference]
+ Chopin_2005
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ 936
+ c2
+ P335
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/abil.md b/content/3.defense-systems/abil.md
index 2453dab6..de80bf27 100644
--- a/content/3.defense-systems/abil.md
+++ b/content/3.defense-systems/abil.md
@@ -52,11 +52,30 @@ dataUrl: /abil/AbiL,AbiL__AbiLii,0,V-plddts_86.69766.pdb
::
## Experimental validation
-
-AbiL systems were experimentally validated using:
-
-A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2 (Chopin et al., 2005)
-
+<mermaid>
+graph LR;
+ Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
+ Origin_0[lactococcal plasmid
+<a href='https://ncbi.nlm.nih.gov/protein/AAB53710.1'>AAB53710.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/AAB53711.1'>AAB53711.1</a>] --> Expressed_0[lactococci ]
+ Expressed_0[lactococci ] ----> 936 & c2
+ subgraph Title1[Reference]
+ Chopin_2005
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ 936
+ c2
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/abin.md b/content/3.defense-systems/abin.md
index f356f965..63964f3f 100644
--- a/content/3.defense-systems/abin.md
+++ b/content/3.defense-systems/abin.md
@@ -44,11 +44,30 @@ dataUrl: /abin/AbiN__AbiN-plddts_84.27216.pdb
::
## Experimental validation
-
-AbiN systems were experimentally validated using:
-
-A system from *lactococcal prophage* in *lactococci* has an anti-phage effect against 936, c2 (Chopin et al., 2005)
-
+<mermaid>
+graph LR;
+ Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
+ Origin_0[lactococcal prophage
+<a href='https://ncbi.nlm.nih.gov/protein/CAA72648.1'>CAA72648.1</a>] --> Expressed_0[lactococci]
+ Expressed_0[lactococci] ----> 936 & c2
+ subgraph Title1[Reference]
+ Chopin_2005
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ 936
+ c2
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/abio.md b/content/3.defense-systems/abio.md
index 5547f58a..116db721 100644
--- a/content/3.defense-systems/abio.md
+++ b/content/3.defense-systems/abio.md
@@ -45,11 +45,30 @@ dataUrl: /abio/AbiO__AbiO-plddts_87.43501.pdb
::
## Experimental validation
-
-AbiO systems were experimentally validated using:
-
-A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2 (Chopin et al., 2005)
-
+<mermaid>
+graph LR;
+ Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
+ Origin_0[lactococcal plasmid
+<a href='https://ncbi.nlm.nih.gov/protein/insideplasmid:I61427.1'>insideplasmid:I61427.1</a>] --> Expressed_0[lactococci]
+ Expressed_0[lactococci] ----> 936 & c2
+ subgraph Title1[Reference]
+ Chopin_2005
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ 936
+ c2
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/abip2.md b/content/3.defense-systems/abip2.md
index c0f80220..a1a13f67 100644
--- a/content/3.defense-systems/abip2.md
+++ b/content/3.defense-systems/abip2.md
@@ -45,13 +45,38 @@ dataUrl: /abip2/AbiP2__AbiP2-plddts_93.08218.pdb
::
## Experimental validation
-
-AbiP2 systems were experimentally validated using:
-
-Subsystem RT-Abi-P2 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T5 (Gao et al., 2020)
-
-A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936 (Chopin et al., 2005)
-
+<mermaid>
+graph LR;
+ Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
+ Origin_0[ RT-Abi-P2
+Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_047657908.1'>WP_047657908.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T5
+ Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_1
+ Origin_1[lactococcal plasmid
+<a href='https://ncbi.nlm.nih.gov/protein/WP_045971693.1'>WP_045971693.1</a>] --> Expressed_1[lactococci]
+ Expressed_1[lactococci] ----> 936
+ subgraph Title1[Reference]
+ Gao_2020
+ Chopin_2005
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_1
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_1
+end
+ subgraph Title4[Phage infected]
+ T5
+ 936
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/abiq.md b/content/3.defense-systems/abiq.md
index dab1ef15..4408fb70 100644
--- a/content/3.defense-systems/abiq.md
+++ b/content/3.defense-systems/abiq.md
@@ -45,11 +45,30 @@ dataUrl: /abiq/AbiQ__AbiQ-plddts_90.84212.pdb
::
## Experimental validation
-
-AbiQ systems were experimentally validated using:
-
-A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2 (Chopin et al., 2005)
-
+<mermaid>
+graph LR;
+ Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
+ Origin_0[lactococcal plasmid
+<a href='https://ncbi.nlm.nih.gov/protein/AAC98713.1'>AAC98713.1</a>] --> Expressed_0[lactococci]
+ Expressed_0[lactococci] ----> 936 & c2
+ subgraph Title1[Reference]
+ Chopin_2005
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ 936
+ c2
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/abir.md b/content/3.defense-systems/abir.md
index b856d890..06b6bb93 100644
--- a/content/3.defense-systems/abir.md
+++ b/content/3.defense-systems/abir.md
@@ -59,11 +59,30 @@ dataUrl: /abir/AbiR,AbiR__AbiRc,0,V-plddts_86.60767.pdb
::
## Experimental validation
-
-AbiR systems were experimentally validated using:
-
-A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against c2 (Chopin et al., 2005)
-
+<mermaid>
+graph LR;
+ Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
+ Origin_0[lactococcal plasmid
+<a href='https://ncbi.nlm.nih.gov/protein/AAF75619.1'>AAF75619.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/AAF75618.1'>AAF75618.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/AAF75617.1'>AAF75617.1</a>] --> Expressed_0[lactococci]
+ Expressed_0[lactococci] ----> c2
+ subgraph Title1[Reference]
+ Chopin_2005
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ c2
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/abit.md b/content/3.defense-systems/abit.md
index 296cfe9b..78fc1724 100644
--- a/content/3.defense-systems/abit.md
+++ b/content/3.defense-systems/abit.md
@@ -52,11 +52,30 @@ dataUrl: /abit/AbiT,AbiT__AbiTii,0,V-plddts_88.46375.pdb
::
## Experimental validation
-
-AbiT systems were experimentally validated using:
-
-A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, P335 (Chopin et al., 2005)
-
+<mermaid>
+graph LR;
+ Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
+ Origin_0[lactococcal plasmid
+<a href='https://ncbi.nlm.nih.gov/protein/AAN60762.1'>AAN60762.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/AAN60763.1'>AAN60763.1</a>] --> Expressed_0[lactococci]
+ Expressed_0[lactococci] ----> 936 & P335
+ subgraph Title1[Reference]
+ Chopin_2005
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ 936
+ P335
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/abiu.md b/content/3.defense-systems/abiu.md
index f01863b3..97814afc 100644
--- a/content/3.defense-systems/abiu.md
+++ b/content/3.defense-systems/abiu.md
@@ -45,11 +45,31 @@ dataUrl: /abiu/AbiU__AbiU-plddts_84.61928.pdb
::
## Experimental validation
-
-AbiU systems were experimentally validated using:
-
-A system from *lactococcal plasmid* in *lactococci* has an anti-phage effect against 936, c2, P335 (Chopin et al., 2005)
-
+<mermaid>
+graph LR;
+ Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
+ Origin_0[lactococcal plasmid
+<a href='https://ncbi.nlm.nih.gov/protein/AAG17058.'>AAG17058.</a>] --> Expressed_0[lactococci]
+ Expressed_0[lactococci] ----> 936 & c2 & P335
+ subgraph Title1[Reference]
+ Chopin_2005
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ 936
+ c2
+ P335
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/abiv.md b/content/3.defense-systems/abiv.md
index 36136ea3..93da9479 100644
--- a/content/3.defense-systems/abiv.md
+++ b/content/3.defense-systems/abiv.md
@@ -45,11 +45,37 @@ dataUrl: /abiv/AbiV__AbiV-plddts_93.56204.pdb
::
## Experimental validation
-
-AbiV systems were experimentally validated using:
-
-A system from *Lactococcus lactis* in *Lactococcus lactis* has an anti-phage effect against sk1, p2, jj50, P008, bIL170, c2, bIL67, ml3, eb1 (Haaber et al., 2008)
-
+<mermaid>
+graph LR;
+ Haaber_2008[<a href='https://doi.org/10.1128/AEM.00780-08'>Haaber et al., 2008</a>] --> Origin_0
+ Origin_0[Lactococcus lactis
+<a href='https://ncbi.nlm.nih.gov/protein/AAK16428.1'>AAK16428.1</a>] --> Expressed_0[Lactococcus lactis]
+ Expressed_0[Lactococcus lactis] ----> sk1 & p2 & jj50 & P008 & bIL170 & c2 & bIL67 & ml3 & eb1
+ subgraph Title1[Reference]
+ Haaber_2008
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ sk1
+ p2
+ jj50
+ P008
+ bIL170
+ c2
+ bIL67
+ ml3
+ eb1
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/abiz.md b/content/3.defense-systems/abiz.md
index 4497aa72..2757a76e 100644
--- a/content/3.defense-systems/abiz.md
+++ b/content/3.defense-systems/abiz.md
@@ -44,11 +44,38 @@ dataUrl: /abiz/AbiZ__AbiZ-plddts_78.85683.pdb
::
## Experimental validation
-
-AbiZ systems were experimentally validated using:
-
-A system from *Lactococcus lactis* in *Lactococcus lactis* has an anti-phage effect against Phi31.2, ul36, phi31, phi48, phi31.1, Q30, Q36, Q33, phi50, phi48 (Durmaz et al., 2007)
-
+<mermaid>
+graph LR;
+ Durmaz_2007[<a href='https://doi.org/10.1128/JB.00904-06'>Durmaz and Klaenhammer, 2007</a>] --> Origin_0
+ Origin_0[Lactococcus lactis
+<a href='https://ncbi.nlm.nih.gov/protein/ABI93964.1'>ABI93964.1</a>] --> Expressed_0[Lactococcus lactis]
+ Expressed_0[Lactococcus lactis] ----> Phi31.2 & ul36 & phi31 & phi48 & phi31.1 & Q30 & Q36 & Q33 & phi50 & phi48
+ subgraph Title1[Reference]
+ Durmaz_2007
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ Phi31.2
+ ul36
+ phi31
+ phi48
+ phi31.1
+ Q30
+ Q36
+ Q33
+ phi50
+ phi48
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/aditi.md b/content/3.defense-systems/aditi.md
index f7a1e705..ea0db2cb 100644
--- a/content/3.defense-systems/aditi.md
+++ b/content/3.defense-systems/aditi.md
@@ -52,11 +52,31 @@ dataUrl: /aditi/Aditi,Aditi__DitB,0,V-plddts_90.75274.pdb
::
## Experimental validation
-
-Aditi systems were experimentally validated using:
-
-A system from *Saccharibacillus kuerlensis* in *Bacillus subtilis* has an anti-phage effect against phi105, Rho14, SPP1 (Millman et al., 2022)
-
+<mermaid>
+graph LR;
+ Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
+ Origin_0[Saccharibacillus kuerlensis
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2519017023'>2519017023</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2519017022'>2519017022</a>] --> Expressed_0[Bacillus subtilis]
+ Expressed_0[Bacillus subtilis] ----> phi105 & Rho14 & SPP1
+ subgraph Title1[Reference]
+ Millman_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ phi105
+ Rho14
+ SPP1
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/avs.md b/content/3.defense-systems/avs.md
index 064794de..d181694b 100644
--- a/content/3.defense-systems/avs.md
+++ b/content/3.defense-systems/avs.md
@@ -134,42 +134,204 @@ dataUrls:
## Experimental validation
-Avs systems were experimentally validated using:
+<mermaid>
+graph LR;
+ Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
+ Origin_0[ SIR2-STAND
+Escherichia fergusonii's PICI EfCIRHB19-C05
+<a href='https://ncbi.nlm.nih.gov/protein/QML19490.1'>QML19490.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T4 & Lambda & HK97 & HK544 & HK578 & T7
+ Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
+ Origin_0[ SIR2-STAND
+Escherichia fergusonii's PICI EfCIRHB19-C05
+<a href='https://ncbi.nlm.nih.gov/protein/QML19490.1'>QML19490.1</a>] --> Expressed_1[Salmonella enterica]
+ Expressed_1 ----> P22 & BTP1 & ES18 & det7
+ Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
+ Origin_0[ SIR2-STAND
+Escherichia fergusonii's PICI EfCIRHB19-C05
+<a href='https://ncbi.nlm.nih.gov/protein/QML19490.1'>QML19490.1</a>] --> Expressed_2[Klebsiella pneumoniae]
+ Expressed_2[Klebsiella pneumoniae] ----> Pokey
+ Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_1
+ Origin_1[ Metallo beta-lactamase + protease + STAND type 1
+Erwinia piriflorinigrans
+<a href='https://ncbi.nlm.nih.gov/protein/WP_023654314.1'>WP_023654314.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_084007836.1'>WP_084007836.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/WP_023654316.1'>WP_023654316.1</a>] --> Expressed_3[Escherichia coli]
+ Expressed_3[Escherichia coli] ----> P1
+ Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_2
+ Origin_2[ STAND type 2
+Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_063118745.1'>WP_063118745.1</a>] --> Expressed_4[Escherichia coli]
+ Expressed_4[Escherichia coli] ----> T4 & P1
+ Gao_2022[<a href='https://doi.org/10.1126/science.abm4096'>Gao et al., 2022</a>] --> Origin_2
+ Origin_2[ EcAvs2
+Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_063118745.1'>WP_063118745.1</a>] --> Expressed_4[Escherichia coli]
+ Expressed_4[Escherichia coli] ----> T7 & PhiV-1 & P1 & T4 & T5 & ZL-19
+ Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_3
+ Origin_3[ DUF4297-STAND type 3
+Salmonella enterica
+<a href='https://ncbi.nlm.nih.gov/protein/WP_126523998.1'>WP_126523998.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_126523997.1'>WP_126523997.1</a>] --> Expressed_5[Escherichia coli]
+ Expressed_5[Escherichia coli] ----> T2 & T3 & T7 & PhiV-1
+ Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_4
+ Origin_4[ Mrr-STAND type 4
+Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_044068927.1'>WP_044068927.1</a>] --> Expressed_6[Escherichia coli]
+ Expressed_6[Escherichia coli] ----> T3 & T7 & PhiV-1
+ Gao_2022[<a href='https://doi.org/10.1126/science.abm4096'>Gao et al., 2022</a>] --> Origin_4
+ Origin_4[ EcAvs4
+Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_044068927.1'>WP_044068927.1</a>] --> Expressed_6[Escherichia coli]
+ Expressed_6[Escherichia coli] ----> T7 & PhiV-1 & ZL-19
+ Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_5
+ Origin_5[ SIR2-STAND type 5
+Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_001515187.1'>WP_001515187.1</a>] --> Expressed_7[Escherichia coli]
+ Expressed_7[Escherichia coli] ----> T2
+ Gao_2022[<a href='https://doi.org/10.1126/science.abm4096'>Gao et al., 2022</a>] --> Origin_6
+ Origin_6[ SeAvs1
+Salmonella enterica
+<a href='https://ncbi.nlm.nih.gov/protein/ECC9552481.1'>ECC9552481.1</a>] --> Expressed_8[Escherichia coli]
+ Expressed_8[Escherichia coli] ----> P1 & ZL-19
+ Gao_2022[<a href='https://doi.org/10.1126/science.abm4096'>Gao et al., 2022</a>] --> Origin_7
+ Origin_7[ EcAvs1
+Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_060615938.1'>WP_060615938.1</a>] --> Expressed_9[Escherichia coli]
+ Expressed_9[Escherichia coli] ----> ZL-19
+ Gao_2022[<a href='https://doi.org/10.1126/science.abm4096'>Gao et al., 2022</a>] --> Origin_8
+ Origin_8[ EpAvs1
+Erwinia piriflorinigrans
+<a href='https://ncbi.nlm.nih.gov/protein/WP_048696970.1'>WP_048696970.1</a>] --> Expressed_10[Escherichia coli]
+ Expressed_10[Escherichia coli] ----> P1 & Lambda & ZL-19
+ Gao_2022[<a href='https://doi.org/10.1126/science.abm4096'>Gao et al., 2022</a>] --> Origin_9
+ Origin_9[ SeAvs3
+Salmonella enterica
+<a href='https://ncbi.nlm.nih.gov/protein/WP_126523998.1'>WP_126523998.1</a>] --> Expressed_11[Escherichia coli]
+ Expressed_11[Escherichia coli] ----> T7 & PhiV-1 & ZL-19
+ Gao_2022[<a href='https://doi.org/10.1126/science.abm4096'>Gao et al., 2022</a>] --> Origin_10
+ Origin_10[ KvAvs3
+Klebsiella variicola
+<a href='https://ncbi.nlm.nih.gov/protein/WP_139964370.1'>WP_139964370.1</a>] --> Expressed_12[Escherichia coli]
+ Expressed_12[Escherichia coli] ----> P1 & ZL-19
+ Gao_2022[<a href='https://doi.org/10.1126/science.abm4096'>Gao et al., 2022</a>] --> Origin_11
+ Origin_11[ Ec2Avs2
+Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_001017806.1'>WP_001017806.1</a>] --> Expressed_13[Escherichia coli]
+ Expressed_13[Escherichia coli] ----> P1
+ Gao_2022[<a href='https://doi.org/10.1126/science.abm4096'>Gao et al., 2022</a>] --> Origin_12
+ Origin_12[ Ec2Avs4
+Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/EEW5978513.1'>EEW5978513.1</a>] --> Expressed_14[Escherichia coli]
+ Expressed_14[Escherichia coli] ----> T7 & PhiV-1 & ZL-19
+ Gao_2022[<a href='https://doi.org/10.1126/science.abm4096'>Gao et al., 2022</a>] --> Origin_13
+ Origin_13[ KpAvs4
+Klebsiella pneumoniae
+<a href='https://ncbi.nlm.nih.gov/protein/WP_087775949.1'>WP_087775949.1</a>] --> Expressed_15[Escherichia coli]
+ Expressed_15[Escherichia coli] ----> ZL-19
+ Gao_2022[<a href='https://doi.org/10.1126/science.abm4096'>Gao et al., 2022</a>] --> Origin_14
+ Origin_14[ CcAvs4
+Corallococcus coralloides
+<a href='https://ncbi.nlm.nih.gov/protein/WP_083892326.1'>WP_083892326.1</a>] --> Expressed_16[Escherichia coli]
+ Expressed_16[Escherichia coli] ----> T7
+ subgraph Title1[Reference]
+ Fillol-Salom_2022
+ Gao_2020
+ Gao_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_0
+ Origin_0
+ Origin_1
+ Origin_2
+ Origin_2
+ Origin_3
+ Origin_4
+ Origin_4
+ Origin_5
+ Origin_6
+ Origin_7
+ Origin_8
+ Origin_9
+ Origin_10
+ Origin_11
+ Origin_12
+ Origin_13
+ Origin_14
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_1
+ Expressed_2
+ Expressed_3
+ Expressed_4
+ Expressed_4
+ Expressed_5
+ Expressed_6
+ Expressed_6
+ Expressed_7
+ Expressed_8
+ Expressed_9
+ Expressed_10
+ Expressed_11
+ Expressed_12
+ Expressed_13
+ Expressed_14
+ Expressed_15
+ Expressed_16
+end
+ subgraph Title4[Phage infected]
+ T4
+ Lambda
+ HK97
+ HK544
+ HK578
+ T7
+ P22
+ BTP1
+ ES18
+ det7
+ Pokey
+ P1
+ T4
+ P1
+ T7
+ PhiV-1
+ P1
+ T4
+ T5
+ ZL-19
+ T2
+ T3
+ T7
+ PhiV-1
+ T3
+ T7
+ PhiV-1
+ T7
+ PhiV-1
+ ZL-19
+ T2
+ P1
+ ZL-19
+ ZL-19
+ P1
+ Lambda
+ ZL-19
+ T7
+ PhiV-1
+ ZL-19
+ P1
+ ZL-19
+ P1
+ T7
+ PhiV-1
+ ZL-19
+ ZL-19
+ T7
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
-Subsystem SIR2-STAND with a system from *Escherichia fergusonii's PICI (EfCIRHB19-C05)* in *Escherichia coli* has an anti-phage effect against T4, Lambda, HK97, HK544, HK578, T7 (Fillol-Salom et al., 2022)
-
-Subsystem SIR2-STAND with a system from *Escherichia fergusonii's PICI (EfCIRHB19-C05)* in *Salmonella enterica * has an anti-phage effect against P22, BTP1, ES18, det7 (Fillol-Salom et al., 2022)
-
-Subsystem SIR2-STAND with a system from *Escherichia fergusonii's PICI (EfCIRHB19-C05)* in *Klebsiella pneumoniae * has an anti-phage effect against Pokey (Fillol-Salom et al., 2022)
-
-Subsystem Metallo beta-lactamase + protease + STAND (Type 1) with a system from *Erwinia piriflorinigrans* in *Escherichia coli* has an anti-phage effect against P1 (Gao et al., 2020)
-
-Subsystem STAND (Type 2) with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T4, P1 (Gao et al., 2020)
-
-Subsystem DUF4297-STAND (Type 3) with a system from *Salmonella enterica* in *Escherichia coli* has an anti-phage effect against T2, T3, T7, PhiV-1 (Gao et al., 2020)
-
-Subsystem Mrr-STAND (Type 4) with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T3, T7, PhiV-1 (Gao et al., 2020)
-
-Subsystem SIR2-STAND (Type 5) with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2 (Gao et al., 2020)
-
-Subsystem SeAvs1 with a system from *Salmonella enterica* in *Escherichia coli* has an anti-phage effect against P1, ZL-19 (Gao et al., 2022)
-
-Subsystem EcAcs1 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against ZL-19 (Gao et al., 2022)
-
-Subsystem EpAvs1 with a system from *Erwinia piriflorinigrans* in *Escherichia coli* has an anti-phage effect against P1, Lambda, , ZL-19 (Gao et al., 2022)
-
-Subsystem SeAvs3 with a system from *Salmonella enterica* in *Escherichia coli* has an anti-phage effect against T7, PhiV-1, ZL-19 (Gao et al., 2022)
-
-Subsystem KvAvs3 with a system from *Klebsiella variicola* in *Escherichia coli* has an anti-phage effect against P1, ZL-19 (Gao et al., 2022)
-
-Subsystem EcAvs2 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T7, PhiV-1, P1, T4, T5, ZL-19 (Gao et al., 2022)
-
-Subsystem Ec2Avs2 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against P1 (Gao et al., 2022)
-
-Subsystem EcAvs4 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T7, PhiV-1, ZL-19 (Gao et al., 2022)
-
-Subsystem Ec2Avs4 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T7, PhiV-1, ZL-19 (Gao et al., 2022)
-
-Subsystem KpAvs4 with a system from *Klebsiella pneumoniae* in *Escherichia coli* has an anti-phage effect against ZL-19 (Gao et al., 2022)
-
-Subsystem CcAvs4 with a system from *Corallococcus coralloides* in *Escherichia coli* has an anti-phage effect against T7 (Gao et al., 2022)
diff --git a/content/3.defense-systems/azaca.md b/content/3.defense-systems/azaca.md
index 51d8cf1f..9394c42e 100644
--- a/content/3.defense-systems/azaca.md
+++ b/content/3.defense-systems/azaca.md
@@ -59,13 +59,40 @@ dataUrl: /azaca/Azaca,Azaca__ZacC,0,V-plddts_86.69875.pdb
::
## Experimental validation
-
-Azaca systems were experimentally validated using:
-
-A system from *Bacillus massilioanorexius* in *Escherichia coli* has an anti-phage effect against T2, T4, T6 (Millman et al., 2022)
-
-A system from *Bacillus massilioanorexius* in *Bacillus subtilis* has an anti-phage effect against SBSphiC (Millman et al., 2022)
-
+<mermaid>
+graph LR;
+ Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
+ Origin_0[Bacillus massilioanorexius
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2547646535'>2547646535</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2547646536'>2547646536</a>,
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2547646537'>2547646537</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T2 & T4 & T6
+ Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
+ Origin_0[Bacillus massilioanorexius
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2547646535'>2547646535</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2547646536'>2547646536</a>,
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2547646537'>2547646537</a>] --> Expressed_1[Bacillus subtilis]
+ Expressed_1[Bacillus subtilis] ----> SBSphiC
+ subgraph Title1[Reference]
+ Millman_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_1
+end
+ subgraph Title4[Phage infected]
+ T2
+ T4
+ T6
+ SBSphiC
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/borvo.md b/content/3.defense-systems/borvo.md
index 2b6c3368..731d84b6 100644
--- a/content/3.defense-systems/borvo.md
+++ b/content/3.defense-systems/borvo.md
@@ -45,11 +45,32 @@ dataUrl: /borvo/Borvo__BovA-plddts_90.79263.pdb
::
## Experimental validation
-
-Borvo systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T5, SECphi4, SECphi6, SECphi18 (Millman et al., 2022)
-
+<mermaid>
+graph LR;
+ Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2646127138'>2646127138</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T5 & SECphi4 & SECphi6 & SECphi18
+ subgraph Title1[Reference]
+ Millman_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T5
+ SECphi4
+ SECphi6
+ SECphi18
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/brex.md b/content/3.defense-systems/brex.md
index c627abc0..03ba456f 100644
--- a/content/3.defense-systems/brex.md
+++ b/content/3.defense-systems/brex.md
@@ -282,20 +282,49 @@ dataUrl: /brex/BREX_VI,BREX_brxA,0,DF-plddts_93.93224.pdb
## Experimental validation
-BREX systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against Lambda (Gao et al., 2020 ; Gordeeva et al., 2017)
-
-A system from *Bacillus cereus* in *Bacillus subtilis* has an anti-phage effect against SPbeta, SP16, Zeta, phi3T, SPO2, SPO1, SP82G :ref{doi=10.15252/embj.201489455}
-
-
-## Relevant Abstracts
-
-## Referencesqq
-
-**1. Goldfarb T, Sberro H, Weinstock E, Cohen O, Doron S, Charpak-Amikam Y, Afik S, Ofir G, Sorek R. BREX is a novel phage resistance system widespread in microbial genomes. EMBO J. 2015 Jan 13;34(2):169-83. doi: 10.15252/embj.201489455. Epub 2014 Dec 1. PMID: 25452498; PMCID: PMC4337064.**
-
-**2. Nunes-Alves C. Bacterial physiology: putting the 'BREX' on phage replication. Nat Rev Microbiol. 2015 Mar;13(3):129. doi: 10.1038/nrmicro3437. Epub 2015 Feb 2. PMID: 25639679.**
-
-**3. Sumby P, Smith MC. Phase variation in the phage growth limitation system of Streptomyces coelicolor A3(2). J Bacteriol. 2003;185(15):4558-4563. doi:10.1128/JB.185.15.4558-4563.2003**
-
+<mermaid>
+graph LR;
+ Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
+ Gordeeva_2017[<a href='https://doi.org/10.1093/nar/gky1125'>Gordeeva et al., 2019</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_085962535.1'>WP_085962535.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_000566901.1'>WP_000566901.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/WP_001019648.1'>WP_001019648.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_021524842.1'>WP_021524842.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/WP_001180895.1'>WP_001180895.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_001193074.1'>WP_001193074.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> Lambda
+ Goldfarb_2015[<a href='https://doi.org/10.15252/embj.201489455'>Goldfarb et al., 2015</a>] --> Origin_1
+ Origin_1[Bacillus cereus
+<a href='https://ncbi.nlm.nih.gov/protein/ZP_02596040.1'>ZP_02596040.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/ZP_02596039.1'>ZP_02596039.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/ZP_02596038.1'>ZP_02596038.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/ZP_02596037.1'>ZP_02596037.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/ZP_02596036.1'>ZP_02596036.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/ZP_02596035.1'>ZP_02596035.1</a>] --> Expressed_1[Bacillus subtilis ]
+ Expressed_1[Bacillus subtilis ] ----> SPbeta & SP16 & Zeta & phi3T & SPO2 & SPO1 & SP82G
+ subgraph Title1[Reference]
+ Gao_2020
+ Gordeeva_2017
+ Goldfarb_2015
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_0
+ Origin_1
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_0
+ Expressed_1
+end
+ subgraph Title4[Phage infected]
+ Lambda
+ Lambda
+ SPbeta
+ SP16
+ Zeta
+ phi3T
+ SPO2
+ SPO1
+ SP82G
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
diff --git a/content/3.defense-systems/bsta.md b/content/3.defense-systems/bsta.md
index 9d021f99..8d75ac00 100644
--- a/content/3.defense-systems/bsta.md
+++ b/content/3.defense-systems/bsta.md
@@ -68,19 +68,64 @@ dataUrl: /bsta/BstA__BstA2-plddts_92.11235.pdb
::
## Experimental validation
-
-BstA systems were experimentally validated using:
-
-A system from *Salmonella Typhimurium's BTP1 prophage* in *Salmonella Typhimurium* has an anti-phage effect against P22, ES18, 9NA (Owen et al., 2021)
-
-A system from *Salmonella Typhimurium's BTP1 prophage* in *Escherichia coli* has an anti-phage effect against P22, ES18, 9NA (Owen et al., 2021)
-
-A system from *Klebsiella pneumoniae* in *Salmonella Typhimurium* has an anti-phage effect against BTP1, P22, ES18, P22 HT, 9NA, Felix O1 (Owen et al., 2021)
-
-A system from *Escherichia coli* in *Salmonella Typhimurium* has an anti-phage effect against BTP1, P22, ES18, P22 HT, 9NA (Owen et al., 2021)
-
-A system from *Salmonella Typhimurium's BTP1* in *Escherichia coli* has an anti-phage effect against Lambda, Phi80, P1vir, T7 (Owen et al., 2021)
-
+<mermaid>
+graph LR;
+ Owen_2021[<a href='https://doi.org/10.1016/j.chom.2021.09.002'>Owen et al., 2021</a>] --> Origin_0
+ Origin_0[Salmonella Typhimurium's BTP1 prophage
+<a href='https://ncbi.nlm.nih.gov/protein/CBG23363.1'>CBG23363.1</a>] --> Expressed_0[Salmonella Typhimurium]
+ Expressed_0[Salmonella Typhimurium] ----> P22 & ES18 & 9NA
+ Owen_2021[<a href='https://doi.org/10.1016/j.chom.2021.09.002'>Owen et al., 2021</a>] --> Origin_0
+ Origin_0[Salmonella Typhimurium's BTP1 prophage
+<a href='https://ncbi.nlm.nih.gov/protein/CBG23363.1'>CBG23363.1</a>] --> Expressed_3[Escherichia coli]
+ Expressed_3[Escherichia coli] ----> Lambda & Phi80 & P1vir & T7
+ Owen_2021[<a href='https://doi.org/10.1016/j.chom.2021.09.002'>Owen et al., 2021</a>] --> Origin_1
+ Origin_1[Klebsiella pneumoniae
+<a href='https://ncbi.nlm.nih.gov/protein/CDO13226.1'>CDO13226.1</a>] --> Expressed_1[Salmonella Typhimurium]
+ Expressed_1[Salmonella Typhimurium] ----> BTP1 & P22 & ES18 & P22HT & 9NA & FelixO1
+ Owen_2021[<a href='https://doi.org/10.1016/j.chom.2021.09.002'>Owen et al., 2021</a>] --> Origin_2
+ Origin_2[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_000026554.1'>WP_000026554.1</a>] --> Expressed_2[Salmonella Typhimurium]
+ Expressed_2[Salmonella Typhimurium] ----> BTP1 & P22 & ES18 & P22HT & 9NA
+ subgraph Title1[Reference]
+ Owen_2021
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_0
+ Origin_1
+ Origin_2
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_3
+ Expressed_1
+ Expressed_2
+end
+ subgraph Title4[Phage infected]
+ P22
+ ES18
+ 9NA
+ Lambda
+ Phi80
+ P1vir
+ T7
+ BTP1
+ P22
+ ES18
+ P22HT
+ 9NA
+ FelixO1
+ BTP1
+ P22
+ ES18
+ P22HT
+ 9NA
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/bunzi.md b/content/3.defense-systems/bunzi.md
index 9fc80b18..ba99511a 100644
--- a/content/3.defense-systems/bunzi.md
+++ b/content/3.defense-systems/bunzi.md
@@ -51,11 +51,30 @@ dataUrl: /bunzi/Bunzi,Bunzi__BnzB,0,V-plddts_86.79774.pdb
::
## Experimental validation
-
-Bunzi systems were experimentally validated using:
-
-A system from *Ligilactobacillus animalis* in *Bacillus subtilis* has an anti-phage effect against AR9 (Jumbo), PBS1 (Jumbo) (Millman et al., 2022)
-
+<mermaid>
+graph LR;
+ Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
+ Origin_0[Ligilactobacillus animalis
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2658999466'>2658999466</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2658999467'>2658999467</a>] --> Expressed_0[Bacillus subtilis]
+ Expressed_0[Bacillus subtilis] ----> AR9 & PBS1
+ subgraph Title1[Reference]
+ Millman_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ AR9
+ PBS1
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/butters_gp30_gp31.md b/content/3.defense-systems/butters_gp30_gp31.md
index 48881175..4a9cc52e 100644
--- a/content/3.defense-systems/butters_gp30_gp31.md
+++ b/content/3.defense-systems/butters_gp30_gp31.md
@@ -30,6 +30,30 @@ dataUrl: /butters_gp30_gp31/Butters_gp30_gp31__Butters_gp31-plddts_84.75463.pdb
---
::
+## Experimental validation
+<mermaid>
+graph LR;
+ Mageeney_2020[<a href='https://doi.org/10.1128/mSystems.00534-20'>Mageeney et al., 2020</a>] --> Origin_0
+ Origin_0[Mycobacterium phage Butters
+<a href='https://ncbi.nlm.nih.gov/protein/YP_007869841.1'>YP_007869841.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/YP_007869842.1'>YP_007869842.1</a>] --> Expressed_0[Mycobacterium smegmatis]
+ Expressed_0[Mycobacterium smegmatis] ----> PurpleHazeandAlma
+ subgraph Title1[Reference]
+ Mageeney_2020
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ PurpleHazeandAlma
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstract
::relevant-abstracts
---
diff --git a/content/3.defense-systems/butters_gp57r.md b/content/3.defense-systems/butters_gp57r.md
index ad95f49b..e619aa40 100644
--- a/content/3.defense-systems/butters_gp57r.md
+++ b/content/3.defense-systems/butters_gp57r.md
@@ -23,6 +23,37 @@ dataUrl: /butters_gp57r/Butters_gp57r__gp57r-plddts_90.7432.pdb
---
::
+## Experimental validation
+<mermaid>
+graph LR;
+ Mohammed_2023[<a href='https://doi.org/10.1101/2023.01.03.522681'>Mohammed et al., 2023</a>] --> Origin_0
+ Origin_0[Mycobacterium phage Butters
+<a href='https://ncbi.nlm.nih.gov/protein/YP_009304936.1'>YP_009304936.1</a>] --> Expressed_0[Mycobacterium smegmatis mc2 155]
+ Expressed_0[Mycobacterium smegmatis mc2 155] ----> Island3 & Brujita & Gyzlar & LHTSCC & Norz & PurpleHaze & Perplexer & Bud
+ subgraph Title1[Reference]
+ Mohammed_2023
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ Island3
+ Brujita
+ Gyzlar
+ LHTSCC
+ Norz
+ PurpleHaze
+ Perplexer
+ Bud
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstract
::relevant-abstracts
---
diff --git a/content/3.defense-systems/caprel.md b/content/3.defense-systems/caprel.md
index 7ed9c7fa..f4092172 100644
--- a/content/3.defense-systems/caprel.md
+++ b/content/3.defense-systems/caprel.md
@@ -57,15 +57,47 @@ dataUrl: /caprel/CapRel__CapRel-plddts_90.09132.pdb
::
## Experimental validation
-
-CapRel systems were experimentally validated using:
-
-A system from *Salmonella phage SJ46* in *Escherichia coli* has an anti-phage effect against T2, T4, T6, RB69, SECphi27 (Zhang et al., 2022)
-
-A system from *Enterobacter chengduensis* in *Escherichia coli* has an anti-phage effect against T7 (Zhang et al., 2022)
-
-A system from *Klebsiella pneumoniae* in *Escherichia coli* has an anti-phage effect against SECphi18 (Zhang et al., 2022)
-
+<mermaid>
+graph LR;
+ Zhang_2022[<a href='https://doi.org/10.1038/s41586-022-05444-z'>Zhang et al., 2022</a>] --> Origin_0
+ Origin_0[Salmonella phage SJ46
+<a href='https://ncbi.nlm.nih.gov/protein/WP_001749390.1'>WP_001749390.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & RB69 & SECphi27
+ Zhang_2022[<a href='https://doi.org/10.1038/s41586-022-05444-z'>Zhang et al., 2022</a>] --> Origin_1
+ Origin_1[Enterobacter chengduensis
+<a href='https://ncbi.nlm.nih.gov/protein/WP_001749390.1'>WP_001749390.1</a>] --> Expressed_1[Escherichia coli]
+ Expressed_1[Escherichia coli] ----> T7
+ Zhang_2022[<a href='https://doi.org/10.1038/s41586-022-05444-z'>Zhang et al., 2022</a>] --> Origin_2
+ Origin_2[Klebsiella pneumoniae
+<a href='https://ncbi.nlm.nih.gov/protein/WP_0235711397.1'>WP_0235711397.1</a>] --> Expressed_2[Escherichia coli]
+ Expressed_2[Escherichia coli] ----> SECphi18
+ subgraph Title1[Reference]
+ Zhang_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_1
+ Origin_2
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_1
+ Expressed_2
+end
+ subgraph Title4[Phage infected]
+ T2
+ T4
+ T6
+ RB69
+ SECphi27
+ T7
+ SECphi18
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/cbass.md b/content/3.defense-systems/cbass.md
index 12f93515..1c5ab459 100644
--- a/content/3.defense-systems/cbass.md
+++ b/content/3.defense-systems/cbass.md
@@ -168,17 +168,62 @@ dataUrl: /cbass/CBASS_IV,CBASS__TGT,0,DF-plddts_93.84001.pdb
::
## Experimental validation
-
-CBASS systems were experimentally validated using:
-
-A system from *Vibrio cholerae* in *Escherichia coli* has an anti-phage effect against P1, T2 (Cohen et al., 2019)
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against P1, T2, T4, T5, T6, LambdaVir (Cohen et al., 2019)
-
-A system from *Enterobacter cloacae* in *Escherichia coli* has an anti-phage effect against T2, T7 (Lowey et al., 2020)
-
-A system from *Pseudomonas aeruginosa* in *Pseudomonas aeruginosa* has an anti-phage effect against PaMx41, PaMx33, PaMx35, PaMx43 (Huiting et al., 2022)
-
+<mermaid>
+graph LR;
+ Cohen_2019[<a href='https://doi.org/10.1038/s41586-019-1605-5'>Cohen et al., 2019</a>] --> Origin_0
+ Origin_0[Vibrio cholerae
+<a href='https://ncbi.nlm.nih.gov/protein/WP_001901330.1'>WP_001901330.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_001133548.1'>WP_001133548.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/WP_001884104.1'>WP_001884104.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_223225479.1'>WP_223225479.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> P1 & T2
+ Cohen_2019[<a href='https://doi.org/10.1038/s41586-019-1605-5'>Cohen et al., 2019</a>] --> Origin_1
+ Origin_1[Escherichia coli] --> Expressed_1[Escherichia coli]
+ Expressed_1[Escherichia coli] ----> P1 & T2 & T4 & T5 & T6 & LambdaVir
+ Lowey_2020[<a href='https://doi.org/10.1016/j.cell.2020.05.019'>Lowey et al., 2020</a>] --> Origin_2
+ Origin_2[Enterobacter cloacae
+<a href='https://ncbi.nlm.nih.gov/protein/WP_032676399.1'>WP_032676399.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_032676400.1'>WP_032676400.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/WP_050010101.1'>WP_050010101.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_157903655.1'>WP_157903655.1</a>] --> Expressed_2[Escherichia coli]
+ Expressed_2[Escherichia coli] ----> T2 & T7
+ Huiting_2022[<a href='https://doi.org/10.1016/j.cell.2022.12.041'>Huiting et al., 2023</a>] --> Origin_3
+ Origin_3[Pseudomonas aeruginosa] --> Expressed_3[Pseudomonas aeruginosa]
+ Expressed_3[Pseudomonas aeruginosa] ----> PaMx41 & PaMx33 & PaMx35 & PaMx43
+ subgraph Title1[Reference]
+ Cohen_2019
+ Lowey_2020
+ Huiting_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_1
+ Origin_2
+ Origin_3
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_1
+ Expressed_2
+ Expressed_3
+end
+ subgraph Title4[Phage infected]
+ P1
+ T2
+ P1
+ T2
+ T4
+ T5
+ T6
+ LambdaVir
+ T2
+ T7
+ PaMx41
+ PaMx33
+ PaMx35
+ PaMx43
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/charlie_gp32.md b/content/3.defense-systems/charlie_gp32.md
index 45d8ee98..78ac40bf 100644
--- a/content/3.defense-systems/charlie_gp32.md
+++ b/content/3.defense-systems/charlie_gp32.md
@@ -23,6 +23,30 @@ dataUrl: /charlie_gp32/Charlie_gp32__gp32-plddts_82.99758.pdb
---
::
+## Experimental validation
+<mermaid>
+graph LR;
+ Dedrick_2017[<a href='https://doi.org/10.1038/nmicrobiol.2016.251'>Dedrick et al., 2017</a>] --> Origin_0
+ Origin_0[Mycobacterium phage Charlie
+<a href='https://ncbi.nlm.nih.gov/protein/YP_009017028.1'>YP_009017028.1</a>] --> Expressed_0[Mycobacterium smegmatis]
+ Expressed_0[Mycobacterium smegmatis] ----> thephageChe9c
+ subgraph Title1[Reference]
+ Dedrick_2017
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ thephageChe9c
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstract
::relevant-abstracts
---
diff --git a/content/3.defense-systems/dartg.md b/content/3.defense-systems/dartg.md
index 79546aa6..adf9b92b 100644
--- a/content/3.defense-systems/dartg.md
+++ b/content/3.defense-systems/dartg.md
@@ -52,11 +52,31 @@ dataUrl: /dartg/DarTG,DarTG_DarT,0,DF-plddts_94.62475.pdb
::
## Experimental validation
-
-DarTG systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against RB69, T5, SECphi18, Lust (Leroux et al., 2022)
-
+<mermaid>
+graph LR;
+ Leroux_2022[<a href='https://doi.org/10.1038/s41564-022-01153-5'>LeRoux et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia coli strain C7] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> RB69 & T5 & SECphi18 & Lust
+ subgraph Title1[Reference]
+ Leroux_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ RB69
+ T5
+ SECphi18
+ Lust
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/dazbog.md b/content/3.defense-systems/dazbog.md
index c771b8e9..e4148981 100644
--- a/content/3.defense-systems/dazbog.md
+++ b/content/3.defense-systems/dazbog.md
@@ -67,13 +67,41 @@ dataUrl: /dazbog/Dazbog,Dazbog__DzbB,0,V-plddts_93.82789.pdb
::
## Experimental validation
-
-Dazbog systems were experimentally validated using:
-
-A system from *Bacillus cereus* in *Escherichia coli* has an anti-phage effect against T2, T4, T6, T5, T7 (Millman et al., 2022)
-
-A system from *Bacillus cereus* in *Bacillus subtilis* has an anti-phage effect against Fado, SPR (Millman et al., 2022)
-
+<mermaid>
+graph LR;
+ Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
+ Origin_0[Bacillus cereus
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2689007484'>2689007484</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2689007485'>2689007485</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & T5 & T7
+ Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
+ Origin_0[Bacillus cereus
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2689007484'>2689007484</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2689007485'>2689007485</a>] --> Expressed_1[Bacillus subtilis]
+ Expressed_1[Bacillus subtilis] ----> Fado & SPR
+ subgraph Title1[Reference]
+ Millman_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_1
+end
+ subgraph Title4[Phage infected]
+ T2
+ T4
+ T6
+ T5
+ T7
+ Fado
+ SPR
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/dctpdeaminase.md b/content/3.defense-systems/dctpdeaminase.md
index d8a12c5a..fefe8bcf 100644
--- a/content/3.defense-systems/dctpdeaminase.md
+++ b/content/3.defense-systems/dctpdeaminase.md
@@ -55,19 +55,76 @@ dataUrl: /dctpdeaminase/dCTPdeaminase__dCTPdeaminase-plddts_91.37723.pdb
::
## Experimental validation
-
-dCTPdeaminase systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T5, SECphi4, SECphi6, SECphi18, T2, T4, T6, T7 (Tal et al., 2022)
-
-Subsystem AvcID with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T3, SECphi17, SECphi18, SECphi27 (Hsueh et al., 2022)
-
-Subsystem AvcID with a system from *Proteus mirabilis* in *Escherichia coli* has an anti-phage effect against T4 (Hsueh et al., 2022)
-
-Subsystem AvcID with a system from *Vibrio parahaemolyticus* in *Escherichia coli* has an anti-phage effect against T3, T5, T6, SECphi18 (Hsueh et al., 2022)
-
-Subsystem AvcID with a system from *Vibrio cholerae* in *Escherichia coli* has an anti-phage effect against T2, T3 (Hsueh et al., 2022)
-
+<mermaid>
+graph LR;
+ Tal_2022[<a href='https://doi.org/10.1038/s41564-022-01158-0'>Tal et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_045268677.1'>WP_045268677.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T5 & SECphi4 & SECphi6 & SECphi18 & T2 & T4 & T6 & T7
+ Hsueh_2022[<a href='https://doi.org/10.1038/s41564-022-01162-4'>Hsueh et al., 2022</a>] --> Origin_1
+ Origin_1[ AvcID
+Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_096882215.1'>WP_096882215.1</a>] --> Expressed_1[Escherichia coli]
+ Expressed_1[Escherichia coli] ----> T3 & SECphi17 & SECphi18 & SECphi27
+ Hsueh_2022[<a href='https://doi.org/10.1038/s41564-022-01162-4'>Hsueh et al., 2022</a>] --> Origin_2
+ Origin_2[ AvcID
+Proteus mirabilis
+<a href='https://ncbi.nlm.nih.gov/protein/WP_108717204.1'>WP_108717204.1</a>] --> Expressed_2[Escherichia coli]
+ Expressed_2[Escherichia coli] ----> T4
+ Hsueh_2022[<a href='https://doi.org/10.1038/s41564-022-01162-4'>Hsueh et al., 2022</a>] --> Origin_3
+ Origin_3[ AvcID
+Vibrio parahaemolyticus
+<a href='https://ncbi.nlm.nih.gov/protein/WP_020839904.1'>WP_020839904.1</a>] --> Expressed_3[Escherichia coli]
+ Expressed_3[Escherichia coli] ----> T3 & T5 & T6 & SECphi18
+ Hsueh_2022[<a href='https://doi.org/10.1038/s41564-022-01162-4'>Hsueh et al., 2022</a>] --> Origin_4
+ Origin_4[ AvcID
+Vibrio cholerae
+<a href='https://ncbi.nlm.nih.gov/protein/WP_001901328.1'>WP_001901328.1</a>] --> Expressed_4[Escherichia coli]
+ Expressed_4[Escherichia coli] ----> T2 & T3
+ subgraph Title1[Reference]
+ Tal_2022
+ Hsueh_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_1
+ Origin_2
+ Origin_3
+ Origin_4
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_1
+ Expressed_2
+ Expressed_3
+ Expressed_4
+end
+ subgraph Title4[Phage infected]
+ T5
+ SECphi4
+ SECphi6
+ SECphi18
+ T2
+ T4
+ T6
+ T7
+ T3
+ SECphi17
+ SECphi18
+ SECphi27
+ T4
+ T3
+ T5
+ T6
+ SECphi18
+ T2
+ T3
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/detocs.md b/content/3.defense-systems/detocs.md
index 1b4eaa8d..cc4a24bf 100644
--- a/content/3.defense-systems/detocs.md
+++ b/content/3.defense-systems/detocs.md
@@ -34,12 +34,49 @@ While 80% of Detocs operons encode PNP effectors, in a minority of these operons
Detocs is encoded in Proteobacteria, Bacteroidetes, Firmicutes, Planctomycetes and Chloroflexi phyla.
## Experimental validation
-Detocs was experimentally validated using:
-
-* A system from Vibrio alginolyticus UCD-32C that has defense activity against phages T2, T4, T5, T6 and SECphi27 (Rousset et al., 2023).
-
-* A system from Enterobacter cloacae JD6301 that has defense activity against phages T2, T4, T5, T7, SECphi4, SECphi6, SECphi18 and SECphi27 (Rousset et al., 2023).
-
+<mermaid>
+graph LR;
+ Rousset_2023[<a href='https://doi.org/10.1016/j.cell.2023.07.020'>Rousset et al., 2023</a>] --> Origin_0
+ Origin_0[Vibrio alginolyticus
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2645761408'>2645761408</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2645761407'>2645761407</a>,
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2645761406'>2645761406</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T2 & T4 & T5 & T6
+ Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_1
+ Origin_1[ Detocs Hydrolase
+Enterobacter cloacae
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2540965173'>2540965173</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2540965172'>2540965172</a>,
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2540965171'>2540965171</a>] --> Expressed_1[Escherichia coli]
+ Expressed_1[Escherichia coli] ----> SECPhi27 & T5 & SECPhi18 & SECPhi6 & T2 & T4 & T7
+ subgraph Title1[Reference]
+ Rousset_2023
+ Millman_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_1
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_1
+end
+ subgraph Title4[Phage infected]
+ T2
+ T4
+ T5
+ T6
+ SECPhi27
+ T5
+ SECPhi18
+ SECPhi6
+ T2
+ T4
+ T7
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Structure
### Detocs
diff --git a/content/3.defense-systems/dgtpase.md b/content/3.defense-systems/dgtpase.md
index b3413fc8..9c346e97 100644
--- a/content/3.defense-systems/dgtpase.md
+++ b/content/3.defense-systems/dgtpase.md
@@ -45,17 +45,72 @@ dataUrl: /dgtpase/dGTPase__Sp_dGTPase-plddts_94.35719.pdb
::
## Experimental validation
-
-dGTPase systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T5, SECphi4, SECphi6, SECphi18, SECphi27, T7 (Tal et al., 2022)
-
-A system from *Mesorhizobium ssp.* in *Escherichia coli* has an anti-phage effect against SECphi4, SECphi6, SECphi18, SECphi27, T7 (Tal et al., 2022)
-
-A system from *Pseudoalteromonas luteoviolacea* in *Escherichia coli* has an anti-phage effect against T5, SECphi4, SECphi6, SECphi18, SECphi27, T2 (Tal et al., 2022)
-
-A system from *Shewanella putrefaciens* in *Escherichia coli* has an anti-phage effect against T5, SECphi4, SECphi6, SECphi18, SECphi27, T2, T6, T7, SECphi17 (Tal et al., 2022)
-
+<mermaid>
+graph LR;
+ Tal_2022[<a href='https://doi.org/10.1038/s41564-022-01158-0'>Tal et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2704680458'>2704680458</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T5 & SECphi4 & SECphi6 & SECphi18 & SECphi27 & T7
+ Tal_2022[<a href='https://doi.org/10.1038/s41564-022-01158-0'>Tal et al., 2022</a>] --> Origin_1
+ Origin_1[Mesorhizobium ssp.
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2522901616'>2522901616</a>] --> Expressed_1[Escherichia coli]
+ Expressed_1[Escherichia coli] ----> SECphi4 & SECphi6 & SECphi18 & SECphi27 & T7
+ Tal_2022[<a href='https://doi.org/10.1038/s41564-022-01158-0'>Tal et al., 2022</a>] --> Origin_2
+ Origin_2[Pseudoalteromonas luteoviolacea
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2731093246'>2731093246</a>] --> Expressed_2[Escherichia coli]
+ Expressed_2[Escherichia coli] ----> T5 & SECphi4 & SECphi6 & SECphi18 & SECphi27 & T2
+ Tal_2022[<a href='https://doi.org/10.1038/s41564-022-01158-0'>Tal et al., 2022</a>] --> Origin_3
+ Origin_3[Shewanella putrefaciens
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2524134135'>2524134135</a>] --> Expressed_3[Escherichia coli]
+ Expressed_3[Escherichia coli] ----> T5 & SECphi4 & SECphi6 & SECphi18 & SECphi27 & T2 & T6 & T7 & SECphi17
+ subgraph Title1[Reference]
+ Tal_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_1
+ Origin_2
+ Origin_3
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_1
+ Expressed_2
+ Expressed_3
+end
+ subgraph Title4[Phage infected]
+ T5
+ SECphi4
+ SECphi6
+ SECphi18
+ SECphi27
+ T7
+ SECphi4
+ SECphi6
+ SECphi18
+ SECphi27
+ T7
+ T5
+ SECphi4
+ SECphi6
+ SECphi18
+ SECphi27
+ T2
+ T5
+ SECphi4
+ SECphi6
+ SECphi18
+ SECphi27
+ T2
+ T6
+ T7
+ SECphi17
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/disarm.md b/content/3.defense-systems/disarm.md
index 295c7d93..c1453e04 100644
--- a/content/3.defense-systems/disarm.md
+++ b/content/3.defense-systems/disarm.md
@@ -56,13 +56,66 @@ Among the 22k complete genomes of RefSeq, this system is present in 341 genomes
*Proportion of genome encoding the DISARM system for the 14 phyla with more than 50 genomes in the RefSeq database.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.*
## Experimental validation
-
-DISARM systems were experimentally validated using:
-
-A system from *Bacillus paralicheniformis* in *Bacillus subtilis* has an anti-phage effect against SPO1, phi3T, SpBeta, SPR, phi105, rho14, SPP1, phi29 , Nf (Doron et al., 2018; Ofir et al., 2017)
-
-A system from *Serratia sp. SCBI* in *Escherichia coli* has an anti-phage effect against T1, Nami, T7, M13 (Aparicio-Maldonado et al., 2021)
-
+<mermaid>
+graph LR;
+ Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_0
+ Ofir_2017[<a href='https://doi.org/10.1038/s41564-017-0051-0'>Ofir et al., 2018</a>] --> Origin_0
+ Origin_0[Bacillus paralicheniformis
+<a href='https://ncbi.nlm.nih.gov/protein/WP_020450479.1'>WP_020450479.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_020450481.1'>WP_020450481.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/WP_020450482.1'>WP_020450482.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_025810358.1'>WP_025810358.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/WP_020450478.1'>WP_020450478.1</a>] --> Expressed_0[Bacillus subtilis]
+ Expressed_0[Bacillus subtilis] ----> SPO1 & phi3T & SpBeta & SPR & phi105 & rho14 & SPP1 & phi29 & Nf
+ Aparicio-Maldonado_2021[<a href='https://doi.org/10.1101/2021.12.28.474362'>Aparicio-Maldonado et al., 2021</a>] --> Origin_1
+ Origin_1[Serratia sp. SCBI
+<a href='https://ncbi.nlm.nih.gov/protein/WP_071883521.1'>WP_071883521.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_255352645.1'>WP_255352645.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/WP_304413583.1'>WP_304413583.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_198036332.1'>WP_198036332.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/WP_042783584.1'>WP_042783584.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_071883524.1'>WP_071883524.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/WP_071883525.1'>WP_071883525.1</a>] --> Expressed_1[Escherichia coli]
+ Expressed_1[Escherichia coli] ----> T1 & Nami & T7 & M13
+ subgraph Title1[Reference]
+ Doron_2018
+ Ofir_2017
+ Aparicio-Maldonado_2021
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_0
+ Origin_1
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_0
+ Expressed_1
+end
+ subgraph Title4[Phage infected]
+ SPO1
+ phi3T
+ SpBeta
+ SPR
+ phi105
+ rho14
+ SPP1
+ phi29
+ Nf
+ SPO1
+ phi3T
+ SpBeta
+ SPR
+ phi105
+ rho14
+ SPP1
+ phi29
+ Nf
+ T1
+ Nami
+ T7
+ M13
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/dnd.md b/content/3.defense-systems/dnd.md
index a6e2ffb0..0c4f171b 100644
--- a/content/3.defense-systems/dnd.md
+++ b/content/3.defense-systems/dnd.md
@@ -135,11 +135,29 @@ dataUrl: /dnd/Dnd_ABCDEFGH,Dnd__DndE,0,DF-plddts_95.24932.pdb
::
## Experimental validation
-
-Dnd systems were experimentally validated using:
-
-Subsystem DndCDEA-PbeABCD with a system from *Halalkalicoccus jeotgali* in *Natrinema sp. CJ7-F* has an anti-phage effect against SNJ1 (Xiong et al., 2019)
-
+<mermaid>
+graph LR;
+ Xiong_2019[<a href='https://doi.org/10.1038/s41467-019-09390-9'>Xiong et al., 2019</a>] --> Origin_0
+ Origin_0[ DndCDEA-PbeABCD
+Halalkalicoccus jeotgali] --> Expressed_0[Natrinema sp. CJ7-F]
+ Expressed_0[Natrinema sp. CJ7-F] ----> SNJ1
+ subgraph Title1[Reference]
+ Xiong_2019
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ SNJ1
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/dodola.md b/content/3.defense-systems/dodola.md
index 83277bd8..69795322 100644
--- a/content/3.defense-systems/dodola.md
+++ b/content/3.defense-systems/dodola.md
@@ -52,11 +52,29 @@ dataUrl: /dodola/Dodola,Dodola__DolB,0,V-plddts_92.53304.pdb
::
## Experimental validation
-
-Dodola systems were experimentally validated using:
-
-A system from *Bacillus cereus* in *Bacillus subtilis* has an anti-phage effect against SPP1 (Millman et al., 2022)
-
+<mermaid>
+graph LR;
+ Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
+ Origin_0[Bacillus cereus
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2625022793'>2625022793</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2625022793'>2625022793</a>] --> Expressed_0[Bacillus subtilis]
+ Expressed_0[Bacillus subtilis] ----> SPP1
+ subgraph Title1[Reference]
+ Millman_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ SPP1
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/drt.md b/content/3.defense-systems/drt.md
index c2247f60..748644c8 100644
--- a/content/3.defense-systems/drt.md
+++ b/content/3.defense-systems/drt.md
@@ -159,25 +159,114 @@ dataUrl: /drt/DRT_5__drt5-plddts_90.89502.pdb
::
## Experimental validation
-
-DRT systems were experimentally validated using:
-
-Subsystem RT-nitrilase (UG1) (Type 1) with a system from *Klebsiella pneumoniae* in *Escherichia coli* has an anti-phage effect against T2, T4, T5 (Gao et al., 2020)
-
-Subsystem RT (UG2) (Type 2) with a system from *Salmonella enterica* in *Escherichia coli* has an anti-phage effect against T5, T2 (Gao et al., 2020; Mestre et al., 2022)
-
-Subsystem RT (UG3) + RT (UG8) (Type 3) with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T5, Lambda (Gao et al., 2020)
-
-Subsystem RT (UG15) (Type 4) with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T5, T3, T7, Phi-V1, ZL19 (Gao et al., 2020; Mestre et al., 2022)
-
-Subsystem RT (UG16) (Type 5) with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2 (Gao et al., 2020)
-
-Subsystem RT (UG10) (Type 7) with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T5, ZL-19 (Mestre et al., 2022)
-
-Subsystem RT(UG7) (Type 8) with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T5 (Mestre et al., 2022)
-
-Subsystem RT (UG28) (Type 9) with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T5, ZL-19 (Mestre et al., 2022)
-
+<mermaid>
+graph LR;
+ Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
+ Origin_0[ RT-nitrilase UG1 Type 1
+Klebsiella pneumoniae
+<a href='https://ncbi.nlm.nih.gov/protein/WP_115196278.1'>WP_115196278.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_040189938.1'>WP_040189938.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T2 & T4 & T5
+ Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_1
+ Mestre_2022[<a href='https://doi.org/10.1093/nar/gkac467'>Mestre et al., 2022</a>] --> Origin_1
+ Origin_1[ RT UG2 Type 2
+Salmonella enterica
+<a href='https://ncbi.nlm.nih.gov/protein/WP_012737279.1'>WP_012737279.1</a>] --> Expressed_1[Escherichia coli]
+ Expressed_1[Escherichia coli] ----> T5 & T2
+ Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_2
+ Origin_2[ RT UG3 + RT UG8 type 3
+Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_087902017.1'>WP_087902017.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_062891751.1'>WP_062891751.1</a>] --> Expressed_2[Escherichia coli]
+ Expressed_2[Escherichia coli] ----> T2 & T5 & Lambda
+ Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_3
+ Mestre_2022[<a href='https://doi.org/10.1093/nar/gkac467'>Mestre et al., 2022</a>] --> Origin_3
+ Origin_3[ RT UG15 Type 4
+Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/GCK53192.1'>GCK53192.1</a>] --> Expressed_3[Escherichia coli]
+ Expressed_3[Escherichia coli] ----> T5 & T3 & T7 & Phi-V1 & ZL19
+ Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_4
+ Origin_4[ RT UG16 Type 5
+Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_001524904.1'>WP_001524904.1</a>] --> Expressed_4[Escherichia coli]
+ Expressed_4[Escherichia coli] ----> T2
+ Mestre_2022[<a href='https://doi.org/10.1093/nar/gkac467'>Mestre et al., 2022</a>] --> Origin_5
+ Origin_5[ RT UG10 Type 7
+Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_096936834.1'>WP_096936834.1</a>] --> Expressed_5[Escherichia coli]
+ Expressed_5[Escherichia coli] ----> T2 & T5 & ZL-19
+ Mestre_2022[<a href='https://doi.org/10.1093/nar/gkac467'>Mestre et al., 2022</a>] --> Origin_6
+ Origin_6[ RT UG7 Type 8
+Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_123894217.1'>WP_123894217.1</a>] --> Expressed_6[Escherichia coli]
+ Expressed_6[Escherichia coli] ----> T2 & T5
+ Mestre_2022[<a href='https://doi.org/10.1093/nar/gkac467'>Mestre et al., 2022</a>] --> Origin_7
+ Origin_7[ RT UG28 Type 9
+Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/EAO1508900.1'>EAO1508900.1</a>] --> Expressed_7[Escherichia coli]
+ Expressed_7[Escherichia coli] ----> T2 & T5 & ZL-19
+ subgraph Title1[Reference]
+ Gao_2020
+ Mestre_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_1
+ Origin_1
+ Origin_2
+ Origin_3
+ Origin_3
+ Origin_4
+ Origin_5
+ Origin_6
+ Origin_7
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_1
+ Expressed_1
+ Expressed_2
+ Expressed_3
+ Expressed_3
+ Expressed_4
+ Expressed_5
+ Expressed_6
+ Expressed_7
+end
+ subgraph Title4[Phage infected]
+ T2
+ T4
+ T5
+ T5
+ T2
+ T5
+ T2
+ T2
+ T5
+ Lambda
+ T5
+ T3
+ T7
+ Phi-V1
+ ZL19
+ T5
+ T3
+ T7
+ Phi-V1
+ ZL19
+ T2
+ T2
+ T5
+ ZL-19
+ T2
+ T5
+ T2
+ T5
+ ZL-19
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/druantia.md b/content/3.defense-systems/druantia.md
index 7306c6b0..960d3f77 100644
--- a/content/3.defense-systems/druantia.md
+++ b/content/3.defense-systems/druantia.md
@@ -127,11 +127,56 @@ dataUrl: /druantia/Druantia_III,Druantia__DruE_3,0,DF-plddts_83.26091.pdb
::
## Experimental validation
-
-Druantia systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T5, P1, Lambda, T3, T7, PhiV-1, Lambdavir, SECphi18, SECphi27 (Gao et al., 2020; Doron et al., 2018)
-
+<mermaid>
+graph LR;
+ Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
+ Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/ERA40829.1'>ERA40829.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/ERA40830.1'>ERA40830.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/ERA40831.1'>ERA40831.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/ERA40832.1'>ERA40832.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/ERA40833.1'>ERA40833.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T2 & T4 & T5 & P1 & Lambda & T3 & T7 & PhiV-1 & Lambdavir & SECphi18 & SECphi27
+ subgraph Title1[Reference]
+ Gao_2020
+ Doron_2018
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T2
+ T4
+ T5
+ P1
+ Lambda
+ T3
+ T7
+ PhiV-1
+ Lambdavir
+ SECphi18
+ SECphi27
+ T2
+ T4
+ T5
+ P1
+ Lambda
+ T3
+ T7
+ PhiV-1
+ Lambdavir
+ SECphi18
+ SECphi27
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/dsr.md b/content/3.defense-systems/dsr.md
index 22ee59e3..183e491a 100644
--- a/content/3.defense-systems/dsr.md
+++ b/content/3.defense-systems/dsr.md
@@ -58,17 +58,57 @@ dataUrl: /dsr/Dsr_II__Dsr2-plddts_86.62203.pdb
::
## Experimental validation
-
-Dsr systems were experimentally validated using:
-
-Subsystem DSR1 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T3, T7, PhiV-1 (Gao et al., 2020)
-
-Subsystem DSR2 with a system from *Cronobacter sakazakii* in *Escherichia coli* has an anti-phage effect against Lambda (Gao et al., 2020)
-
-Subsystem DSR2 with a system from *Bacillus subtilis* in *Bacillus subtilis * has an anti-phage effect against SPR (Garb et al., 2022)
-
-Subsystem DSR1 with a system from *Bacillus subtilis* in *Bacillus subtilis * has an anti-phage effect against phi29 (Garb et al., 2022)
-
+<mermaid>
+graph LR;
+ Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
+ Origin_0[ DSR1
+Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_029488749.1'>WP_029488749.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T3 & T7 & PhiV-1
+ Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_1
+ Origin_1[ DSR2
+Cronobacter sakazakii
+<a href='https://ncbi.nlm.nih.gov/protein/WP_015387030.1'>WP_015387030.1</a>] --> Expressed_1[Escherichia coli]
+ Expressed_1[Escherichia coli] ----> Lambda
+ Garb_2022[<a href='https://doi.org/10.1038/s41564-022-01207-8'>Garb et al., 2022</a>] --> Origin_2
+ Origin_2[ DSR2
+Bacillus subtilis
+<a href='https://ncbi.nlm.nih.gov/protein/WP_029317421.1'>WP_029317421.1</a>] --> Expressed_2[Bacillus subtilis ]
+ Expressed_2[Bacillus subtilis ] ----> SPR
+ Garb_2022[<a href='https://doi.org/10.1038/s41564-022-01207-8'>Garb et al., 2022</a>] --> Origin_3
+ Origin_3[ DSR1
+Bacillus subtilis
+<a href='https://ncbi.nlm.nih.gov/protein/WP_053564071.1'>WP_053564071.1</a>] --> Expressed_3[Bacillus subtilis]
+ Expressed_3[Bacillus subtilis] ----> phi29
+ subgraph Title1[Reference]
+ Gao_2020
+ Garb_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_1
+ Origin_2
+ Origin_3
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_1
+ Expressed_2
+ Expressed_3
+end
+ subgraph Title4[Phage infected]
+ T3
+ T7
+ PhiV-1
+ Lambda
+ SPR
+ phi29
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/eleos.md b/content/3.defense-systems/eleos.md
index d60586e6..fab1f736 100644
--- a/content/3.defense-systems/eleos.md
+++ b/content/3.defense-systems/eleos.md
@@ -53,12 +53,30 @@ dataUrl: /eleos/Eleos,Eleos__LeoBC,0,V-plddts_83.32056.pdb
::
## Experimental validation
-
-Eleos systems were experimentally validated using:
-
-A system from *Bacillus vietnamensis* in *Bacillus subtilis* has an anti-phage effect against AR9 (Jumbo), PBS1(Jumbo) (Millman et al., 2022)
-
-
+<mermaid>
+graph LR;
+ Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
+ Origin_0[Bacillus vietnamensis
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2732656981'>2732656981</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2732656980'>2732656980</a>] --> Expressed_0[Bacillus subtilis]
+ Expressed_0[Bacillus subtilis] ----> AR9 & PBS1
+ subgraph Title1[Reference]
+ Millman_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ AR9
+ PBS1
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/fs_giy_yig.md b/content/3.defense-systems/fs_giy_yig.md
index 5cde4e31..91987d8b 100644
--- a/content/3.defense-systems/fs_giy_yig.md
+++ b/content/3.defense-systems/fs_giy_yig.md
@@ -23,6 +23,39 @@ dataUrl: /fs_giy_yig/FS_GIY_YIG__GIY_YIG-plddts_93.05664.pdb
---
::
+## Experimental validation
+<mermaid>
+graph LR;
+ Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
+ Origin_0[Klebsiella pneumoniae
+<a href='https://ncbi.nlm.nih.gov/protein/WP_071843248.1'>WP_071843248.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> HK97 & HK544
+ Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
+ Origin_0[Klebsiella pneumoniae
+<a href='https://ncbi.nlm.nih.gov/protein/WP_071843248.1'>WP_071843248.1</a>] --> Expressed_1[Salmonella enterica]
+ Expressed_1[Salmonella enterica] ----> P22 & BTP1
+ subgraph Title1[Reference]
+ Fillol-Salom_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_1
+end
+ subgraph Title4[Phage infected]
+ HK97
+ HK544
+ P22
+ BTP1
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstract
::relevant-abstracts
---
diff --git a/content/3.defense-systems/fs_hepn_tm.md b/content/3.defense-systems/fs_hepn_tm.md
index e147130b..f6d2095e 100644
--- a/content/3.defense-systems/fs_hepn_tm.md
+++ b/content/3.defense-systems/fs_hepn_tm.md
@@ -30,6 +30,32 @@ dataUrl: /fs_hepn_tm/FS_HEPN_TM__TM-plddts_90.28126.pdb
---
::
+## Experimental validation
+<mermaid>
+graph LR;
+ Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
+ Origin_0[Staphylococcus saprophyticus
+<a href='https://ncbi.nlm.nih.gov/protein/RXS01966.1'>RXS01966.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RXS01965.1'>RXS01965.1</a>] --> Expressed_0[Staphylococcus aureus]
+ Expressed_0[Staphylococcus aureus] ----> ΦSA2 & Φ12 & ΦSLT
+ subgraph Title1[Reference]
+ Fillol-Salom_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ ΦSA2
+ Φ12
+ ΦSLT
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstract
::relevant-abstracts
---
diff --git a/content/3.defense-systems/fs_hp.md b/content/3.defense-systems/fs_hp.md
index ee17cc9a..98a3aa0a 100644
--- a/content/3.defense-systems/fs_hp.md
+++ b/content/3.defense-systems/fs_hp.md
@@ -23,6 +23,38 @@ dataUrl: /fs_hp/FS_HP__HP-plddts_94.44828.pdb
---
::
+## Experimental validation
+<mermaid>
+graph LR;
+ Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia fergusonii
+<a href='https://ncbi.nlm.nih.gov/protein/QML19489.1'>QML19489.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> HK578
+ Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia fergusonii
+<a href='https://ncbi.nlm.nih.gov/protein/QML19489.1'>QML19489.1</a>] --> Expressed_1[Salmonella enterica]
+ Expressed_1[Salmonella enterica] ----> P22 & ES18
+ subgraph Title1[Reference]
+ Fillol-Salom_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_1
+end
+ subgraph Title4[Phage infected]
+ HK578
+ P22
+ ES18
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstract
::relevant-abstracts
---
diff --git a/content/3.defense-systems/fs_hp_sdh_sah.md b/content/3.defense-systems/fs_hp_sdh_sah.md
index 49fb231d..e4bd1790 100644
--- a/content/3.defense-systems/fs_hp_sdh_sah.md
+++ b/content/3.defense-systems/fs_hp_sdh_sah.md
@@ -31,6 +31,30 @@ dataUrl: /fs_hp_sdh_sah/FS_HP_SDH_sah__SDH_sah-plddts_95.32024.pdb
---
::
+## Experimental validation
+<mermaid>
+graph LR;
+ Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
+ Origin_0[Klebsiella pneumoniae
+<a href='https://ncbi.nlm.nih.gov/protein/BBW89085.1'>BBW89085.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/BBW89084.1'>BBW89084.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T4
+ subgraph Title1[Reference]
+ Fillol-Salom_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T4
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstract
::relevant-abstracts
---
diff --git a/content/3.defense-systems/fs_hsdr_like.md b/content/3.defense-systems/fs_hsdr_like.md
index ad60e69e..48fea2a4 100644
--- a/content/3.defense-systems/fs_hsdr_like.md
+++ b/content/3.defense-systems/fs_hsdr_like.md
@@ -30,6 +30,45 @@ dataUrl: /fs_hsdr_like/FS_HsdR_like__HdrR-plddts_88.7069.pdb
---
::
+## Experimental validation
+<mermaid>
+graph LR;
+ Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
+ Origin_0[Klebsiella pneumoniae
+<a href='https://ncbi.nlm.nih.gov/protein/QFH39805.1'>QFH39805.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RXS01985.1'>RXS01985.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T5 & Lambda & HK97 & HK544 & HK544 & HK578 & T7
+ Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
+ Origin_0[Klebsiella pneumoniae
+<a href='https://ncbi.nlm.nih.gov/protein/QFH39805.1'>QFH39805.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RXS01985.1'>RXS01985.1</a>] --> Expressed_1[Salmonella enterica]
+ Expressed_1[Salmonella enterica] ----> P22 & BTP1 & ES18
+ subgraph Title1[Reference]
+ Fillol-Salom_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_1
+end
+ subgraph Title4[Phage infected]
+ T5
+ Lambda
+ HK97
+ HK544
+ HK544
+ HK578
+ T7
+ P22
+ BTP1
+ ES18
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstract
::relevant-abstracts
---
diff --git a/content/3.defense-systems/fs_sma.md b/content/3.defense-systems/fs_sma.md
index 55512c53..a5b0c029 100644
--- a/content/3.defense-systems/fs_sma.md
+++ b/content/3.defense-systems/fs_sma.md
@@ -24,6 +24,47 @@ dataUrl: /fs_sma/FS_Sma__Sma-plddts_94.14969.pdb
---
::
+## Experimental validation
+<mermaid>
+graph LR;
+ Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
+ Origin_0[Staphylococcus aureus' PICI SaPIpT1028
+<a href='https://ncbi.nlm.nih.gov/protein/RXS01985.1'>RXS01985.1</a>] --> Expressed_0[Staphylococcus aureus]
+ Expressed_0[Staphylococcus aureus] ----> 80alpha & phiNM1 & phiNM2 & phi53 & phi55 & phi6199 & phi7206 & phi6490 & phiSLT & Sushi & phi2339 & phi96 & ROSA & phi11 & phi12 & phi85 & phi7094 & phiSA2
+ subgraph Title1[Reference]
+ Fillol-Salom_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ 80alpha
+ phiNM1
+ phiNM2
+ phi53
+ phi55
+ phi6199
+ phi7206
+ phi6490
+ phiSLT
+ Sushi
+ phi2339
+ phi96
+ ROSA
+ phi11
+ phi12
+ phi85
+ phi7094
+ phiSA2
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstract
::relevant-abstracts
---
diff --git a/content/3.defense-systems/gabija.md b/content/3.defense-systems/gabija.md
index d961bb83..df8a8f72 100644
--- a/content/3.defense-systems/gabija.md
+++ b/content/3.defense-systems/gabija.md
@@ -62,15 +62,49 @@ dataUrl: /gabija/Gabija,Gabija__GajA,0,V-plddts_86.08162.pdb
::
## Experimental validation
-
-Gabija systems were experimentally validated using:
-
-A system from *Bacillus cereus* in *Bacillus subtilis* has an anti-phage effect against SBSphiC, SpBeta, phi105, rho14, phi29 (Doron et al., 2018)
-
-A system from *Bacillus cereus* in *Bacillus subtilis* has an anti-phage effect against SpBeta, phi105 (Doron et al., 2018)
-
-A system from *Bacillus cereus* in *Escherichia coli* has an anti-phage effect against T7 (Cheng et al., 2021)
-
+<mermaid>
+graph LR;
+ Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_0
+ Origin_0[Bacillus cereus strain VD045
+<a href='https://ncbi.nlm.nih.gov/protein/EJR29742.1'>EJR29742.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/EJR29743.1'>EJR29743.1</a>] --> Expressed_0[Bacillus subtilis]
+ Expressed_0[Bacillus subtilis] ----> SBSphiC & SpBeta & phi105 & rho14 & phi29
+ Cheng_2021[<a href='https://doi.org/10.1093/nar/gkab277'>Cheng et al., 2021</a>] --> Origin_0
+ Origin_0[Bacillus cereus strain VD045
+<a href='https://ncbi.nlm.nih.gov/protein/EJR29742.1'>EJR29742.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/EJR29743.1'>EJR29743.1</a>] --> Expressed_2[Escherichia coli]
+ Expressed_2[Escherichia coli] ----> T7
+ Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_1
+ Origin_1[Bacillus cereus strain HuB5-5
+<a href='https://ncbi.nlm.nih.gov/protein/EJQ91274.1'>EJQ91274.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/EJQ91275.1'>EJQ91275.1</a>] --> Expressed_1[Bacillus subtilis]
+ Expressed_1[Bacillus subtilis] ----> SpBeta & phi105
+ subgraph Title1[Reference]
+ Doron_2018
+ Cheng_2021
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_0
+ Origin_1
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_2
+ Expressed_1
+end
+ subgraph Title4[Phage infected]
+ SBSphiC
+ SpBeta
+ phi105
+ rho14
+ phi29
+ T7
+ SpBeta
+ phi105
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/gao_ape.md b/content/3.defense-systems/gao_ape.md
index 22b3714d..38f502cd 100644
--- a/content/3.defense-systems/gao_ape.md
+++ b/content/3.defense-systems/gao_ape.md
@@ -44,11 +44,34 @@ dataUrl: /gao_ape/Gao_Ape__ApeA-plddts_90.44181.pdb
::
## Experimental validation
-
-Gao_Ape systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T5, T3, T7, PhiV-1 (Gao et al., 2020)
-
+<mermaid>
+graph LR;
+ Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_000706972.1'>WP_000706972.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T2 & T4 & T5 & T3 & T7 & PhiV-1
+ subgraph Title1[Reference]
+ Gao_2020
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T2
+ T4
+ T5
+ T3
+ T7
+ PhiV-1
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/gao_her.md b/content/3.defense-systems/gao_her.md
index 87bee93f..b1909eaf 100644
--- a/content/3.defense-systems/gao_her.md
+++ b/content/3.defense-systems/gao_her.md
@@ -72,13 +72,45 @@ dataUrl: /gao_her/Gao_Her_SIR,Gao_Her_SIR__SIR2,0,V-plddts_87.76893.pdb
::
## Experimental validation
-
-Gao_Her systems were experimentally validated using:
-
-Subsystem SIR2 + HerA with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against Lambda, T3, T7, PhiV-1 (Gao et al., 2020)
-
-Subsystem DUF4297 + HerA with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T4, P1, Lambda, T3, T7 (Gao et al., 2020)
-
+<mermaid>
+graph LR;
+ Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
+ Origin_0[ SIR2 + HerA
+Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_021577682.1'>WP_021577682.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_021577683.1'>WP_021577683.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> Lambda & T3 & T7 & PhiV-1
+ Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_1
+ Origin_1[ DUF4297 + HerA
+Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_016239655.1'>WP_016239655.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_016239654.1'>WP_016239654.1</a>] --> Expressed_1[Escherichia coli]
+ Expressed_1[Escherichia coli] ----> T4 & P1 & Lambda & T3 & T7
+ subgraph Title1[Reference]
+ Gao_2020
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_1
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_1
+end
+ subgraph Title4[Phage infected]
+ Lambda
+ T3
+ T7
+ PhiV-1
+ T4
+ P1
+ Lambda
+ T3
+ T7
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/gao_hhe.md b/content/3.defense-systems/gao_hhe.md
index 2ad765ff..9b9f35cd 100644
--- a/content/3.defense-systems/gao_hhe.md
+++ b/content/3.defense-systems/gao_hhe.md
@@ -45,11 +45,32 @@ dataUrl: /gao_hhe/Gao_Hhe__HheA-plddts_81.41701.pdb
::
## Experimental validation
-
-Gao_Hhe systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against Lambda, T3, T7, PhiV-1 (Gao et al., 2020)
-
+<mermaid>
+graph LR;
+ Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_032200272.1'>WP_032200272.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> Lambda & T3 & T7 & PhiV-1
+ subgraph Title1[Reference]
+ Gao_2020
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ Lambda
+ T3
+ T7
+ PhiV-1
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/gao_iet.md b/content/3.defense-systems/gao_iet.md
index 29aab706..9c749adf 100644
--- a/content/3.defense-systems/gao_iet.md
+++ b/content/3.defense-systems/gao_iet.md
@@ -52,11 +52,32 @@ dataUrl: /gao_iet/Gao_Iet,Gao_Iet__IetS,0,V-plddts_90.4167.pdb
::
## Experimental validation
-
-Gao_Iet systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against Lambda, T3, T7, PhiV-1 (Gao et al., 2020)
-
+<mermaid>
+graph LR;
+ Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_000385105.1'>WP_000385105.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_001551050.1'>WP_001551050.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> Lambda & T3 & T7 & PhiV-1
+ subgraph Title1[Reference]
+ Gao_2020
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ Lambda
+ T3
+ T7
+ PhiV-1
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/gao_mza.md b/content/3.defense-systems/gao_mza.md
index e8eab809..1a41eb4c 100644
--- a/content/3.defense-systems/gao_mza.md
+++ b/content/3.defense-systems/gao_mza.md
@@ -73,11 +73,35 @@ dataUrl: /gao_mza/Gao_Mza,Gao_Mza__MzaE,0,V-plddts_87.92462.pdb
::
## Experimental validation
-
-Gao_Mza systems were experimentally validated using:
-
-A system from *Salmonella enterica* in *Escherichia coli* has an anti-phage effect against T2, T4, T5, Lambda, M13 (Gao et al., 2020)
-
+<mermaid>
+graph LR;
+ Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
+ Origin_0[Salmonella enterica
+<a href='https://ncbi.nlm.nih.gov/protein/VEA06816.1'>VEA06816.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/VEA06814.1'>VEA06814.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/VEA06812.1'>VEA06812.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/VEA06810.1'>VEA06810.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/VEA06808.1'>VEA06808.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T2 & T4 & T5 & Lambda & M13
+ subgraph Title1[Reference]
+ Gao_2020
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T2
+ T4
+ T5
+ Lambda
+ M13
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/gao_ppl.md b/content/3.defense-systems/gao_ppl.md
index 818c4a67..bcc350b9 100644
--- a/content/3.defense-systems/gao_ppl.md
+++ b/content/3.defense-systems/gao_ppl.md
@@ -44,11 +44,32 @@ dataUrl: /gao_ppl/Gao_Ppl__PplA-plddts_89.89639.pdb
::
## Experimental validation
-
-Gao_Ppl systems were experimentally validated using:
-
-A system from *Salmonella enterica* in *Escherichia coli* has an anti-phage effect against Lambda, T3, T7, PhiV-1 (Gao et al., 2020)
-
+<mermaid>
+graph LR;
+ Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
+ Origin_0[Salmonella enterica
+<a href='https://ncbi.nlm.nih.gov/protein/STM52149.1'>STM52149.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> Lambda & T3 & T7 & PhiV-1
+ subgraph Title1[Reference]
+ Gao_2020
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ Lambda
+ T3
+ T7
+ PhiV-1
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/gao_qat.md b/content/3.defense-systems/gao_qat.md
index 3199a3e1..80833dfa 100644
--- a/content/3.defense-systems/gao_qat.md
+++ b/content/3.defense-systems/gao_qat.md
@@ -66,11 +66,31 @@ dataUrl: /gao_qat/Gao_Qat,Gao_Qat__QatD,0,V-plddts_94.78681.pdb
::
## Experimental validation
-
-Gao_Qat systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against P1, Lambda (Gao et al., 2020)
-
+<mermaid>
+graph LR;
+ Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/STG85056.1'>STG85056.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/STG85057.1'>STG85057.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/STG85058.1'>STG85058.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/STG85059.1'>STG85059.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> P1 & Lambda
+ subgraph Title1[Reference]
+ Gao_2020
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ P1
+ Lambda
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/gao_rl.md b/content/3.defense-systems/gao_rl.md
index a4c90e5b..3372c763 100644
--- a/content/3.defense-systems/gao_rl.md
+++ b/content/3.defense-systems/gao_rl.md
@@ -66,11 +66,32 @@ dataUrl: /gao_rl/Gao_RL,Gao_RL__RL_D,0,V-plddts_85.47115.pdb
::
## Experimental validation
-
-Gao_RL systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against P1, Lambda, M13 (Gao et al., 2020)
-
+<mermaid>
+graph LR;
+ Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_000860009.1'>WP_000860009.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_001044652.1'>WP_001044652.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/WP_001207938.1'>WP_001207938.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_000985714.1'>WP_000985714.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> P1 & Lambda & M13
+ subgraph Title1[Reference]
+ Gao_2020
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ P1
+ Lambda
+ M13
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/gao_tery.md b/content/3.defense-systems/gao_tery.md
index 7d4f8c1c..e82990dc 100644
--- a/content/3.defense-systems/gao_tery.md
+++ b/content/3.defense-systems/gao_tery.md
@@ -58,11 +58,32 @@ dataUrl: /gao_tery/Gao_TerY,Gao_TerY__TerYC,0,V-plddts_81.328.pdb
::
## Experimental validation
-
-Gao_TerY systems were experimentally validated using:
-
-A system from *Citrobacter gillenii* in *Escherichia coli* has an anti-phage effect against T3, T7, PhiV-1 (Gao et al., 2020)
-
+<mermaid>
+graph LR;
+ Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
+ Origin_0[Citrobacter gillenii
+<a href='https://ncbi.nlm.nih.gov/protein/WP_115257868.1'>WP_115257868.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_115257869.1'>WP_115257869.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/WP_115257870.1'>WP_115257870.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T3 & T7 & PhiV-1
+ subgraph Title1[Reference]
+ Gao_2020
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T3
+ T7
+ PhiV-1
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/gao_tmn.md b/content/3.defense-systems/gao_tmn.md
index 339529f5..f3b8512e 100644
--- a/content/3.defense-systems/gao_tmn.md
+++ b/content/3.defense-systems/gao_tmn.md
@@ -44,11 +44,32 @@ dataUrl: /gao_tmn/Gao_Tmn__TmnA-plddts_82.0142.pdb
::
## Experimental validation
-
-Gao_Tmn systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, P1, PhiV-1, PhiX (Gao et al., 2020)
-
+<mermaid>
+graph LR;
+ Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_001683567.1'>WP_001683567.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T2 & P1 & PhiV-1 & PhiX
+ subgraph Title1[Reference]
+ Gao_2020
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T2
+ P1
+ PhiV-1
+ PhiX
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/gao_upx.md b/content/3.defense-systems/gao_upx.md
index 61497b90..2fd2dd49 100644
--- a/content/3.defense-systems/gao_upx.md
+++ b/content/3.defense-systems/gao_upx.md
@@ -44,11 +44,30 @@ dataUrl: /gao_upx/Gao_Upx__UpxA-plddts_90.66658.pdb
::
## Experimental validation
-
-Gao_Upx systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against P1, PhiV-1(Gao et al., 2020)
-
+<mermaid>
+graph LR;
+ Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_060647174.1'>WP_060647174.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> P1 & PhiV-1
+ subgraph Title1[Reference]
+ Gao_2020
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ P1
+ PhiV-1
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/gaps1.md b/content/3.defense-systems/gaps1.md
index ead7f405..32bbf872 100644
--- a/content/3.defense-systems/gaps1.md
+++ b/content/3.defense-systems/gaps1.md
@@ -23,6 +23,31 @@ dataUrl: /gaps1/GAPS1__GAPS1-plddts_91.57482.pdb
---
::
+## Experimental validation
+<mermaid>
+graph LR;
+ Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0
+ Origin_0[Vibrio parahaemolyticus
+<a href='https://ncbi.nlm.nih.gov/protein/WP_005477165.1'>WP_005477165.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T7 & P1-vir
+ subgraph Title1[Reference]
+ Mahata_2023
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T7
+ P1-vir
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstract
::relevant-abstracts
---
diff --git a/content/3.defense-systems/gaps2.md b/content/3.defense-systems/gaps2.md
index 361f3889..63084664 100644
--- a/content/3.defense-systems/gaps2.md
+++ b/content/3.defense-systems/gaps2.md
@@ -24,6 +24,31 @@ dataUrl: /gaps2/GAPS2__GAPS2-plddts_87.94657.pdb
---
::
+## Experimental validation
+<mermaid>
+graph LR;
+ Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0
+ Origin_0[Vibrio parahaemolyticus
+<a href='https://ncbi.nlm.nih.gov/protein/WP_174208646.1'>WP_174208646.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> P1-vir & Lambda-vir
+ subgraph Title1[Reference]
+ Mahata_2023
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ P1-vir
+ Lambda-vir
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstract
::relevant-abstracts
---
diff --git a/content/3.defense-systems/gaps4.md b/content/3.defense-systems/gaps4.md
index c8474543..fa50666d 100644
--- a/content/3.defense-systems/gaps4.md
+++ b/content/3.defense-systems/gaps4.md
@@ -30,6 +30,33 @@ dataUrl: /gaps4/GAPS4__GAPS4b-plddts_86.45931.pdb
---
::
+## Experimental validation
+<mermaid>
+graph LR;
+ Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0
+ Origin_0[Vibrio parahaemolyticus
+<a href='https://ncbi.nlm.nih.gov/protein/WP_055466293.1'>WP_055466293.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_055466294.1'>WP_055466294.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T7 & T4 & P1-vir & Lambda-vir
+ subgraph Title1[Reference]
+ Mahata_2023
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T7
+ T4
+ P1-vir
+ Lambda-vir
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstract
::relevant-abstracts
---
diff --git a/content/3.defense-systems/gaps6.md b/content/3.defense-systems/gaps6.md
index 558f7076..59a008cf 100644
--- a/content/3.defense-systems/gaps6.md
+++ b/content/3.defense-systems/gaps6.md
@@ -30,6 +30,33 @@ dataUrl: /gaps6/GAPS6__GAPS6b-plddts_90.04892.pdb
---
::
+## Experimental validation
+<mermaid>
+graph LR;
+ Mahata_2023[<a href='https://doi.org/10.1101/2023.03.28.534373'>Mahata et al., 2023</a>] --> Origin_0
+ Origin_0[Vibrio parahaemolyticus
+<a href='https://ncbi.nlm.nih.gov/protein/WP_248387294.1'>WP_248387294.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_248387295.1'>WP_248387295.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T7 & T4 & P1-vir & Lambda-vir
+ subgraph Title1[Reference]
+ Mahata_2023
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T7
+ T4
+ P1-vir
+ Lambda-vir
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstract
::relevant-abstracts
---
diff --git a/content/3.defense-systems/gasdermin.md b/content/3.defense-systems/gasdermin.md
index 9e92e61c..09df1a0e 100644
--- a/content/3.defense-systems/gasdermin.md
+++ b/content/3.defense-systems/gasdermin.md
@@ -79,11 +79,32 @@ dataUrl: /gasdermin/GasderMIN__bGSDM1-plddts_65.95252.pdb
::
## Experimental validation
-
-GasderMIN systems were experimentally validated using:
-
-A system from *Lysobacter enzymogenes* in *Escherichia coli* has an anti-phage effect against T5, T4, T6 (Johnson et al., 2022)
-
+<mermaid>
+graph LR;
+ Johnson_2022[<a href='https://doi.org/10.1371/journal.pgen.1010065'>Johnson et al., 2022</a>] --> Origin_0
+ Origin_0[Lysobacter enzymogenes
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2841794907'>2841794907</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2841794908'>2841794908</a>,
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2841794909'>2841794909</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2841794910'>2841794910</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T5 & T4 & T6
+ subgraph Title1[Reference]
+ Johnson_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T5
+ T4
+ T6
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/hachiman.md b/content/3.defense-systems/hachiman.md
index fec562a1..61e57840 100644
--- a/content/3.defense-systems/hachiman.md
+++ b/content/3.defense-systems/hachiman.md
@@ -60,13 +60,46 @@ dataUrl: /hachiman/Hachiman.Hachiman__HamB.0.V-plddts_88.00493.pdb
::
## Experimental validation
-
-Hachiman systems were experimentally validated using:
-
-A system from *Bacillus cereus* in *Bacillus subtilis* has an anti-phage effect against SBSphiJ, phi3T, SPbeta, SPR, phi105, rho14, phi29 (Doron et al., 2018)
-
-Subsystem Hachiman Type II with a system from *Sphingopyxis witflariensis* in *Escherichia coli* has an anti-phage effect against T3, PVP-SE1 (Payne et al., 2021)
-
+<mermaid>
+graph LR;
+ Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_0
+ Origin_0[Bacillus cereus
+<a href='https://ncbi.nlm.nih.gov/protein/KLA13163.1'>KLA13163.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/KLA13162.1'>KLA13162.1</a>] --> Expressed_0[Bacillus subtilis]
+ Expressed_0[Bacillus subtilis] ----> SBSphiJ & phi3T & SPbeta & SPR & phi105 & rho14 & phi29
+ Payne_2021[<a href='https://doi.org/10.1093/nar/gkab883'>Payne et al., 2021</a>] --> Origin_1
+ Origin_1[ Hachiman Type II
+Sphingopyxis witflariensis
+<a href='https://ncbi.nlm.nih.gov/protein/WP_201791916.1'>WP_201791916.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_201791915.1'>WP_201791915.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/WP_088473955.1'>WP_088473955.1</a>] --> Expressed_1[Escherichia coli]
+ Expressed_1[Escherichia coli] ----> T3 & PVP-SE1
+ subgraph Title1[Reference]
+ Doron_2018
+ Payne_2021
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_1
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_1
+end
+ subgraph Title4[Phage infected]
+ SBSphiJ
+ phi3T
+ SPbeta
+ SPR
+ phi105
+ rho14
+ phi29
+ T3
+ PVP-SE1
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/hna.md b/content/3.defense-systems/hna.md
index a2a47871..7996c39d 100644
--- a/content/3.defense-systems/hna.md
+++ b/content/3.defense-systems/hna.md
@@ -24,6 +24,42 @@ dataUrl: /hna/Hna__Hna-plddts_91.2064.pdb
---
::
+## Experimental validation
+<mermaid>
+graph LR;
+ Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_0
+ Origin_0[Sinorhizobium meliloti
+<a href='https://ncbi.nlm.nih.gov/protein/AAK65868.1'>AAK65868.1</a>] --> Expressed_0[Sinorhizobium meliloti]
+ Expressed_0[Sinorhizobium meliloti] ----> 5A & 3K
+ Sather_2023[<a href='https://doi.org/10.1016/j.chom.2023.01.010'>Sather et al., 2023</a>] --> Origin_1
+ Origin_1[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/RDP84117.1'>RDP84117.1</a>] --> Expressed_1[Escherichia coli]
+ Expressed_1[Escherichia coli] ----> T3 & T4 & T7 & HK97
+ subgraph Title1[Reference]
+ Doron_2018
+ Sather_2023
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_1
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_1
+end
+ subgraph Title4[Phage infected]
+ 5A
+ 3K
+ T3
+ T4
+ T7
+ HK97
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstract
::relevant-abstracts
---
diff --git a/content/3.defense-systems/isg15-like.md b/content/3.defense-systems/isg15-like.md
index 6bfea784..294a5c22 100644
--- a/content/3.defense-systems/isg15-like.md
+++ b/content/3.defense-systems/isg15-like.md
@@ -182,19 +182,87 @@ dataUrl: /isg15-like/ISG15-like,ISG15-like__BilD,0,V-plddts_93.10226.pdb
::
## Experimental validation
-
-ISG15-like systems were experimentally validated using:
-
-A system from *Collimonas sp. OK412* in *Escherichia coli* has an anti-phage effect against T2, T4, T6, T5, SECphi4, SECphi6, SECphi18, SECphi27, T7, SECphi17 (Millman et al., 2022)
-
-A system from *Caulobacter sp. Root343* in *Escherichia coli* has an anti-phage effect against T4, T6, T5, SECphi4, SECphi6, SECphi18, SECphi27, T7, SECphi17 (Millman et al., 2022)
-
-A system from *Cupriavidus sp. SHE* in *Escherichia coli* has an anti-phage effect against T2, T4, T6, T5, SECphi4, SECphi6, SECphi18, SECphi27 (Millman et al., 2022)
-
-A system from *Paraburkholderia caffeinilytica* in *Escherichia coli* has an anti-phage effect against T6, SECphi27 (Millman et al., 2022)
-
-A system from *Thiomonas sp. FB-6* in *Escherichia coli* has an anti-phage effect against SECphi27 (Millman et al., 2022)
-
+<mermaid>
+graph LR;
+ Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
+ Origin_0[Collimonas sp. OK412
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2609810443'>2609810443</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2609810442'>2609810442</a>,
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2609810441'>2609810441</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2609810440'>2609810440</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & T5 & SECphi4 & SECphi6 & SECphi18 & SECphi27 & T7 & SECphi17
+ Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_1
+ Origin_1[Caulobacter sp. Root343
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2644236682'>2644236682</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2644236681'>2644236681</a>,
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2644236680'>2644236680</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2644236679'>2644236679</a>] --> Expressed_1[Escherichia coli]
+ Expressed_1[Escherichia coli] ----> T4 & T6 & T5 & SECphi4 & SECphi6 & SECphi18 & SECphi27 & T7 & SECphi17
+ Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_2
+ Origin_2[Cupriavidus sp. SHE
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2654619719'>2654619719</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2654619720'>2654619720</a>,
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2654619721'>2654619721</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2654619722'>2654619722</a>] --> Expressed_2[Escherichia coli]
+ Expressed_2[Escherichia coli] ----> T2 & T4 & T6 & T5 & SECphi4 & SECphi6 & SECphi18 & SECphi27
+ Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_3
+ Origin_3[Paraburkholderia caffeinilytica
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2843959492'>2843959492</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2843959493'>2843959493</a>,
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2843959494'>2843959494</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2843959495'>2843959495</a>] --> Expressed_3[Escherichia coli]
+ Expressed_3[Escherichia coli] ----> T6 & SECphi27
+ Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_4
+ Origin_4[Thiomonas sp. FB-6
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2523655165'>2523655165</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2523655166'>2523655166</a>,
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2523655167'>2523655167</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2523655168'>2523655168</a>] --> Expressed_4[Escherichia coli]
+ Expressed_4[Escherichia coli] ----> SECphi27
+ subgraph Title1[Reference]
+ Millman_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_1
+ Origin_2
+ Origin_3
+ Origin_4
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_1
+ Expressed_2
+ Expressed_3
+ Expressed_4
+end
+ subgraph Title4[Phage infected]
+ T2
+ T4
+ T6
+ T5
+ SECphi4
+ SECphi6
+ SECphi18
+ SECphi27
+ T7
+ SECphi17
+ T4
+ T6
+ T5
+ SECphi4
+ SECphi6
+ SECphi18
+ SECphi27
+ T7
+ SECphi17
+ T2
+ T4
+ T6
+ T5
+ SECphi4
+ SECphi6
+ SECphi18
+ SECphi27
+ T6
+ SECphi27
+ SECphi27
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/jukab.md b/content/3.defense-systems/jukab.md
index 0aec5c30..93e66c06 100644
--- a/content/3.defense-systems/jukab.md
+++ b/content/3.defense-systems/jukab.md
@@ -31,6 +31,30 @@ dataUrl: /jukab/JukAB__JukB-plddts_67.28863.pdb
---
::
+## Experimental validation
+<mermaid>
+graph LR;
+ Li_2022[<a href='https://doi.org/10.1101/2022.09.17.508391'>Li et al., 2022</a>] --> Origin_0
+ Origin_0[Pseudomonas aeruginosa
+<a href='https://ncbi.nlm.nih.gov/protein/WP_003137195.1'>WP_003137195.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_003137196.1'>WP_003137196.1</a>] --> Expressed_0[Pseudomonas aeruginosa]
+ Expressed_0[Pseudomonas aeruginosa] ----> ΦΚZ
+ subgraph Title1[Reference]
+ Li_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ ΦΚZ
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstract
::relevant-abstracts
---
diff --git a/content/3.defense-systems/kiwa.md b/content/3.defense-systems/kiwa.md
index 2c6e98b1..c27a42ee 100644
--- a/content/3.defense-systems/kiwa.md
+++ b/content/3.defense-systems/kiwa.md
@@ -52,11 +52,30 @@ dataUrl: /kiwa/Kiwa,Kiwa__KwaB,0,V-plddts_93.65136.pdb
::
## Experimental validation
-
-Kiwa systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against LambdaVir, SECphi18 (Doron et al., 2018)
-
+<mermaid>
+graph LR;
+ Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/AEZ43441.1'>AEZ43441.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/AEZ43440.1'>AEZ43440.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> LambdaVir & SECphi18
+ subgraph Title1[Reference]
+ Doron_2018
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ LambdaVir
+ SECphi18
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/lamassu-fam.md b/content/3.defense-systems/lamassu-fam.md
index 296df2a8..de297dd3 100644
--- a/content/3.defense-systems/lamassu-fam.md
+++ b/content/3.defense-systems/lamassu-fam.md
@@ -319,27 +319,114 @@ dataUrl: /lamassu-fam/Lamassu-Sir2,Lamassu-Fam__LmuC_acc_Sir2,0,DF-plddts_85.947
::
## Experimental validation
-
-Lamassu-Fam systems were experimentally validated using:
-
-A system from *Bacillus sp. NIO-1130* in *Bacillus subtilis* has an anti-phage effect against phi3T, SpBeta, SPR (Doron et al., 2018)
-
-A system from *Bacillus cereus* in *Bacillus subtilis* has an anti-phage effect against SpBeta (Doron et al., 2018)
-
-Subsystem LmuB+LmuC+Hydrolase+ Protease with a system from *Bacillus cereus* in *Escherichia coli* has an anti-phage effect against T4 (Millman et al., 2022)
-
-Subsystem LmuB+LmuC+Hydrolase+ Protease with a system from *Bacillus cereus* in *Bacillus subtilis* has an anti-phage effect against SpBeta, phi105, Rho14, SPP1, phi29 (Millman et al., 2022)
-
-Subsystem LmuB+LmuC+Mrr endonuclease with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against LambdaVir, SECphi27 (Millman et al., 2022)
-
-Subsystem LmuB+LmuC+PDDEXK nuclease with a system from *Bacillus cereus* in *Escherichia coli* has an anti-phage effect against LambdaVir (Millman et al., 2022)
-
-Subsystem LmuB+LmuC+PDDEXK nuclease with a system from *Bacillus sp. UNCCL81* in *Escherichia coli* has an anti-phage effect against LambdaVir (Millman et al., 2022)
-
-Subsystem LmuA+LmuC+LmuB with a system from *Janthinobacterium agaricidamnosum* in *Escherichia coli* has an anti-phage effect against T1, T3, T7, LambdaVir, PVP-SE1 (Payne et al., 2021)
-
-Subsystem DdmABC with a system from *Vibrio cholerae* in *Escherichia coli* has an anti-phage effect against P1, Lambda (Jaskólska et al., 2022)
-
+<mermaid>
+graph LR;
+ Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_0
+ Origin_0[Bacillus sp. NIO-1130
+<a href='https://ncbi.nlm.nih.gov/protein/SCC38433.1'>SCC38433.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/SCC38445.1'>SCC38445.1</a>] --> Expressed_0[Bacillus subtilis]
+ Expressed_0[Bacillus subtilis] ----> phi3T & SpBeta & SPR
+ Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_1
+ Origin_1[Bacillus cereus
+<a href='https://ncbi.nlm.nih.gov/protein/EJR12435.1'>EJR12435.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/EJR12434.1'>EJR12434.1</a>] --> Expressed_1[Bacillus subtilis]
+ Expressed_1[Bacillus subtilis] ----> SpBeta
+ Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_2
+ Origin_2[ LmuB+LmuC+Hydrolase Protease
+Bacillus cereus
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2624999254'>2624999254</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2624999255'>2624999255</a>,
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2624999257'>2624999257</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2624999256'>2624999256</a>] --> Expressed_2[Escherichia coli]
+ Expressed_2[Escherichia coli] ----> T4
+ Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_2
+ Origin_2[ LmuB+LmuC+Hydrolase Protease
+Bacillus cereus
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2624999254'>2624999254</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2624999255'>2624999255</a>,
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2624999257'>2624999257</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2624999256'>2624999256</a>] --> Expressed_3[Bacillus subtilis]
+ Expressed_3[Bacillus subtilis] ----> SpBeta & phi105 & Rho14 & SPP1 & phi29
+ Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_3
+ Origin_3[ LmuB+LmuC+Mrr endonuclease
+Escherichia coli
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=646870492'>646870492</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=646870494'>646870494</a>,
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=646870493'>646870493</a>] --> Expressed_4[Escherichia coli]
+ Expressed_4[Escherichia coli] ----> LambdaVir & SECphi27
+ Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_4
+ Origin_4[ LmuB+LmuC+PDDEXK nuclease
+Bacillus cereus
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2729045962'>2729045962</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2729045961'>2729045961</a>,
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2729045960'>2729045960</a>] --> Expressed_5[Escherichia coli]
+ Expressed_5[Escherichia coli] ----> LambdaVir
+ Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_5
+ Origin_5[ LmuB+LmuC+PDDEXK nuclease
+Bacillus sp. UNCCL81
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2595091739'>2595091739</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2595091740'>2595091740</a>,
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2595091741'>2595091741</a>] --> Expressed_6[Escherichia coli]
+ Expressed_6[Escherichia coli] ----> LambdaVir
+ Payne_2021[<a href='https://doi.org/10.1093/nar/gkab883'>Payne et al., 2021</a>] --> Origin_6
+ Origin_6[ LmuA+LmuC+LmuB
+Janthinobacterium agaricidamnosum
+<a href='https://ncbi.nlm.nih.gov/protein/WP_038488270.1'>WP_038488270.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_038488273.1'>WP_038488273.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/WP_156484105.1'>WP_156484105.1</a>] --> Expressed_7[Escherichia coli]
+ Expressed_7[Escherichia coli] ----> T1 & T3 & T7 & LambdaVir & PVP-SE1
+ Jaskolska_2022[<a href='https://doi.org/10.1038/s41586-022-04546-y'>Jaskólska et al., 2022</a>] --> Origin_7
+ Origin_7[ DdmABC
+Vibrio cholerae
+<a href='https://ncbi.nlm.nih.gov/protein/WP_000466016.1'>WP_000466016.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_000917213.1'>WP_000917213.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/WP_000654528.1'>WP_000654528.1</a>] --> Expressed_8[Escherichia coli]
+ Expressed_8[Escherichia coli] ----> P1 & Lambda
+ subgraph Title1[Reference]
+ Doron_2018
+ Millman_2022
+ Payne_2021
+ Jaskolska_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_1
+ Origin_2
+ Origin_2
+ Origin_3
+ Origin_4
+ Origin_5
+ Origin_6
+ Origin_7
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_1
+ Expressed_2
+ Expressed_3
+ Expressed_4
+ Expressed_5
+ Expressed_6
+ Expressed_7
+ Expressed_8
+end
+ subgraph Title4[Phage infected]
+ phi3T
+ SpBeta
+ SPR
+ SpBeta
+ T4
+ SpBeta
+ phi105
+ Rho14
+ SPP1
+ phi29
+ LambdaVir
+ SECphi27
+ LambdaVir
+ LambdaVir
+ T1
+ T3
+ T7
+ LambdaVir
+ PVP-SE1
+ P1
+ Lambda
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/lit.md b/content/3.defense-systems/lit.md
index 55ddaf31..e64c9beb 100644
--- a/content/3.defense-systems/lit.md
+++ b/content/3.defense-systems/lit.md
@@ -45,11 +45,29 @@ dataUrl: /lit/Lit__Lit-plddts_91.19971.pdb
::
## Experimental validation
-
-Lit systems were experimentally validated using:
-
-A system from *Escherichia coli defective prophage e14* in *Escherichia coli* has an anti-phage effect against T4 (Yu and Snyder, 1994)
-
+<mermaid>
+graph LR;
+ Yu_1994[<a href='https://doi.org/10.1073/pnas.91.2.802'>Yu and Snyder, 1994</a>] --> Origin_0
+ Origin_0[Escherichia coli defective prophage e14
+<a href='https://ncbi.nlm.nih.gov/protein/WP_001257372.1'>WP_001257372.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T4
+ subgraph Title1[Reference]
+ Yu_1994
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T4
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/mads.md b/content/3.defense-systems/mads.md
index ae2362ba..48874bf7 100644
--- a/content/3.defense-systems/mads.md
+++ b/content/3.defense-systems/mads.md
@@ -66,6 +66,33 @@ dataUrl: /mads/MADS__mad8-plddts_82.23514.pdb
---
::
+## Experimental validation
+<mermaid>
+graph LR;
+ Maestri_2023[<a href='https://doi.org/10.1101/2023.03.30.534895'>Maestri et al., 2023</a>] --> Origin_0
+ Origin_0[Pseudomonas aeruginosa
+<a href='https://ncbi.nlm.nih.gov/protein/WP_058876987.1'>WP_058876987.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_058876988.1'>WP_058876988.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/WP_058876989.1'>WP_058876989.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_058876990.1'>WP_058876990.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/WP_058876991.1'>WP_058876991.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_058876992.1'>WP_058876992.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/WP_124170283.1'>WP_124170283.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_201267341.1'>WP_201267341.1</a>] --> Expressed_0[Pseudomonas aeruginosa]
+ Expressed_0[Pseudomonas aeruginosa] ----> DMS3vir
+ subgraph Title1[Reference]
+ Maestri_2023
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ DMS3vir
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstract
::relevant-abstracts
---
diff --git a/content/3.defense-systems/mazef.md b/content/3.defense-systems/mazef.md
index 2ca8dee2..40898500 100644
--- a/content/3.defense-systems/mazef.md
+++ b/content/3.defense-systems/mazef.md
@@ -13,6 +13,30 @@ tableColumns:
## To do
+## Experimental validation
+<mermaid>
+graph LR;
+ Maestri_2023[<a href='https://doi.org/10.1101/2023.03.30.534895'>Maestri et al., 2023</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_000581937.1'>WP_000581937.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_000254738.1'>WP_000254738.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> P1
+ subgraph Title1[Reference]
+ Maestri_2023
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ P1
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstract
::relevant-abstracts
---
diff --git a/content/3.defense-systems/menshen.md b/content/3.defense-systems/menshen.md
index 85131b62..bc38138c 100644
--- a/content/3.defense-systems/menshen.md
+++ b/content/3.defense-systems/menshen.md
@@ -59,13 +59,40 @@ dataUrl: /menshen/Menshen,Menshen__NsnC,0,V-plddts_91.07244.pdb
::
## Experimental validation
-
-Menshen systems were experimentally validated using:
-
-A system from *Solibacillus silvestris* in *Escherichia coli* has an anti-phage effect against T2, T4, T6 (Millman et al., 2022)
-
-A system from *Solibacillus silvestris* in *Bacillus subtilis* has an anti-phage effect against Fado (Millman et al., 2022)
-
+<mermaid>
+graph LR;
+ Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
+ Origin_0[Solibacillus silvestris
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2562294789'>2562294789</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2562294790'>2562294790</a>,
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2562294791'>2562294791</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T2 & T4 & T6
+ Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
+ Origin_0[Solibacillus silvestris
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2562294789'>2562294789</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2562294790'>2562294790</a>,
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2562294791'>2562294791</a>] --> Expressed_1[Bacillus subtilis]
+ Expressed_1[Bacillus subtilis] ----> Fado
+ subgraph Title1[Reference]
+ Millman_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_1
+end
+ subgraph Title4[Phage infected]
+ T2
+ T4
+ T6
+ Fado
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/mmb_gp29_gp30.md b/content/3.defense-systems/mmb_gp29_gp30.md
index 8be0aab3..bca819f0 100644
--- a/content/3.defense-systems/mmb_gp29_gp30.md
+++ b/content/3.defense-systems/mmb_gp29_gp30.md
@@ -30,6 +30,32 @@ dataUrl: /mmb_gp29_gp30/MMB_gp29_gp30__gp30-plddts_65.6043.pdb
---
::
+## Experimental validation
+<mermaid>
+graph LR;
+ Dedrick_2017[<a href='https://doi.org/10.1038/nmicrobiol.2016.251'>Dedrick et al., 2017</a>] --> Origin_0
+ Origin_0[Mycobacterium MMB phage
+<a href='https://ncbi.nlm.nih.gov/protein/YP_009006630.1'>YP_009006630.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/YP_009006631.2'>YP_009006631.2</a>] --> Expressed_0[Mycobacterium smegmatis mc2 155]
+ Expressed_0[Mycobacterium smegmatis mc2 155] ----> Bxz2 & Tweety & TM4
+ subgraph Title1[Reference]
+ Dedrick_2017
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ Bxz2
+ Tweety
+ TM4
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstract
::relevant-abstracts
---
diff --git a/content/3.defense-systems/mok_hok_sok.md b/content/3.defense-systems/mok_hok_sok.md
index 3e6c4834..c4e67479 100644
--- a/content/3.defense-systems/mok_hok_sok.md
+++ b/content/3.defense-systems/mok_hok_sok.md
@@ -45,11 +45,30 @@ dataUrl: /mok_hok_sok/Mok_Hok_Sok__Hok-plddts_80.98652.pdb
::
## Experimental validation
-
-Mok_Hok_Sok systems were experimentally validated using:
-
-A system from *R1 plasmid of Salmonella paratyphi* in *Escherichia coli* has an anti-phage effect against T4, LambdaVir (Pecota and Wood, 1996)
-
+<mermaid>
+graph LR;
+ Pecota_1996[<a href='https://doi.org/10.1128/jb.178.7.2044-2050.1996'>Pecota and Wood, 1996</a>] --> Origin_0
+ Origin_0[R1 plasmid of Salmonella paratyphi
+<a href='https://ncbi.nlm.nih.gov/protein/WP_001372321.1'>WP_001372321.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T4 & LambdaVir
+ subgraph Title1[Reference]
+ Pecota_1996
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T4
+ LambdaVir
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/mokosh.md b/content/3.defense-systems/mokosh.md
index 45a48f56..5373c9a0 100644
--- a/content/3.defense-systems/mokosh.md
+++ b/content/3.defense-systems/mokosh.md
@@ -81,13 +81,51 @@ dataUrl: /mokosh/Mokosh_TypeII__MkoC-plddts_90.69139.pdb
::
## Experimental validation
-
-Mokosh systems were experimentally validated using:
-
-Subsystem Type I with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6, LambdaVir, T5, SECphi27 (Millman et al., 2022)
-
-Subsystem Type II with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against SECphi17 (Millman et al., 2022)
-
+<mermaid>
+graph LR;
+ Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
+ Origin_0[ Type I
+Escherichia coli
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2597791081'>2597791081</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2597791080'>2597791080</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & LambdaVir & T5 & SECphi27
+ Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_1
+ Origin_1[ Type I
+Escherichia coli
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2720391838'>2720391838</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2720391839'>2720391839</a>] --> Expressed_1[Escherichia coli]
+ Expressed_1[Escherichia coli] ----> LambdaVir
+ Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_2
+ Origin_2[ Type II
+Escherichia coli
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2586378093'>2586378093</a>] --> Expressed_2[Escherichia coli]
+ Expressed_2[Escherichia coli] ----> SECphi17
+ subgraph Title1[Reference]
+ Millman_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_1
+ Origin_2
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_1
+ Expressed_2
+end
+ subgraph Title4[Phage infected]
+ T2
+ T4
+ T6
+ LambdaVir
+ T5
+ SECphi27
+ LambdaVir
+ SECphi17
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/mqsrac.md b/content/3.defense-systems/mqsrac.md
index dfb6b3cf..d15f98df 100644
--- a/content/3.defense-systems/mqsrac.md
+++ b/content/3.defense-systems/mqsrac.md
@@ -29,5 +29,30 @@ Among the 22k complete genomes of RefSeq, this system is present in 26 genomes (
*Proportion of genome encoding the MqsRAC system for the 14 phyla with more than 50 genomes in the RefSeq database.*
+## Experimental validation
+<mermaid>
+graph LR;
+ Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia coli strain C496_10
+<a href='https://ncbi.nlm.nih.gov/protein/WP_157899945.1'>WP_157899945.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_021568457.1'>WP_021568457.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/WP_024222007.1'>WP_024222007.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T2
+ subgraph Title1[Reference]
+ Vassallo_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T2
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
diff --git a/content/3.defense-systems/nhi.md b/content/3.defense-systems/nhi.md
index 44b87275..a3d556b0 100644
--- a/content/3.defense-systems/nhi.md
+++ b/content/3.defense-systems/nhi.md
@@ -45,19 +45,69 @@ dataUrl: /nhi/Nhi__Nhi-plddts_83.89425.pdb
::
## Experimental validation
-
-Nhi systems were experimentally validated using:
-
-Subsystem Nhi-like with a system from *Bacillus cereus* in *Bacillus subtilis* has an anti-phage effect against phi3T, SpBeta, SPR (Millman et al., 2022)
-
-A system from *Staphylococcus epidermidis* in *Staphylococcus epidermidis* has an anti-phage effect against JBug18, Pike, CNPx (Bari et al., 2022)
-
-A system from *Staphylococcus epidermidis* in *Staphylococcus aureus* has an anti-phage effect against Lorac (Bari et al., 2022)
-
-A system from *Staphylococcus aureus* in *Staphylococcus aureus* has an anti-phage effect against Lorac (Bari et al., 2022)
-
-A system from *Vibrio vulnificus* in *Staphylococcus aureus* has an anti-phage effect against Lorac (Bari et al., 2022)
-
+<mermaid>
+graph LR;
+ Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
+ Origin_0[ Nhi-like
+Bacillus cereus] --> Expressed_0[Bacillus subtilis]
+ Expressed_0[Bacillus subtilis] ----> phi3T & SpBeta & SPR
+ Bari_2022[<a href='https://doi.org/10.1016/j.chom.2022.03.001'>Bari et al., 2022</a>] --> Origin_1
+ Origin_1[Staphylococcus epidermidis
+<a href='https://ncbi.nlm.nih.gov/protein/AAW53361.1'>AAW53361.1</a>] --> Expressed_1[Staphylococcus epidermidis]
+ Expressed_1[Staphylococcus epidermidis] ----> JBug18 & Pike & CNPx
+ Bari_2022[<a href='https://doi.org/10.1016/j.chom.2022.03.001'>Bari et al., 2022</a>] --> Origin_1
+ Origin_1[Staphylococcus epidermidis
+<a href='https://ncbi.nlm.nih.gov/protein/AAW53361.1'>AAW53361.1</a>] --> Expressed_2[Staphylococcus aureus]
+ Expressed_2[Staphylococcus aureus] ----> Lorac
+ Bari_2022[<a href='https://doi.org/10.1016/j.chom.2022.03.001'>Bari et al., 2022</a>] --> Origin_2
+ Origin_2[Staphylococcus aureus
+<a href='https://ncbi.nlm.nih.gov/protein/WP_000632676.1'>WP_000632676.1</a>] --> Expressed_3[Staphylococcus aureus]
+ Expressed_3[Staphylococcus aureus] ----> Lorac
+ Bari_2022[<a href='https://doi.org/10.1016/j.chom.2022.03.001'>Bari et al., 2022</a>] --> Origin_3
+ Origin_3[Staphylococcus aureus
+<a href='https://ncbi.nlm.nih.gov/protein/WP_045177897.1'>WP_045177897.1</a>] --> Expressed_4[Staphylococcus aureus]
+ Expressed_4[Staphylococcus aureus] ----> Lorac
+ Bari_2022[<a href='https://doi.org/10.1016/j.chom.2022.03.001'>Bari et al., 2022</a>] --> Origin_4
+ Origin_4[Vibrio vulnificus
+<a href='https://ncbi.nlm.nih.gov/protein/WP_101958732.1'>WP_101958732.1</a>] --> Expressed_5[Staphylococcus aureus]
+ Expressed_5[Staphylococcus aureus] ----> Lorac
+ subgraph Title1[Reference]
+ Millman_2022
+ Bari_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_1
+ Origin_1
+ Origin_2
+ Origin_3
+ Origin_4
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_1
+ Expressed_2
+ Expressed_3
+ Expressed_4
+ Expressed_5
+end
+ subgraph Title4[Phage infected]
+ phi3T
+ SpBeta
+ SPR
+ JBug18
+ Pike
+ CNPx
+ Lorac
+ Lorac
+ Lorac
+ Lorac
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/nixi.md b/content/3.defense-systems/nixi.md
index 0058acc8..37bd0096 100644
--- a/content/3.defense-systems/nixi.md
+++ b/content/3.defense-systems/nixi.md
@@ -44,11 +44,29 @@ dataUrl: /nixi/NixI__NixI-plddts_92.38782.pdb
::
## Experimental validation
-
-NixI systems were experimentally validated using:
-
-A system from *Vibrio cholerae* in *Vibrio cholerae* has an anti-phage effect against ICP1 (Legault et al., 2022)
-
+<mermaid>
+graph LR;
+ Legault_2022[<a href='https://doi.org/10.1093/nar/gkac002'>LeGault et al., 2022</a>] --> Origin_0
+ Origin_0[Vibrio cholerae
+<a href='https://ncbi.nlm.nih.gov/protein/WP_045177897.1'>WP_045177897.1</a>] --> Expressed_0[Vibrio cholerae]
+ Expressed_0[Vibrio cholerae] ----> ICP1
+ subgraph Title1[Reference]
+ Legault_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ ICP1
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/nlr.md b/content/3.defense-systems/nlr.md
index 930fd169..ec0e51e0 100644
--- a/content/3.defense-systems/nlr.md
+++ b/content/3.defense-systems/nlr.md
@@ -58,27 +58,117 @@ dataUrl: /nlr/NLR_like_bNACHT09__NLR_like_bNACHT09-plddts_85.63627.pdb
::
## Experimental validation
-
-NLR systems were experimentally validated using:
-
-Subsystem bNACHT01 with a system from *Klebsiella pneumoniae* in *Escherichia coli* has an anti-phage effect against T4, T5, T6 (Kibby et al., 2022)
-
-Subsystem bNACHT02 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T7, MS2 (Kibby et al., 2022)
-
-Subsystem bNACHT11 with a system from *Klebsiella pneumoniae* in *Escherichia coli* has an anti-phage effect against T2, T4, T6 (Kibby et al., 2022)
-
-Subsystem bNACHT12 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T4, T6, MS2 (Kibby et al., 2022)
-
-Subsystem bNACHT23 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T6, T5 (Kibby et al., 2022)
-
-Subsystem bNACHT25 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6, LambdaVir, MS2 (Kibby et al., 2022)
-
-Subsystem bNACHT32 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6, LambdaVir, MS2 (Kibby et al., 2022)
-
-Subsystem bNACHT67 with a system from *Klebsiella michiganensis* in *Escherichia coli* has an anti-phage effect against T2, T4 (Kibby et al., 2022)
-
-Subsystem bNACHT09 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T5, LambdaVir, T3, T7 (Kibby et al., 2022)
-
+<mermaid>
+graph LR;
+ Kibby_2022[<a href='https://doi.org/10.1101/2022.07.19.500537'>Kibby et al., 2022</a>] --> Origin_0
+ Origin_0[ bNACHT01
+Klebsiella pneumoniae
+<a href='https://ncbi.nlm.nih.gov/protein/WP_015632533.1'>WP_015632533.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T4 & T5 & T6
+ Kibby_2022[<a href='https://doi.org/10.1101/2022.07.19.500537'>Kibby et al., 2022</a>] --> Origin_1
+ Origin_1[ bNACHT02
+Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_021557529.1'>WP_021557529.1</a>] --> Expressed_1[Escherichia coli]
+ Expressed_1[Escherichia coli] ----> T7 & MS2
+ Kibby_2022[<a href='https://doi.org/10.1101/2022.07.19.500537'>Kibby et al., 2022</a>] --> Origin_2
+ Origin_2[ bNACHT11
+Klebsiella pneumoniae
+<a href='https://ncbi.nlm.nih.gov/protein/WP_114260439.1'>WP_114260439.1</a>] --> Expressed_2[Escherichia coli]
+ Expressed_2[Escherichia coli] ----> T2 & T4 & T6
+ Kibby_2022[<a href='https://doi.org/10.1101/2022.07.19.500537'>Kibby et al., 2022</a>] --> Origin_3
+ Origin_3[ bNACHT12
+Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_021519735.1'>WP_021519735.1</a>] --> Expressed_3[Escherichia coli]
+ Expressed_3[Escherichia coli] ----> T4 & T6 & MS2
+ Kibby_2022[<a href='https://doi.org/10.1101/2022.07.19.500537'>Kibby et al., 2022</a>] --> Origin_4
+ Origin_4[ bNACHT23
+Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_000433597.1'>WP_000433597.1</a>] --> Expressed_4[Escherichia coli]
+ Expressed_4[Escherichia coli] ----> T2 & T6 & T5
+ Kibby_2022[<a href='https://doi.org/10.1101/2022.07.19.500537'>Kibby et al., 2022</a>] --> Origin_5
+ Origin_5[ bNACHT25
+Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_001702659.1'>WP_001702659.1</a>] --> Expressed_5[Escherichia coli]
+ Expressed_5[Escherichia coli] ----> T2 & T4 & T6 & LambdaVir & MS2
+ Kibby_2022[<a href='https://doi.org/10.1101/2022.07.19.500537'>Kibby et al., 2022</a>] --> Origin_6
+ Origin_6[ bNACHT32
+Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_057688292'>WP_057688292</a>] --> Expressed_6[Escherichia coli]
+ Expressed_6[Escherichia coli] ----> T2 & T4 & T6 & LambdaVir & MS2
+ Kibby_2022[<a href='https://doi.org/10.1101/2022.07.19.500537'>Kibby et al., 2022</a>] --> Origin_7
+ Origin_7[ bNACHT67
+Klebsiella michiganensis
+<a href='https://ncbi.nlm.nih.gov/protein/WP_064381242'>WP_064381242</a>] --> Expressed_7[Escherichia coli]
+ Expressed_7[Escherichia coli] ----> T2 & T4
+ Kibby_2022[<a href='https://doi.org/10.1101/2022.07.19.500537'>Kibby et al., 2022</a>] --> Origin_8
+ Origin_8[ bNACHT09
+Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_087866631'>WP_087866631</a>] --> Expressed_8[Escherichia coli]
+ Expressed_8[Escherichia coli] ----> T2 & T4 & T5 & LambdaVir & T3 & T7
+ subgraph Title1[Reference]
+ Kibby_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_1
+ Origin_2
+ Origin_3
+ Origin_4
+ Origin_5
+ Origin_6
+ Origin_7
+ Origin_8
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_1
+ Expressed_2
+ Expressed_3
+ Expressed_4
+ Expressed_5
+ Expressed_6
+ Expressed_7
+ Expressed_8
+end
+ subgraph Title4[Phage infected]
+ T4
+ T5
+ T6
+ T7
+ MS2
+ T2
+ T4
+ T6
+ T4
+ T6
+ MS2
+ T2
+ T6
+ T5
+ T2
+ T4
+ T6
+ LambdaVir
+ MS2
+ T2
+ T4
+ T6
+ LambdaVir
+ MS2
+ T2
+ T4
+ T2
+ T4
+ T5
+ LambdaVir
+ T3
+ T7
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/old_exonuclease.md b/content/3.defense-systems/old_exonuclease.md
index 185ea8ba..d87f647b 100644
--- a/content/3.defense-systems/old_exonuclease.md
+++ b/content/3.defense-systems/old_exonuclease.md
@@ -45,11 +45,32 @@ dataUrl: /old_exonuclease/Old_exonuclease__Old_exonuclease-plddts_88.62156.pdb
::
## Experimental validation
-
-Old_exonuclease systems were experimentally validated using:
-
-A system from *Enterobacteria phage P2* in *Escherichia coli* has an anti-phage effect against Lambda, T4, LF82_P8, Al505_P2 (Rousset et al., 2022)
-
+<mermaid>
+graph LR;
+ Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0
+ Origin_0[Enterobacteria phage P2
+<a href='https://ncbi.nlm.nih.gov/protein/NP_046798.1'>NP_046798.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> Lambda & T4 & LF82_P8 & Al505_P2
+ subgraph Title1[Reference]
+ Rousset_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ Lambda
+ T4
+ LF82_P8
+ Al505_P2
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
**Rousset, F. et al. Phages and their satellites encode hotspots of antiviral systems. Cell Host & Microbe 30, 740-753.e5 (2022).**
diff --git a/content/3.defense-systems/olokun.md b/content/3.defense-systems/olokun.md
index 92aa955a..11c9a4ca 100644
--- a/content/3.defense-systems/olokun.md
+++ b/content/3.defense-systems/olokun.md
@@ -51,11 +51,30 @@ dataUrl: /olokun/Olokun,Olokun__OloB,0,V-plddts_85.67714.pdb
::
## Experimental validation
-
-Olokun systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against LambdaVir, SECphi27 (Millman et al., 2022)
-
+<mermaid>
+graph LR;
+ Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2610314205'>2610314205</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2610314206'>2610314206</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> LambdaVir & SECphi27
+ subgraph Title1[Reference]
+ Millman_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ LambdaVir
+ SECphi27
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/pago.md b/content/3.defense-systems/pago.md
index 911f122f..2a24e5df 100644
--- a/content/3.defense-systems/pago.md
+++ b/content/3.defense-systems/pago.md
@@ -107,27 +107,102 @@ dataUrl: /pago/pAgo__pAgo_LongB-plddts_92.47739.pdb
::
## Experimental validation
-
-pAgo systems were experimentally validated using:
-
-Subsystem Ago with a system from *Clostridium butyricum* in *Escherichia coli* has an anti-phage effect against M13, P1vir (Kuzmenko et al., 2020)
-
-A system from *Natronobacterium gregoryi* in *Escherichia coli* has an anti-phage effect against T7 (Xing et al., 2022)
-
-Subsystem GsSir2/Ago with a system from *Geobacter sulfurreducens* in *Escherichia coli* has an anti-phage effect against LambdaVir, SECphi27 (Zaremba et al., 2022)
-
-Subsystem GsSir2/Ago with a system from *Geobacter sulfurreducens* in *Escherichia coli* has an anti-phage effect against LambdaVir, SECphi27 (Zaremba et al., 2022)
-
-Subsystem CcSir2/Ago with a system from *Caballeronia cordobensis* in *Escherichia coli* has an anti-phage effect against LambdaVir (Zaremba et al., 2022)
-
-Subsystem PgSir2/Ago with a system from *araburkholderia graminis* in *Escherichia coli* has an anti-phage effect against LambdaVir, SECphi27 (Zaremba et al., 2022)
-
-Subsystem Ago with a system from *Exiguobacterium marinum* in *Escherichia coli* has an anti-phage effect against P1vir (Lisitskaya et al., 2022)
-
-Subsystem Sir2/Ago with a system from *Geobacter sulfurreducens* in *Escherichia coli* has an anti-phage effect against LambdaVir (Garb et al., 2022)
-
-Subsystem SiAgo/Aga1/Aga2 with a system from *Sulfolobus islandicus* in *Sulfolobus islandicus* has an anti-phage effect against SMV1 (Zeng et al., 2021)
-
+<mermaid>
+graph LR;
+ Kuzmenko_2020[<a href='https://doi.org/10.1038/s41586-020-2605-1'>Kuzmenko et al., 2020</a>] --> Origin_0
+ Origin_0[ Ago
+Clostridium butyricum
+<a href='https://ncbi.nlm.nih.gov/protein/WP_045143632.1'>WP_045143632.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> M13 & P1vir
+ Xing_2022[<a href='https://doi.org/10.1128/mbio.03656-21'>Xing et al., 2022</a>] --> Origin_1
+ Origin_1[Natronobacterium gregoryi
+<a href='https://ncbi.nlm.nih.gov/protein/WP_005580376.1'>WP_005580376.1</a>] --> Expressed_1[Escherichia coli]
+ Expressed_1[Escherichia coli] ----> T7
+ Zaremba_2022[<a href='https://doi.org/10.1038/s41564-022-01239-0'>Zaremba et al., 2022</a>] --> Origin_2
+ Origin_2[ GsSir2/Ago
+Geobacter sulfurreducens
+<a href='https://ncbi.nlm.nih.gov/protein/WP_010942012.1'>WP_010942012.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_010942011.1'>WP_010942011.1</a>] --> Expressed_2[Escherichia coli]
+ Expressed_2[Escherichia coli] ----> LambdaVir & SECphi27
+ Zaremba_2022[<a href='https://doi.org/10.1038/s41564-022-01239-0'>Zaremba et al., 2022</a>] --> Origin_2
+ Origin_2[ GsSir2/Ago
+Geobacter sulfurreducens
+<a href='https://ncbi.nlm.nih.gov/protein/WP_010942012.1'>WP_010942012.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_010942011.1'>WP_010942011.1</a>] --> Expressed_2[Escherichia coli]
+ Expressed_2[Escherichia coli] ----> LambdaVir & SECphi27
+ Zaremba_2022[<a href='https://doi.org/10.1038/s41564-022-01239-0'>Zaremba et al., 2022</a>] --> Origin_3
+ Origin_3[ CcSir2/Ago
+Caballeronia cordobensis
+<a href='https://ncbi.nlm.nih.gov/protein/WP_053571900.1'>WP_053571900.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_053571899.1'>WP_053571899.1</a>] --> Expressed_3[Escherichia coli]
+ Expressed_3[Escherichia coli] ----> LambdaVir
+ Zaremba_2022[<a href='https://doi.org/10.1038/s41564-022-01239-0'>Zaremba et al., 2022</a>] --> Origin_4
+ Origin_4[ PgSir2/Ago
+Paraburkholderia graminis
+<a href='https://ncbi.nlm.nih.gov/protein/WP_006053074.1'>WP_006053074.1</a>] --> Expressed_4[Escherichia coli]
+ Expressed_4[Escherichia coli] ----> LambdaVir & SECphi27
+ Lisitskaya_2022[<a href='https://doi.org/10.1093/nar/gkad290'>Lisitskaya et al., 2023</a>] --> Origin_5
+ Origin_5[ Ago
+Exiguobacterium marinum] --> Expressed_5[Escherichia coli]
+ Expressed_5[Escherichia coli] ----> P1vir
+ Garb_2022[<a href='https://doi.org/10.1038/s41564-022-01207-8'>Garb et al., 2022</a>] --> Origin_6
+ Origin_6[ Sir2/Ago
+Geobacter sulfurreducens
+<a href='https://ncbi.nlm.nih.gov/protein/NP_952413'>NP_952413</a>, <a href='https://ncbi.nlm.nih.gov/protein/NP_952414'>NP_952414</a>] --> Expressed_6[Escherichia coli]
+ Expressed_6[Escherichia coli] ----> LambdaVir
+ Zeng_2021[<a href='https://doi.org/10.1016/j.chom.2022.04.015'>Zeng et al., 2022</a>] --> Origin_7
+ Origin_7[ SiAgo/Aga1/Aga2
+Sulfolobus islandicus
+<a href='https://ncbi.nlm.nih.gov/protein/WP_012735993.1'>WP_012735993.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_012718851.1'>WP_012718851.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/WP_012735992.1'>WP_012735992.1</a>] --> Expressed_7[Sulfolobus islandicus]
+ Expressed_7[Sulfolobus islandicus] ----> SMV1
+ subgraph Title1[Reference]
+ Kuzmenko_2020
+ Xing_2022
+ Zaremba_2022
+ Lisitskaya_2022
+ Garb_2022
+ Zeng_2021
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_1
+ Origin_2
+ Origin_2
+ Origin_3
+ Origin_4
+ Origin_5
+ Origin_6
+ Origin_7
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_1
+ Expressed_2
+ Expressed_2
+ Expressed_3
+ Expressed_4
+ Expressed_5
+ Expressed_6
+ Expressed_7
+end
+ subgraph Title4[Phage infected]
+ M13
+ P1vir
+ T7
+ LambdaVir
+ SECphi27
+ LambdaVir
+ SECphi27
+ LambdaVir
+ LambdaVir
+ SECphi27
+ P1vir
+ LambdaVir
+ SMV1
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/panchino_gp28.md b/content/3.defense-systems/panchino_gp28.md
index c6d2ad59..8a94f856 100644
--- a/content/3.defense-systems/panchino_gp28.md
+++ b/content/3.defense-systems/panchino_gp28.md
@@ -24,6 +24,34 @@ dataUrl: /panchino_gp28/Panchino_gp28__gp28-plddts_90.80762.pdb
---
::
+## Experimental validation
+<mermaid>
+graph LR;
+ Dedrick_2017[<a href='https://doi.org/10.1038/nmicrobiol.2016.251'>Dedrick et al., 2017</a>] --> Origin_0
+ Origin_0[Mycobacterium Panchino phage
+<a href='https://ncbi.nlm.nih.gov/protein/YP_009304936.1'>YP_009304936.1</a>] --> Expressed_0[Mycobacterium smegmatis mc2 155]
+ Expressed_0[Mycobacterium smegmatis mc2 155] ----> Tweety & TM4 & Bruita & U2 & 244
+ subgraph Title1[Reference]
+ Dedrick_2017
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ Tweety
+ TM4
+ Bruita
+ U2
+ 244
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstract
::relevant-abstracts
---
diff --git a/content/3.defense-systems/paris.md b/content/3.defense-systems/paris.md
index afc2c846..4a08c649 100644
--- a/content/3.defense-systems/paris.md
+++ b/content/3.defense-systems/paris.md
@@ -104,13 +104,47 @@ dataUrl: /paris/PARIS_I_merge__AAA_15_DUF4435-plddts_85.1867.pdb
::
## Experimental validation
-
-Paris systems were experimentally validated using:
-
-Subsystem Paris 1 with a system from *Escherichia coli (P4 loci)* in *Escherichia coli* has an anti-phage effect against Lambda, T4, CLB_P2, LF82_P8, Al505_P2, T7 (Rousset et al., 2022)
-
-Subsystem Paris 2 with a system from *Escherichia coli (P4 loci)* in *Escherichia coli* has an anti-phage effect against Lambda, T4, CLB_P2, LF82_P8, T7 (Rousset et al., 2022)
-
+<mermaid>
+graph LR;
+ Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0
+ Origin_0[ Paris 1
+Escherichia coli P4 loci
+<a href='https://ncbi.nlm.nih.gov/protein/WP_000334847.1'>WP_000334847.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_000342409.1'>WP_000342409.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> Lambda & T4 & CLB_P2 & LF82_P8 & Al505_P2 & T7
+ Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_1
+ Origin_1[ Paris 2
+Escherichia coli P4 loci
+<a href='https://ncbi.nlm.nih.gov/protein/WP_001007866.1'>WP_001007866.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_000093097.1'>WP_000093097.1</a>] --> Expressed_1[Escherichia coli]
+ Expressed_1[Escherichia coli] ----> Lambda & T4 & CLB_P2 & LF82_P8 & T7
+ subgraph Title1[Reference]
+ Rousset_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_1
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_1
+end
+ subgraph Title4[Phage infected]
+ Lambda
+ T4
+ CLB_P2
+ LF82_P8
+ Al505_P2
+ T7
+ Lambda
+ T4
+ CLB_P2
+ LF82_P8
+ T7
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/pd-lambda-1.md b/content/3.defense-systems/pd-lambda-1.md
index 042701a1..4d1dd64a 100644
--- a/content/3.defense-systems/pd-lambda-1.md
+++ b/content/3.defense-systems/pd-lambda-1.md
@@ -45,11 +45,29 @@ dataUrl: /pd-lambda-1/PD-Lambda-1__PD-Lambda-1-plddts_85.64965.pdb
::
## Experimental validation
-
-PD-Lambda-1 systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against LambdaVir (Vassallo et al., 2022)
-
+<mermaid>
+graph LR;
+ Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/RCP76574.1'>RCP76574.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> LambdaVir
+ subgraph Title1[Reference]
+ Vassallo_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ LambdaVir
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/pd-lambda-2.md b/content/3.defense-systems/pd-lambda-2.md
index 15237efb..ef269f27 100644
--- a/content/3.defense-systems/pd-lambda-2.md
+++ b/content/3.defense-systems/pd-lambda-2.md
@@ -59,11 +59,34 @@ dataUrl: /pd-lambda-2/PD-Lambda-2,PD-Lambda-2__PD-Lambda-2_C,0,V-plddts_94.25495
::
## Experimental validation
-
-PD-Lambda-2 systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against LambdaVir, SECphi17, SECphi18, SECphi27, T3 (Vassallo et al., 2022)
-
+<mermaid>
+graph LR;
+ Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/RCO93357.1'>RCO93357.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO93356.1'>RCO93356.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/RCO93355.1'>RCO93355.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> LambdaVir & SECphi17 & SECphi18 & SECphi27 & T3
+ subgraph Title1[Reference]
+ Vassallo_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ LambdaVir
+ SECphi17
+ SECphi18
+ SECphi27
+ T3
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/pd-lambda-3.md b/content/3.defense-systems/pd-lambda-3.md
index d592552a..f2588826 100644
--- a/content/3.defense-systems/pd-lambda-3.md
+++ b/content/3.defense-systems/pd-lambda-3.md
@@ -59,11 +59,30 @@ dataUrl: /pd-lambda-3/PD-Lambda-3,PD-Lambda-3__PD-Lambda-3_C,0,V-plddts_92.92218
::
## Experimental validation
-
-PD-Lambda-3 systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against LambdaVir (Vassallo et al., 2022)
-
+<mermaid>
+graph LR;
+ Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/RCP74640.1'>RCP74640.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCP74641.1'>RCP74641.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/RCP74642.1'>RCP74642.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> LambdaVir
+ subgraph Title1[Reference]
+ Vassallo_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ LambdaVir
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/pd-lambda-4.md b/content/3.defense-systems/pd-lambda-4.md
index 8583dd0b..70847048 100644
--- a/content/3.defense-systems/pd-lambda-4.md
+++ b/content/3.defense-systems/pd-lambda-4.md
@@ -51,11 +51,32 @@ dataUrl: /pd-lambda-4/PD-Lambda-4,PD-Lambda-4__PD-Lambda-4_B,0,V-plddts_81.06371
::
## Experimental validation
-
-PD-Lambda-4 systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T4, LambdaVir, SECphi27, T7 (Vassallo et al., 2022)
-
+<mermaid>
+graph LR;
+ Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/RCP47953.1'>RCP47953.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCP47952.1'>RCP47952.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T4 & LambdaVir & SECphi27 & T7
+ subgraph Title1[Reference]
+ Vassallo_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T4
+ LambdaVir
+ SECphi27
+ T7
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/pd-lambda-5.md b/content/3.defense-systems/pd-lambda-5.md
index 2ed43850..0d0eef96 100644
--- a/content/3.defense-systems/pd-lambda-5.md
+++ b/content/3.defense-systems/pd-lambda-5.md
@@ -52,11 +52,37 @@ dataUrl: /pd-lambda-5/PD-Lambda-5,PD-Lambda-5__PD-Lambda-5_B,0,V-plddts_90.05221
::
## Experimental validation
-
-PD-Lambda-5 systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6, LambdaVir, SECphi17, SECphi18, SECphi27, T3, T7 (Vassallo et al., 2022)
-
+<mermaid>
+graph LR;
+ Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/RCQ13837.1'>RCQ13837.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCQ13838.1'>RCQ13838.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & LambdaVir & SECphi17 & SECphi18 & SECphi27 & T3 & T7
+ subgraph Title1[Reference]
+ Vassallo_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T2
+ T4
+ T6
+ LambdaVir
+ SECphi17
+ SECphi18
+ SECphi27
+ T3
+ T7
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/pd-lambda-6.md b/content/3.defense-systems/pd-lambda-6.md
index 5983f9ae..ac18e18d 100644
--- a/content/3.defense-systems/pd-lambda-6.md
+++ b/content/3.defense-systems/pd-lambda-6.md
@@ -44,11 +44,30 @@ dataUrl: /pd-lambda-6/PD-Lambda-6__PD-Lambda-6-plddts_89.62781.pdb
::
## Experimental validation
-
-PD-Lambda-6 systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against LambdaVir, T5 (Vassallo et al., 2022)
-
+<mermaid>
+graph LR;
+ Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/RRK48647.1'>RRK48647.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> LambdaVir & T5
+ subgraph Title1[Reference]
+ Vassallo_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ LambdaVir
+ T5
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/pd-t4-1.md b/content/3.defense-systems/pd-t4-1.md
index 6ec543d1..5e5426a5 100644
--- a/content/3.defense-systems/pd-t4-1.md
+++ b/content/3.defense-systems/pd-t4-1.md
@@ -45,11 +45,31 @@ dataUrl: /pd-t4-1/PD-T4-1__PD-T4-1-plddts_87.89553.pdb
::
## Experimental validation
-
-PD-T4-1 systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6 (Vassallo et al., 2022)
-
+<mermaid>
+graph LR;
+ Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/RRM93940.1'>RRM93940.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T2 & T4 & T6
+ subgraph Title1[Reference]
+ Vassallo_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T2
+ T4
+ T6
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/pd-t4-10.md b/content/3.defense-systems/pd-t4-10.md
index 09bba3f5..64b7f079 100644
--- a/content/3.defense-systems/pd-t4-10.md
+++ b/content/3.defense-systems/pd-t4-10.md
@@ -51,11 +51,33 @@ dataUrl: /pd-t4-10/PD-T4-10,PD-T4-10__PD-T4-10_B,0,V-plddts_88.59779.pdb
::
## Experimental validation
-
-PD-T4-10 systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6, T5, SECphi27 (Vassallo et al., 2022)
-
+<mermaid>
+graph LR;
+ Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/RCO36089.1'>RCO36089.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO36088.1'>RCO36088.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & T5 & SECphi27
+ subgraph Title1[Reference]
+ Vassallo_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T2
+ T4
+ T6
+ T5
+ SECphi27
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/pd-t4-2.md b/content/3.defense-systems/pd-t4-2.md
index 9c3e67fd..d01d0fdc 100644
--- a/content/3.defense-systems/pd-t4-2.md
+++ b/content/3.defense-systems/pd-t4-2.md
@@ -52,11 +52,32 @@ dataUrl: /pd-t4-2/PD-T4-2,PD-T4-2__PD-T4-2_B,0,DF-plddts_93.48773.pdb
::
## Experimental validation
-
-PD-T4-2 systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6, T5, SECphi27 (Vassallo et al., 2022)
-
+<mermaid>
+graph LR;
+ Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia coli] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & T5 & SECphi27
+ subgraph Title1[Reference]
+ Vassallo_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T2
+ T4
+ T6
+ T5
+ SECphi27
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/pd-t4-3.md b/content/3.defense-systems/pd-t4-3.md
index d5739ccb..9a32464e 100644
--- a/content/3.defense-systems/pd-t4-3.md
+++ b/content/3.defense-systems/pd-t4-3.md
@@ -44,11 +44,31 @@ dataUrl: /pd-t4-3/PD-T4-3__PD-T4-3-plddts_88.02514.pdb
::
## Experimental validation
-
-PD-T4-3 systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6 (Vassallo et al., 2022)
-
+<mermaid>
+graph LR;
+ Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/RCO27183.1'>RCO27183.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T2 & T4 & T6
+ subgraph Title1[Reference]
+ Vassallo_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T2
+ T4
+ T6
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/pd-t4-4.md b/content/3.defense-systems/pd-t4-4.md
index 8a6550d7..21c35ecf 100644
--- a/content/3.defense-systems/pd-t4-4.md
+++ b/content/3.defense-systems/pd-t4-4.md
@@ -52,11 +52,32 @@ dataUrl: /pd-t4-4/PD-T4-4,PD-T4-4__PD-T4-4_B,0,V-plddts_92.18973.pdb
::
## Experimental validation
-
-PD-T4-4 systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6, SECphi17 (Vassallo et al., 2022)
-
+<mermaid>
+graph LR;
+ Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/RCO57999.1'>RCO57999.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCO57988.1'>RCO57988.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & SECphi17
+ subgraph Title1[Reference]
+ Vassallo_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T2
+ T4
+ T6
+ SECphi17
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/pd-t4-5.md b/content/3.defense-systems/pd-t4-5.md
index aab0d33d..ba44a6c3 100644
--- a/content/3.defense-systems/pd-t4-5.md
+++ b/content/3.defense-systems/pd-t4-5.md
@@ -45,11 +45,32 @@ dataUrl: /pd-t4-5/PD-T4-5__PD-T4-5-plddts_94.58803.pdb
::
## Experimental validation
-
-PD-T4-5 systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T4, T6, LambdaVir, T5 (Vassallo et al., 2022)
-
+<mermaid>
+graph LR;
+ Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/RCQ99930.1'>RCQ99930.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T4 & T6 & LambdaVir & T5
+ subgraph Title1[Reference]
+ Vassallo_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T4
+ T6
+ LambdaVir
+ T5
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/pd-t4-6.md b/content/3.defense-systems/pd-t4-6.md
index 7734d40a..f0e618cd 100644
--- a/content/3.defense-systems/pd-t4-6.md
+++ b/content/3.defense-systems/pd-t4-6.md
@@ -45,11 +45,31 @@ dataUrl: /pd-t4-6/PD-T4-6__PD-T4-6-plddts_84.95824.pdb
::
## Experimental validation
-
-PD-T4-6 systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6 (Vassallo et al., 2022)
-
+<mermaid>
+graph LR;
+ Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/RRM76169.1'>RRM76169.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T2 & T4 & T6
+ subgraph Title1[Reference]
+ Vassallo_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T2
+ T4
+ T6
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/pd-t4-7.md b/content/3.defense-systems/pd-t4-7.md
index 8c40ef4b..3cab5dd3 100644
--- a/content/3.defense-systems/pd-t4-7.md
+++ b/content/3.defense-systems/pd-t4-7.md
@@ -44,11 +44,31 @@ dataUrl: /pd-t4-7/PD-T4-7__PD-T4-7-plddts_91.28596.pdb
::
## Experimental validation
-
-PD-T4-7 systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6 (Vassallo et al., 2022)
-
+<mermaid>
+graph LR;
+ Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/RRN43039.1'>RRN43039.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T2 & T4 & T6
+ subgraph Title1[Reference]
+ Vassallo_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T2
+ T4
+ T6
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/pd-t4-8.md b/content/3.defense-systems/pd-t4-8.md
index ebacb14a..3d988e96 100644
--- a/content/3.defense-systems/pd-t4-8.md
+++ b/content/3.defense-systems/pd-t4-8.md
@@ -45,11 +45,33 @@ dataUrl: /pd-t4-8/PD-T4-8__PD-T4-8-plddts_91.39016.pdb
::
## Experimental validation
-
-PD-T4-8 systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6, SECphi18, SECphi27 (Vassallo et al., 2022)
-
+<mermaid>
+graph LR;
+ Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/RCP52534.1'>RCP52534.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & SECphi18 & SECphi27
+ subgraph Title1[Reference]
+ Vassallo_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T2
+ T4
+ T6
+ SECphi18
+ SECphi27
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/pd-t4-9.md b/content/3.defense-systems/pd-t4-9.md
index bf220afd..1ded26e1 100644
--- a/content/3.defense-systems/pd-t4-9.md
+++ b/content/3.defense-systems/pd-t4-9.md
@@ -59,11 +59,32 @@ dataUrl: /pd-t4-9/PD-T4-9,PD-T4-9__PD-T4-9_C,0,V-plddts_93.05735.pdb
::
## Experimental validation
-
-PD-T4-9 systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6 (Vassallo et al., 2022)
-
+<mermaid>
+graph LR;
+ Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/RCP66309.1'>RCP66309.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RCP66310.1'>RCP66310.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/RCP66311.1'>RCP66311.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T2 & T4 & T6
+ subgraph Title1[Reference]
+ Vassallo_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T2
+ T4
+ T6
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/pd-t7-1.md b/content/3.defense-systems/pd-t7-1.md
index 0323f458..356a8ec7 100644
--- a/content/3.defense-systems/pd-t7-1.md
+++ b/content/3.defense-systems/pd-t7-1.md
@@ -44,11 +44,29 @@ dataUrl: /pd-t7-1/PD-T7-1__PD-T7-1-plddts_93.91174.pdb
::
## Experimental validation
-
-PD-T7-1 systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T7(Vassallo et al., 2022)
-
+<mermaid>
+graph LR;
+ Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/RCQ85672.1'>RCQ85672.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T7
+ subgraph Title1[Reference]
+ Vassallo_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T7
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/pd-t7-2.md b/content/3.defense-systems/pd-t7-2.md
index 69f5f63e..96f4acf8 100644
--- a/content/3.defense-systems/pd-t7-2.md
+++ b/content/3.defense-systems/pd-t7-2.md
@@ -52,11 +52,37 @@ dataUrl: /pd-t7-2/PD-T7-2,PD-T7-2__PD-T7-2_B,0,V-plddts_86.88934.pdb
::
## Experimental validation
-
-PD-T7-2 systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6, LambdaVir, T5, SECphi18, SECphi27, T3, T7 (Vassallo et al., 2022)
-
+<mermaid>
+graph LR;
+ Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/RRM73498.1'>RRM73498.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/RRM73410.1'>RRM73410.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & LambdaVir & T5 & SECphi18 & SECphi27 & T3 & T7
+ subgraph Title1[Reference]
+ Vassallo_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T2
+ T4
+ T6
+ LambdaVir
+ T5
+ SECphi18
+ SECphi27
+ T3
+ T7
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/pd-t7-3.md b/content/3.defense-systems/pd-t7-3.md
index 873cfafc..ea981d3e 100644
--- a/content/3.defense-systems/pd-t7-3.md
+++ b/content/3.defense-systems/pd-t7-3.md
@@ -44,11 +44,35 @@ dataUrl: /pd-t7-3/PD-T7-3__PD-T7-3-plddts_89.74752.pdb
::
## Experimental validation
-
-PD-T7-3 systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6, T5, SECphi17, T3, T7 (Vassallo et al., 2022)
-
+<mermaid>
+graph LR;
+ Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/RCP48690.1'>RCP48690.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T2 & T4 & T6 & T5 & SECphi17 & T3 & T7
+ subgraph Title1[Reference]
+ Vassallo_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T2
+ T4
+ T6
+ T5
+ SECphi17
+ T3
+ T7
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/pd-t7-4.md b/content/3.defense-systems/pd-t7-4.md
index 0fba1c7c..7b72b51f 100644
--- a/content/3.defense-systems/pd-t7-4.md
+++ b/content/3.defense-systems/pd-t7-4.md
@@ -45,11 +45,32 @@ dataUrl: /pd-t7-4/PD-T7-4__PD-T7-4-plddts_93.28251.pdb
::
## Experimental validation
-
-PD-T7-4 systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against SECphi18, SECphi27, T3, T7 (Vassallo et al., 2022)
-
+<mermaid>
+graph LR;
+ Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/RRL46918.1'>RRL46918.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> SECphi18 & SECphi27 & T3 & T7
+ subgraph Title1[Reference]
+ Vassallo_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ SECphi18
+ SECphi27
+ T3
+ T7
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/pd-t7-5.md b/content/3.defense-systems/pd-t7-5.md
index a6f14af8..3533e9d2 100644
--- a/content/3.defense-systems/pd-t7-5.md
+++ b/content/3.defense-systems/pd-t7-5.md
@@ -44,11 +44,31 @@ dataUrl: /pd-t7-5/PD-T7-5__PD-T7-5-plddts_92.01228.pdb
::
## Experimental validation
-
-PD-T7-5 systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against SECphi17, T3, T7 (Vassallo et al., 2022)
-
+<mermaid>
+graph LR;
+ Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/RRM82777.1'>RRM82777.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> SECphi17 & T3 & T7
+ subgraph Title1[Reference]
+ Vassallo_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ SECphi17
+ T3
+ T7
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/phrann_gp29_gp30.md b/content/3.defense-systems/phrann_gp29_gp30.md
index 8a874385..69974c40 100644
--- a/content/3.defense-systems/phrann_gp29_gp30.md
+++ b/content/3.defense-systems/phrann_gp29_gp30.md
@@ -31,6 +31,30 @@ Among the 22k complete genomes of RefSeq, this system is present in 314 genomes
*Proportion of genome encoding the phrann_gp29_gp30 system for the 14 phyla with more than 50 genomes in the RefSeq database.*
+## Experimental validation
+<mermaid>
+graph LR;
+ Dedrick_2017[<a href='https://doi.org/10.1038/nmicrobiol.2016.251'>Dedrick et al., 2017</a>] --> Origin_0
+ Origin_0[Mycobacterium phage Phrann
+<a href='https://ncbi.nlm.nih.gov/protein/YP_009304221.1'>YP_009304221.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/YP_009304222.1'>YP_009304222.1</a>] --> Expressed_0[Mycobacterium smegmatis mc2 155]
+ Expressed_0[Mycobacterium smegmatis mc2 155] ----> Tweety
+ subgraph Title1[Reference]
+ Dedrick_2017
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ Tweety
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/pif.md b/content/3.defense-systems/pif.md
index 7cbf6e9a..78931e44 100644
--- a/content/3.defense-systems/pif.md
+++ b/content/3.defense-systems/pif.md
@@ -52,11 +52,29 @@ dataUrl: /pif/Pif,Pif__PifC,0,V-plddts_91.50188.pdb
::
## Experimental validation
-
-Pif systems were experimentally validated using:
-
-A system from *Escherichia coli F-plasmid* in *Escherichia coli* has an anti-phage effect against T7 (Cheng et al., 2004)
-
+<mermaid>
+graph LR;
+ Cheng_2004[<a href='https://doi.org/10.1016/j.virol.2004.06.001'>Cheng et al., 2004</a>] --> Origin_0
+ Origin_0[Escherichia coli F-plasmid
+<a href='https://ncbi.nlm.nih.gov/protein/WP_028985935.1'>WP_028985935.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_028985936.1'>WP_028985936.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T7
+ subgraph Title1[Reference]
+ Cheng_2004
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T7
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/prrc.md b/content/3.defense-systems/prrc.md
index ecc2ad47..105acc27 100644
--- a/content/3.defense-systems/prrc.md
+++ b/content/3.defense-systems/prrc.md
@@ -52,11 +52,32 @@ dataUrl: /prrc/PrrC__PrrC-plddts_86.4815.pdb
::
## Experimental validation
-
-PrrC systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against Lambda, T4 Dec8 (Jabbar and Snyder, 1984)
-
+<mermaid>
+graph LR;
+ Jabbar_1984[<a href='https://doi.org/10.1128/JVI.51.2.522-529.1984'>Jabbar and Snyder, 1984</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_012954793.1'>WP_012954793.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_012954794.1'>WP_012954794.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/WP_012954795.1'>WP_012954795.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_012954796.1'>WP_012954796.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> Lambda & T4 & Dec8
+ subgraph Title1[Reference]
+ Jabbar_1984
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ Lambda
+ T4
+ Dec8
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/psyrta.md b/content/3.defense-systems/psyrta.md
index 5efe4704..140db842 100644
--- a/content/3.defense-systems/psyrta.md
+++ b/content/3.defense-systems/psyrta.md
@@ -52,11 +52,31 @@ dataUrl: /psyrta/PsyrTA,PsyrTA__PsyrT,0,V-plddts_88.00999.pdb
::
## Experimental validation
-
-PsyrTA systems were experimentally validated using:
-
-A system from *Bacillus sp. FJAT-29814* in *Escherichia coli* has an anti-phage effect against T2, T4, T6 (Millman et al., 2022)
-
+<mermaid>
+graph LR;
+ Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
+ Origin_0[Bacillus sp. FJAT-29814
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2746452868'>2746452868</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2746452867'>2746452867</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T2 & T4 & T6
+ subgraph Title1[Reference]
+ Millman_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T2
+ T4
+ T6
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/pycsar.md b/content/3.defense-systems/pycsar.md
index 7a5e184a..9bffd49b 100644
--- a/content/3.defense-systems/pycsar.md
+++ b/content/3.defense-systems/pycsar.md
@@ -68,13 +68,39 @@ dataUrl: /pycsar/Pycsar,Pycsar__AG_cyclase,0,V-plddts_94.90778.pdb
::
## Experimental validation
-
-Pycsar systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T5, P1, LambdaVir, SECphi27 (Tal et al., 2021)
-
-A system from *Xanthomonas perforans* in *Escherichia coli* has an anti-phage effect against T7 (Tal et al., 2021)
-
+<mermaid>
+graph LR;
+ Tal_2021[<a href='https://doi.org/10.1016/j.cell.2021.09.031'>Tal et al., 2021</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2684943848'>2684943848</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2742823945'>2742823945</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T5 & P1 & LambdaVir & SECphi27
+ Tal_2021[<a href='https://doi.org/10.1016/j.cell.2021.09.031'>Tal et al., 2021</a>] --> Origin_1
+ Origin_1[Xanthomonas perforans
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2637229924'>2637229924</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2628816548'>2628816548</a>] --> Expressed_1[Escherichia coli]
+ Expressed_1[Escherichia coli] ----> T7
+ subgraph Title1[Reference]
+ Tal_2021
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_1
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_1
+end
+ subgraph Title4[Phage infected]
+ T5
+ P1
+ LambdaVir
+ SECphi27
+ T7
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/radar.md b/content/3.defense-systems/radar.md
index 55a39eca..8d705fb0 100644
--- a/content/3.defense-systems/radar.md
+++ b/content/3.defense-systems/radar.md
@@ -87,15 +87,61 @@ dataUrl: /radar/radar_II,radar_II__rdrC_II,0,V-plddts_75.42507.pdb
::
## Experimental validation
-
-RADAR systems were experimentally validated using:
-
-A system from *Citrobacter rodentium* in *Escherichia coli* has an anti-phage effect against T2, T4, T5, T3, T6 (Gao et al., 2020; Duncan-Lowey et al., 2022)
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6 (Duncan-Lowey et al., 2022)
-
-A system from *Streptococcus suis* in *Escherichia coli* has an anti-phage effect against T2, T4, T5, T6 (Duncan-Lowey et al., 2022)
-
+<mermaid>
+graph LR;
+ Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
+ Duncan-Lowey_2022[<a href='https://doi.org/10.1016/j.cell.2023.01.012'>Duncan-Lowey et al., 2023</a>] --> Origin_0
+ Origin_0[Citrobacter rodentium
+<a href='https://ncbi.nlm.nih.gov/protein/WP_012906049.1'>WP_012906049.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_012906048.1'>WP_012906048.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T2 & T4 & T5 & T3 & T6
+ Duncan-Lowey_2022[<a href='https://doi.org/10.1016/j.cell.2023.01.012'>Duncan-Lowey et al., 2023</a>] --> Origin_1
+ Origin_1[Escherichia coli
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2548796856'>2548796856</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2548796855'>2548796855</a>] --> Expressed_1[Escherichia coli]
+ Expressed_1[Escherichia coli] ----> T2 & T4 & T6
+ Duncan-Lowey_2022[<a href='https://doi.org/10.1016/j.cell.2023.01.012'>Duncan-Lowey et al., 2023</a>] --> Origin_2
+ Origin_2[Streptococcus suis
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2706833061'>2706833061</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2706833062'>2706833062</a>] --> Expressed_2[Escherichia coli]
+ Expressed_2[Escherichia coli] ----> T2 & T4 & T5 & T6
+ subgraph Title1[Reference]
+ Gao_2020
+ Duncan-Lowey_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_0
+ Origin_1
+ Origin_2
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_0
+ Expressed_1
+ Expressed_2
+end
+ subgraph Title4[Phage infected]
+ T2
+ T4
+ T5
+ T3
+ T6
+ T2
+ T4
+ T5
+ T3
+ T6
+ T2
+ T4
+ T6
+ T2
+ T4
+ T5
+ T6
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/retron.md b/content/3.defense-systems/retron.md
index e977224e..131e6d42 100644
--- a/content/3.defense-systems/retron.md
+++ b/content/3.defense-systems/retron.md
@@ -292,53 +292,248 @@ dataUrl: /retron/Retron_VII_2,Retron__RT_Tot,0,DF-plddts_95.60845.pdb
::
## Experimental validation
-
-Retron systems were experimentally validated using:
-
-Subsystem SLATT + RT_G2_intron with a system from *Klebsiella pneumoniae's PICI (KpCIUCICRE 8)* in *Escherichia coli* has an anti-phage effect against T5, HK97, HK544, HK578, T7 (Fillol-Salom et al., 2022)
-
-Subsystem SLATT + RT_G2_intron with a system from *Klebsiella pneumoniae's PICI (KpCIUCICRE 8)* in *Samonella enterica* has an anti-phage effect against P22, BTP1, ES18 (Fillol-Salom et al., 2022)
-
-Subsystem SLATT + RT_G2_intron with a system from *Klebsiella pneumoniae's PICI (KpCIUCICRE 8)* in *Klebsiella pneumoniae* has an anti-phage effect against Pokey, Raw, Eggy, KaID (Fillol-Salom et al., 2022)
-
-Subsystem RT Ec67 + TOPRIM with a system from *Klebsiella pneumoniae's PICI (KpCIB28906)* in *Escherichia coli* has an anti-phage effect against T4, T5, HK578, T7 (Fillol-Salom et al., 2022)
-
-Subsystem RT Ec67 + TOPRIM with a system from *Klebsiella pneumoniae's PICI (KpCIB28906)* in *Samonella enterica* has an anti-phage effect against det7 (Fillol-Salom et al., 2022)
-
-Subsystem RT Ec67 + TOPRIM with a system from *Klebsiella pneumoniae's PICI (KpCIB28906)* in *Samonella enterica* has an anti-phage effect against Pokey, KalD (Fillol-Salom et al., 2022)
-
-Subsystem Retron-TIR with a system from *Shigella dysenteriae* in *Escherichia coli* has an anti-phage effect against T2, T4, T3, T7, PhiV-1 (Gao et al., 2020)
-
-Subsystem Retron Ec67 + TOPRIM with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T5 (Gao et al., 2020)
-
-Subsystem Retron Ec86 + Nuc_deoxy with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T4 (Gao et al., 2020)
-
-Subsystem Retron Ec78 + ATPase + HNH with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T5 (Gao et al., 2020)
-
-Subsystem Ec73 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against SECphi4, SECphi6, SECphi27, P1, T7 (Millman et al., 2020)
-
-Subsystem Ec86 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T5 (Millman et al., 2020)
-
-Subsystem Ec48 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against Lambda-Vir, T5, T2, T4, T7 (Millman et al., 2020)
-
-Subsystem Ec67 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T5 (Millman et al., 2020)
-
-Subsystem Se72 with a system from *Salmonella enterica* in *Escherichia coli* has an anti-phage effect against Lambda-Vir (Millman et al., 2020)
-
-Subsystem Ec78 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T5 (Millman et al., 2020)
-
-Subsystem Ec83 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T2, T4, T6 (Millman et al., 2020)
-
-Subsystem Vc95 with a system from *Vibrio cholerae* in *Escherichia coli* has an anti-phage effect against T2, T4, T6 (Millman et al., 2020)
-
-Subsystem Retron-Eco8 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against SECphi4, SECphi6, SECphi18, T4, T6, T7 (Millman et al., 2020)
-
-Subsystem Retron-Sen2 with a system from *Salmonella enterica serovar Typhimurium* in *Escherichia coli* has an anti-phage effect against T5 (Bobonis et al., 2022)
-
-Subsystem Retron-Eco9 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against P1vir, T2, T3, T5, T7, Ffm, Br60 (Bobonis et al., 2022)
-
-Subsystem Retron-Eco1 with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T5 (Bobonis et al., 2022)
-
+<mermaid>
+graph LR;
+ Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
+ Origin_0[ SLATT + RT_G2_intron
+Klebsiella pneumoniae's PICI KpCIUCICRE 8
+<a href='https://ncbi.nlm.nih.gov/protein/WP_023301280.1'>WP_023301280.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_023301281.1'>WP_023301281.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T5 & HK97 & HK544 & HK578 & T7
+ Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
+ Origin_0[ SLATT + RT_G2_intron
+Klebsiella pneumoniae's PICI KpCIUCICRE 8
+<a href='https://ncbi.nlm.nih.gov/protein/WP_023301280.1'>WP_023301280.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_023301281.1'>WP_023301281.1</a>] --> Expressed_1[Samonella enterica]
+ Expressed_1[Samonella enterica] ----> P22 & BTP1 & ES18
+ Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
+ Origin_0[ SLATT + RT_G2_intron
+Klebsiella pneumoniae's PICI KpCIUCICRE 8
+<a href='https://ncbi.nlm.nih.gov/protein/WP_023301280.1'>WP_023301280.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_023301281.1'>WP_023301281.1</a>] --> Expressed_2[Klebsiella pneumoniae]
+ Expressed_2[Klebsiella pneumoniae] ----> Pokey & Raw & Eggy & KaID
+ Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_1
+ Origin_1[ RT Ec67 + TOPRIM
+Klebsiella pneumoniae's PICI KpCIB28906
+<a href='https://ncbi.nlm.nih.gov/protein/WP_053810728.1'>WP_053810728.1</a>] --> Expressed_3[Escherichia coli]
+ Expressed_3[Escherichia coli] ----> T4 & T5 & HK578 & T7
+ Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_1
+ Origin_1[ RT Ec67 + TOPRIM
+Klebsiella pneumoniae's PICI KpCIB28906
+<a href='https://ncbi.nlm.nih.gov/protein/WP_053810728.1'>WP_053810728.1</a>] --> Expressed_4[Samonella enterica]
+ Expressed_4[Samonella enterica] ----> det7
+ Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_1
+ Origin_1[ RT Ec67 + TOPRIM
+Klebsiella pneumoniae's PICI KpCIB28906
+<a href='https://ncbi.nlm.nih.gov/protein/WP_053810728.1'>WP_053810728.1</a>] --> Expressed_4[Samonella enterica]
+ Expressed_4[Samonella enterica] ----> Pokey & KalD
+ Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_2
+ Origin_2[ Retron-TIR
+Shigella dysenteriae
+<a href='https://ncbi.nlm.nih.gov/protein/WP_005025120.1'>WP_005025120.1</a>] --> Expressed_5[Escherichia coli]
+ Expressed_5[Escherichia coli] ----> T2 & T4 & T3 & T7 & PhiV-1
+ Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_3
+ Origin_3[ Retron Ec67 + TOPRIM
+Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_000169432.1'>WP_000169432.1</a>] --> Expressed_6[Escherichia coli]
+ Expressed_6[Escherichia coli] ----> T2 & T4 & T5
+ Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_4
+ Origin_4[ Retron Ec86 + Nuc_deoxy
+Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_001034589.1'>WP_001034589.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_001320043.1'>WP_001320043.1</a>] --> Expressed_7[Escherichia coli]
+ Expressed_7[Escherichia coli] ----> T4
+ Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_5
+ Origin_5[ Retron Ec78 + ATPase + HNH
+Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_001549208.1'>WP_001549208.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_001549209.1'>WP_001549209.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/WP_001549210.1'>WP_001549210.1</a>] --> Expressed_8[Escherichia coli]
+ Expressed_8[Escherichia coli] ----> T5
+ Millman_2020[<a href='https://doi.org/10.1038/s41564-020-0777-y'>Millman et al., 2020</a>] --> Origin_6
+ Origin_6[ Ec73
+Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_005025120.1*'>WP_005025120.1*</a>] --> Expressed_9[Escherichia coli]
+ Expressed_9[Escherichia coli] ----> SECphi4 & SECphi6 & SECphi27 & P1 & T7
+ Millman_2020[<a href='https://doi.org/10.1038/s41564-020-0777-y'>Millman et al., 2020</a>] --> Origin_7
+ Origin_7[ Ec86
+Escherichia coli
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2514747571'>2514747571</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2514747569'>2514747569</a>] --> Expressed_10[Escherichia coli]
+ Expressed_10[Escherichia coli] ----> T5
+ Millman_2020[<a href='https://doi.org/10.1038/s41564-020-0777-y'>Millman et al., 2020</a>] --> Origin_8
+ Origin_8[ Ec48
+Escherichia coli
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2642317602'>2642317602</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2642317601'>2642317601</a>] --> Expressed_11[Escherichia coli]
+ Expressed_11[Escherichia coli] ----> Lambda-Vir & T5 & T2 & T4 & T7
+ Millman_2020[<a href='https://doi.org/10.1038/s41564-020-0777-y'>Millman et al., 2020</a>] --> Origin_9
+ Origin_9[ Ec67
+Escherichia coli
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2721121890'>2721121890</a>] --> Expressed_12[Escherichia coli]
+ Expressed_12[Escherichia coli] ----> T5
+ Millman_2020[<a href='https://doi.org/10.1038/s41564-020-0777-y'>Millman et al., 2020</a>] --> Origin_10
+ Origin_10[ Se72
+Salmonella enterica
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2633939248'>2633939248</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2633939247'>2633939247</a>] --> Expressed_13[Escherichia coli]
+ Expressed_13[Escherichia coli] ----> Lambda-Vir
+ Millman_2020[<a href='https://doi.org/10.1038/s41564-020-0777-y'>Millman et al., 2020</a>] --> Origin_11
+ Origin_11[ Ec78
+Escherichia coli
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2647069770'>2647069770</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2647069771'>2647069771</a>,
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2647069772'>2647069772</a>] --> Expressed_14[Escherichia coli]
+ Expressed_14[Escherichia coli] ----> T5
+ Millman_2020[<a href='https://doi.org/10.1038/s41564-020-0777-y'>Millman et al., 2020</a>] --> Origin_12
+ Origin_12[ Ec83
+Escherichia coli
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2712077840'>2712077840</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2712077841'>2712077841</a>,
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2712077841'>2712077841</a>] --> Expressed_15[Escherichia coli]
+ Expressed_15[Escherichia coli] ----> T2 & T4 & T6
+ Millman_2020[<a href='https://doi.org/10.1038/s41564-020-0777-y'>Millman et al., 2020</a>] --> Origin_13
+ Origin_13[ Vc95
+Vibrio cholerae
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2598877024'>2598877024</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2598877023'>2598877023</a>,
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2598877022'>2598877022</a>] --> Expressed_16[Escherichia coli]
+ Expressed_16[Escherichia coli] ----> T2 & T4 & T6
+ Millman_2020[<a href='https://doi.org/10.1038/s41564-020-0777-y'>Millman et al., 2020</a>] --> Origin_14
+ Origin_14[ Retron-Eco8
+Escherichia coli
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2693183786'>2693183786</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2693183785'>2693183785</a>] --> Expressed_17[Escherichia coli]
+ Expressed_17[Escherichia coli] ----> SECphi4 & SECphi6 & SECphi18 & T4 & T6 & T7
+ Bobonis_2022[<a href='https://doi.org/10.1038/s41586-022-05091-4'>Bobonis et al., 2022</a>] --> Origin_15
+ Origin_15[ Retron-Sen2
+Salmonella enterica serovar Typhimurium
+<a href='https://ncbi.nlm.nih.gov/protein/NP_462744.1'>NP_462744.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/NP_462745.3'>NP_462745.3</a>] --> Expressed_18[Escherichia coli]
+ Expressed_18[Escherichia coli] ----> T5
+ Bobonis_2022[<a href='https://doi.org/10.1038/s41586-022-05091-4'>Bobonis et al., 2022</a>] --> Origin_16
+ Origin_16[ Retron-Eco9
+Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_000422112.1'>WP_000422112.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_062914741.1'>WP_062914741.1</a>] --> Expressed_19[Escherichia coli]
+ Expressed_19[Escherichia coli] ----> P1vir & T2 & T3 & T5 & T7 & Ffm & Br60
+ Bobonis_2022[<a href='https://doi.org/10.1038/s41586-022-05091-4'>Bobonis et al., 2022</a>] --> Origin_17
+ Origin_17[ Retron-Eco1
+Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_001320043.1'>WP_001320043.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_001034589.1'>WP_001034589.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/'></a>] --> Expressed_20[Escherichia coli]
+ Expressed_20[Escherichia coli] ----> T5
+ subgraph Title1[Reference]
+ Fillol-Salom_2022
+ Gao_2020
+ Millman_2020
+ Bobonis_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_0
+ Origin_0
+ Origin_1
+ Origin_1
+ Origin_1
+ Origin_2
+ Origin_3
+ Origin_4
+ Origin_5
+ Origin_6
+ Origin_7
+ Origin_8
+ Origin_9
+ Origin_10
+ Origin_11
+ Origin_12
+ Origin_13
+ Origin_14
+ Origin_15
+ Origin_16
+ Origin_17
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_1
+ Expressed_2
+ Expressed_3
+ Expressed_4
+ Expressed_4
+ Expressed_5
+ Expressed_6
+ Expressed_7
+ Expressed_8
+ Expressed_9
+ Expressed_10
+ Expressed_11
+ Expressed_12
+ Expressed_13
+ Expressed_14
+ Expressed_15
+ Expressed_16
+ Expressed_17
+ Expressed_18
+ Expressed_19
+ Expressed_20
+end
+ subgraph Title4[Phage infected]
+ T5
+ HK97
+ HK544
+ HK578
+ T7
+ P22
+ BTP1
+ ES18
+ Pokey
+ Raw
+ Eggy
+ KaID
+ T4
+ T5
+ HK578
+ T7
+ det7
+ Pokey
+ KalD
+ T2
+ T4
+ T3
+ T7
+ PhiV-1
+ T2
+ T4
+ T5
+ T4
+ T5
+ SECphi4
+ SECphi6
+ SECphi27
+ P1
+ T7
+ T5
+ Lambda-Vir
+ T5
+ T2
+ T4
+ T7
+ T5
+ Lambda-Vir
+ T5
+ T2
+ T4
+ T6
+ T2
+ T4
+ T6
+ SECphi4
+ SECphi6
+ SECphi18
+ T4
+ T6
+ T7
+ T5
+ P1vir
+ T2
+ T3
+ T5
+ T7
+ Ffm
+ Br60
+ T5
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/rexab.md b/content/3.defense-systems/rexab.md
index 332b7ab4..bf745019 100644
--- a/content/3.defense-systems/rexab.md
+++ b/content/3.defense-systems/rexab.md
@@ -52,11 +52,30 @@ dataUrl: /rexab/RexAB,RexAB_RexB,0,V-plddts_87.11344.pdb
::
## Experimental validation
-
-RexAB systems were experimentally validated using:
-
-A system from *Escherichia coli lambda prophage* in *Escherichia coli* has an anti-phage effect against T4, Lamboid phages (Parma et al., 1992)
-
+<mermaid>
+graph LR;
+ Parma_1992[<a href='https://doi.org/10.1101/gad.6.3.497'>Parma et al., 1992</a>] --> Origin_0
+ Origin_0[Escherichia coli lambda prophage
+<a href='https://ncbi.nlm.nih.gov/protein/NP_040626.1'>NP_040626.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/NP_040627.1'>NP_040627.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T4 & Lamboidphages
+ subgraph Title1[Reference]
+ Parma_1992
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T4
+ Lamboidphages
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/rloc.md b/content/3.defense-systems/rloc.md
index cf96c958..0ee3e092 100644
--- a/content/3.defense-systems/rloc.md
+++ b/content/3.defense-systems/rloc.md
@@ -45,11 +45,28 @@ dataUrl: /rloc/RloC__RloC-plddts_86.73175.pdb
::
## Experimental validation
-
-RloC systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T4 (Penner et al., 1995)
-
+<mermaid>
+graph LR;
+ Penner_1995[<a href='https://doi.org/10.1006/jmbi.1995.0343'>Penner et al., 1995</a>] --> Origin_0
+ Origin_0[Escherichia coli] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T4
+ subgraph Title1[Reference]
+ Penner_1995
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T4
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/rnlab.md b/content/3.defense-systems/rnlab.md
index 575b7b3d..081ee724 100644
--- a/content/3.defense-systems/rnlab.md
+++ b/content/3.defense-systems/rnlab.md
@@ -52,11 +52,28 @@ dataUrl: /rnlab/RnlAB,RnlAB__RnlB,0,DF-plddts_92.42543.pdb
::
## Experimental validation
-
-RnlAB systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T4 (Koga et al., 2011)
-
+<mermaid>
+graph LR;
+ Koga_2011[<a href='https://doi.org/10.1534/genetics.110.121798'>Koga et al., 2011</a>] --> Origin_0
+ Origin_0[Escherichia coli] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T4
+ subgraph Title1[Reference]
+ Koga_2011
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T4
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/rosmerta.md b/content/3.defense-systems/rosmerta.md
index 4664af1f..47f16a5d 100644
--- a/content/3.defense-systems/rosmerta.md
+++ b/content/3.defense-systems/rosmerta.md
@@ -52,11 +52,30 @@ dataUrl: /rosmerta/RosmerTA,RosmerTA__RmrT,0,V-plddts_84.3404.pdb
::
## Experimental validation
-
-RosmerTA systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against P1, LambdaVir (Millman et al., 2022)
-
+<mermaid>
+graph LR;
+ Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2658042940'>2658042940</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2658042941'>2658042941</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> P1 & LambdaVir
+ subgraph Title1[Reference]
+ Millman_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ P1
+ LambdaVir
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/rst_3hp.md b/content/3.defense-systems/rst_3hp.md
index f57a036e..7bd485dd 100644
--- a/content/3.defense-systems/rst_3hp.md
+++ b/content/3.defense-systems/rst_3hp.md
@@ -58,11 +58,30 @@ dataUrl: /rst_3hp/Rst_3HP,Rst_3HP__Hp3,0,V-plddts_95.1843.pdb
::
## Experimental validation
-
-Rst_3HP systems were experimentally validated using:
-
-A system from *Escherichia coli (P2 loci)* in *Escherichia coli* has an anti-phage effect against P1 (Rousset et al., 2022)
-
+<mermaid>
+graph LR;
+ Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia coli P2 loci
+<a href='https://ncbi.nlm.nih.gov/protein/WP_000508501.1'>WP_000508501.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_112026686.1'>WP_112026686.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/WP_000756244.1'>WP_000756244.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> P1
+ subgraph Title1[Reference]
+ Rousset_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ P1
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/rst_duf4238.md b/content/3.defense-systems/rst_duf4238.md
index af72cbfd..decdcf11 100644
--- a/content/3.defense-systems/rst_duf4238.md
+++ b/content/3.defense-systems/rst_duf4238.md
@@ -45,11 +45,29 @@ dataUrl: /rst_duf4238/Rst_DUF4238__DUF4238_Pers-plddts_94.11236.pdb
::
## Experimental validation
-
-Rst_DUF4238 systems were experimentally validated using:
-
-A system from *Escherichia coli (P2 loci)* in *Escherichia coli* has an anti-phage effect against T7 (Rousset et al., 2022)
-
+<mermaid>
+graph LR;
+ Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia coli P2 loci
+<a href='https://ncbi.nlm.nih.gov/protein/EGB68990.1'>EGB68990.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T7
+ subgraph Title1[Reference]
+ Rousset_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T7
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/rst_gop_beta_cll.md b/content/3.defense-systems/rst_gop_beta_cll.md
index f7e32190..dba4c452 100644
--- a/content/3.defense-systems/rst_gop_beta_cll.md
+++ b/content/3.defense-systems/rst_gop_beta_cll.md
@@ -59,11 +59,31 @@ dataUrl: /rst_gop_beta_cll/Rst_gop_beta_cll,Rst_gop_beta_cll__gop,0,V-plddts_74.
::
## Experimental validation
-
-Rst_gop_beta_cll systems were experimentally validated using:
-
-A system from *Enterobacteria phage P4* in *Escherichia coli* has an anti-phage effect against Lambda, P1 (Rousset et al., 2022)
-
+<mermaid>
+graph LR;
+ Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0
+ Origin_0[Enterobacteria phage P4
+<a href='https://ncbi.nlm.nih.gov/protein/WP_105493229.1'>WP_105493229.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/ENG39111.1'>ENG39111.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/NP_042032.1'>NP_042032.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> Lambda & P1
+ subgraph Title1[Reference]
+ Rousset_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ Lambda
+ P1
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/rst_helicaseduf2290.md b/content/3.defense-systems/rst_helicaseduf2290.md
index 8e94dd2d..1b9d49a8 100644
--- a/content/3.defense-systems/rst_helicaseduf2290.md
+++ b/content/3.defense-systems/rst_helicaseduf2290.md
@@ -52,11 +52,29 @@ dataUrl: /rst_helicaseduf2290/Rst_HelicaseDUF2290,Rst_HelicaseDUF2290__Helicase,
::
## Experimental validation
-
-Rst_HelicaseDUF2290 systems were experimentally validated using:
-
-A system from *Klebsiella pneumoniae (P4 loci)* in *Escherichia coli* has an anti-phage effect against T7 (Rousset et al., 2022)
-
+<mermaid>
+graph LR;
+ Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0
+ Origin_0[Klebsiella pneumoniae P4 loci
+<a href='https://ncbi.nlm.nih.gov/protein/WP_046623503.1'>WP_046623503.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_046623504.1'>WP_046623504.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T7
+ subgraph Title1[Reference]
+ Rousset_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T7
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/rst_hydrolase-3tm.md b/content/3.defense-systems/rst_hydrolase-3tm.md
index 34c3d7c5..55fca2b1 100644
--- a/content/3.defense-systems/rst_hydrolase-3tm.md
+++ b/content/3.defense-systems/rst_hydrolase-3tm.md
@@ -52,11 +52,29 @@ dataUrl: /rst_hydrolase-3tm/Rst_Hydrolase-Tm,Rst_Hydrolase-Tm__Hydrolase-Tm,0,V-
::
## Experimental validation
-
-Rst_Hydrolase-3Tm systems were experimentally validated using:
-
-A system from *Escherichia coli (P4 loci)* in *Escherichia coli* has an anti-phage effect against T7 (Rousset et al., 2022)
-
+<mermaid>
+graph LR;
+ Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia coli P4 loci
+<a href='https://ncbi.nlm.nih.gov/protein/WP_000754434.1'>WP_000754434.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_001401335.1'>WP_001401335.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T7
+ subgraph Title1[Reference]
+ Rousset_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T7
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/rst_rt-nitrilase-tm.md b/content/3.defense-systems/rst_rt-nitrilase-tm.md
index ef862c48..e695d6d4 100644
--- a/content/3.defense-systems/rst_rt-nitrilase-tm.md
+++ b/content/3.defense-systems/rst_rt-nitrilase-tm.md
@@ -52,11 +52,29 @@ dataUrl: /rst_rt-nitrilase-tm/Rst_RT-Tm,Rst_RT-Tm__RT-Tm,0,V-plddts_89.04275.pdb
::
## Experimental validation
-
-Rst_RT-nitrilase-Tm systems were experimentally validated using:
-
-A system from *Escherichia coli (P4 loci)* in *Escherichia coli* has an anti-phage effect against Al505_P2 (Rousset et al., 2022)
-
+<mermaid>
+graph LR;
+ Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia coli P4 loci
+<a href='https://ncbi.nlm.nih.gov/protein/WP_000628823.1'>WP_000628823.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_000094232.1'>WP_000094232.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> Al505_P2
+ subgraph Title1[Reference]
+ Rousset_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ Al505_P2
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/rst_tir-nlr.md b/content/3.defense-systems/rst_tir-nlr.md
index a1bb04a2..9b29b9e6 100644
--- a/content/3.defense-systems/rst_tir-nlr.md
+++ b/content/3.defense-systems/rst_tir-nlr.md
@@ -45,11 +45,34 @@ dataUrl: /rst_tir-nlr/Rst_TIR-NLR__TIR-plddts_88.48123.pdb
::
## Experimental validation
-
-Rst_TIR-NLR systems were experimentally validated using:
-
-A system from *Klebsiella pneumoniae (P4 loci)* in *Escherichia coli* has an anti-phage effect against T4, P1, CLB_P2, LF82_P8, AL505_P2, T7 (Rousset et al., 2022)
-
+<mermaid>
+graph LR;
+ Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_0
+ Origin_0[Klebsiella pneumoniae P4 loci
+<a href='https://ncbi.nlm.nih.gov/protein/WP_044784989.1'>WP_044784989.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T4 & P1 & CLB_P2 & LF82_P8 & AL505_P2 & T7
+ subgraph Title1[Reference]
+ Rousset_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T4
+ P1
+ CLB_P2
+ LF82_P8
+ AL505_P2
+ T7
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/sanata.md b/content/3.defense-systems/sanata.md
index a054e42c..1a7f6d2f 100644
--- a/content/3.defense-systems/sanata.md
+++ b/content/3.defense-systems/sanata.md
@@ -52,11 +52,29 @@ dataUrl: /sanata/SanaTA,SanaTA_SanaT,0,V-plddts_94.5954.pdb
::
## Experimental validation
-
-SanaTA systems were experimentally validated using:
-
-A system from *Shewanella sp. ANA-3* in *Escherichia coli* has an anti-phage effect against T7 (Sberro et al., 2013)
-
+<mermaid>
+graph LR;
+ Sberro_2013[<a href='https://doi.org/10.1016/j.molcel.2013.02.002'>Sberro et al., 2013</a>] --> Origin_0
+ Origin_0[Shewanella sp. ANA-3
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=639720518'>639720518</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=639720519'>639720519</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T7
+ subgraph Title1[Reference]
+ Sberro_2013
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T7
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/sefir.md b/content/3.defense-systems/sefir.md
index 6137599b..fb73b3e6 100644
--- a/content/3.defense-systems/sefir.md
+++ b/content/3.defense-systems/sefir.md
@@ -53,11 +53,29 @@ dataUrl: /sefir/SEFIR__bSEFIR-plddts_89.61831.pdb
::
## Experimental validation
-
-SEFIR systems were experimentally validated using:
-
-A system from *Bacillus sp. NIO-1130* in *Bacillus subtilis* has an anti-phage effect against phi29 (Millman et al., 2022)
-
+<mermaid>
+graph LR;
+ Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
+ Origin_0[Bacillus sp. NIO-1130
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2616229772'>2616229772</a>] --> Expressed_0[Bacillus subtilis]
+ Expressed_0[Bacillus subtilis] ----> phi29
+ subgraph Title1[Reference]
+ Millman_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ phi29
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/septu.md b/content/3.defense-systems/septu.md
index ee3f9144..170028d2 100644
--- a/content/3.defense-systems/septu.md
+++ b/content/3.defense-systems/septu.md
@@ -68,13 +68,38 @@ dataUrl: /septu/Septu,Septu__PtuB,0,V-plddts_95.05244.pdb
::
## Experimental validation
-
-Septu systems were experimentally validated using:
-
-A system from *Bacillus thuringiensis* in *Bacillus subtilis* has an anti-phage effect against SBSphiJ, SBSphiC (Doron et al., 2018)
-
-A system from *Bacillus weihenstephanensis* in *Bacillus subtilis* has an anti-phage effect against SBSphiC, SpBeta (Doron et al., 2018)
-
+<mermaid>
+graph LR;
+ Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_0
+ Origin_0[Bacillus thuringiensis
+<a href='https://ncbi.nlm.nih.gov/protein/AMR85048.1'>AMR85048.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/AMR85049.1'>AMR85049.1</a>] --> Expressed_0[Bacillus subtilis]
+ Expressed_0[Bacillus subtilis] ----> SBSphiJ & SBSphiC
+ Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_1
+ Origin_1[Bacillus weihenstephanensis
+<a href='https://ncbi.nlm.nih.gov/protein/ABY44616.1'>ABY44616.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/ABY44615.1'>ABY44615.1</a>] --> Expressed_1[Bacillus subtilis]
+ Expressed_1[Bacillus subtilis] ----> SBSphiC & SpBeta
+ subgraph Title1[Reference]
+ Doron_2018
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_1
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_1
+end
+ subgraph Title4[Phage infected]
+ SBSphiJ
+ SBSphiC
+ SBSphiC
+ SpBeta
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/shango.md b/content/3.defense-systems/shango.md
index 3314b5d7..1e048aa0 100644
--- a/content/3.defense-systems/shango.md
+++ b/content/3.defense-systems/shango.md
@@ -72,11 +72,31 @@ dataUrl: /shango/Shango,Shango__SngA,0,V-plddts_78.29927.pdb
::
## Experimental validation
-
-Shango systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against LambdaVir, SECphi18 (Millman et al., 2022)
-
+<mermaid>
+graph LR;
+ Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2538938181'>2538938181</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2538938182'>2538938182</a>,
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2538938183'>2538938183</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> LambdaVir & SECphi18
+ subgraph Title1[Reference]
+ Millman_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ LambdaVir
+ SECphi18
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/shedu.md b/content/3.defense-systems/shedu.md
index 25062ee6..a6a15c5f 100644
--- a/content/3.defense-systems/shedu.md
+++ b/content/3.defense-systems/shedu.md
@@ -45,11 +45,32 @@ dataUrl: /shedu/Shedu__SduA-plddts_87.27097.pdb
::
## Experimental validation
-
-Shedu systems were experimentally validated using:
-
-A system from *Bacillus cereus* in *Bacillus subtilis* has an anti-phage effect against phi105, rho14, SPP1, phi29 (Doron et al., 2018)
-
+<mermaid>
+graph LR;
+ Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_0
+ Origin_0[Bacillus cereus
+<a href='https://ncbi.nlm.nih.gov/protein/ACK61957.1'>ACK61957.1</a>] --> Expressed_0[Bacillus subtilis]
+ Expressed_0[Bacillus subtilis] ----> phi105 & rho14 & SPP1 & phi29
+ subgraph Title1[Reference]
+ Doron_2018
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ phi105
+ rho14
+ SPP1
+ phi29
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/shosta.md b/content/3.defense-systems/shosta.md
index 93b01cfd..1e3c7bd8 100644
--- a/content/3.defense-systems/shosta.md
+++ b/content/3.defense-systems/shosta.md
@@ -52,13 +52,41 @@ dataUrl: /shosta/ShosTA,ShosTA__ShosT,0,V-plddts_91.38081.pdb
::
## Experimental validation
-
-ShosTA systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against LambdaVir, SECphi4, SECphi6, SECphi18, T7 (Millman et al., 2022)
-
-A system from *Escherichia coli (P2 loci)* in *Escherichia coli* has an anti-phage effect against Lambda, T7 (Rousset et al., 2022)
-
+<mermaid>
+graph LR;
+ Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2564403099'>2564403099</a>, <a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2564403100'>2564403100</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> LambdaVir & SECphi4 & SECphi6 & SECphi18 & T7
+ Rousset_2022[<a href='https://doi.org/10.1016/j.chom.2022.02.018'>Rousset et al., 2022</a>] --> Origin_1
+ Origin_1[Escherichia coli P2 loci] --> Expressed_1[Escherichia coli]
+ Expressed_1[Escherichia coli] ----> Lambda & T7
+ subgraph Title1[Reference]
+ Millman_2022
+ Rousset_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_1
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_1
+end
+ subgraph Title4[Phage infected]
+ LambdaVir
+ SECphi4
+ SECphi6
+ SECphi18
+ T7
+ Lambda
+ T7
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/sofic.md b/content/3.defense-systems/sofic.md
index 38e1c8de..5023de02 100644
--- a/content/3.defense-systems/sofic.md
+++ b/content/3.defense-systems/sofic.md
@@ -45,11 +45,29 @@ dataUrl: /sofic/SoFic__SoFic-plddts_95.70819.pdb
::
## Experimental validation
-
-SoFIC systems were experimentally validated using:
-
-A system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T5 (Millman et al., 2022)
-
+<mermaid>
+graph LR;
+ Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
+ Origin_0[Escherichia coli
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2533973964'>2533973964</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T5
+ subgraph Title1[Reference]
+ Millman_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T5
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/spbk.md b/content/3.defense-systems/spbk.md
index 50aaf76e..9b9195bc 100644
--- a/content/3.defense-systems/spbk.md
+++ b/content/3.defense-systems/spbk.md
@@ -45,11 +45,29 @@ dataUrl: /spbk/SpbK__SpbK-plddts_78.5012.pdb
::
## Experimental validation
-
-SpbK systems were experimentally validated using:
-
-A system from *Bacillus subtilis* in *Bacillus subtilis* has an anti-phage effect against SPbeta (Johnson et al., 2022)
-
+<mermaid>
+graph LR;
+ Johnson_2022[<a href='https://doi.org/10.1371/journal.pgen.1010065'>Johnson et al., 2022</a>] --> Origin_0
+ Origin_0[Bacillus subtilis
+<a href='https://ncbi.nlm.nih.gov/protein/NP_388381.1'>NP_388381.1</a>] --> Expressed_0[Bacillus subtilis]
+ Expressed_0[Bacillus subtilis] ----> SPbeta
+ subgraph Title1[Reference]
+ Johnson_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ SPbeta
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/sspbcde.md b/content/3.defense-systems/sspbcde.md
index 499b6653..8ca765c7 100644
--- a/content/3.defense-systems/sspbcde.md
+++ b/content/3.defense-systems/sspbcde.md
@@ -110,17 +110,78 @@ dataUrl: /sspbcde/SspBCDE,SspBCDE__SspC,1,V-plddts_84.03334.pdb
::
## Experimental validation
-
-SspBCDE systems were experimentally validated using:
-
-Subsystem SspABCD+SspE with a system from *Vibrio cyclitrophicus* in *Escherichia coli* has an anti-phage effect against T4, T1, JMPW1, JMPW2, EEP, T7 (Xiong et al., 2020)
-
-Subsystem SspBCD+SspE with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T4, T1, JMPW1, JMPW2, EEP, T7, PhiX174 (Xiong et al., 2020)
-
-Subsystem SspBCD+SspE with a system from *Streptomyces yokosukanensis* in *Streptomyces lividans* has an anti-phage effect against JXY1 (Xiong et al., 2020)
-
-Subsystem SspBCD+SspFGH with a system from *Vibrio anguillarum* in *Escherichia coli* has an anti-phage effect against T1, JMPW2, T4, EEP (Wang et al., 2021)
-
+<mermaid>
+graph LR;
+ Xiong_2020[<a href='https://doi.org/10.1038/s41564-020-0700-6'>Xiong et al., 2020</a>] --> Origin_0
+ Origin_0[ SspABCD+SspE
+Vibrio cyclitrophicus
+<a href='https://ncbi.nlm.nih.gov/protein/WP_022570853.1'>WP_022570853.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_016789109.1'>WP_016789109.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/WP_016789110.1'>WP_016789110.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_016789111.1'>WP_016789111.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/WP_016789113.1'>WP_016789113.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_016789114.1'>WP_016789114.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T4 & T1 & JMPW1 & JMPW2 & EEP & T7
+ Xiong_2020[<a href='https://doi.org/10.1038/s41564-020-0700-6'>Xiong et al., 2020</a>] --> Origin_1
+ Origin_1[ SspBCD+SspE
+Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/WP_000429341.1'>WP_000429341.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_000928407.1'>WP_000928407.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/WP_000840786.1'>WP_000840786.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_001424009.1'>WP_001424009.1</a>] --> Expressed_1[Escherichia coli]
+ Expressed_1[Escherichia coli] ----> T4 & T1 & JMPW1 & JMPW2 & EEP & T7 & PhiX174
+ Xiong_2020[<a href='https://doi.org/10.1038/s41564-020-0700-6'>Xiong et al., 2020</a>] --> Origin_2
+ Origin_2[ SspBCD+SspE
+Streptomyces yokosukanensis
+<a href='https://ncbi.nlm.nih.gov/protein/WP_067135675.1'>WP_067135675.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_037642090.1'>WP_037642090.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/WP_208614377.1'>WP_208614377.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_067135521.1'>WP_067135521.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/WP_067135523.1'>WP_067135523.1</a>] --> Expressed_2[Streptomyces lividans]
+ Expressed_2[Streptomyces lividans] ----> JXY1
+ Wang_2021[<a href='https://doi.org/10.1128/mBio.00613-21'>Wang et al., 2021</a>] --> Origin_3
+ Origin_3[ SspBCD+SspFGH
+Vibrio anguillarum
+<a href='https://ncbi.nlm.nih.gov/protein/WP_022570853.1'>WP_022570853.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_016789109.1'>WP_016789109.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/WP_016789110.1'>WP_016789110.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_016789111.1'>WP_016789111.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/WP_017048669.1'>WP_017048669.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/'></a>,
+<a href='https://ncbi.nlm.nih.gov/protein/WP_017048667.1'>WP_017048667.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_017048666.1'>WP_017048666.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/WP_017048665.1'>WP_017048665.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_017048664.1'>WP_017048664.1</a>] --> Expressed_3[Escherichia coli]
+ Expressed_3[Escherichia coli] ----> T1 & JMPW2 & T4 & EEP
+ subgraph Title1[Reference]
+ Xiong_2020
+ Wang_2021
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_1
+ Origin_2
+ Origin_3
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_1
+ Expressed_2
+ Expressed_3
+end
+ subgraph Title4[Phage infected]
+ T4
+ T1
+ JMPW1
+ JMPW2
+ EEP
+ T7
+ T4
+ T1
+ JMPW1
+ JMPW2
+ EEP
+ T7
+ PhiX174
+ JXY1
+ T1
+ JMPW2
+ T4
+ EEP
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/stk2.md b/content/3.defense-systems/stk2.md
index 0ef68de6..f2c36e40 100644
--- a/content/3.defense-systems/stk2.md
+++ b/content/3.defense-systems/stk2.md
@@ -54,13 +54,40 @@ dataUrl: /stk2/Stk2__Stk2-plddts_91.79541.pdb
::
## Experimental validation
-
-Stk2 systems were experimentally validated using:
-
-A system from *Staphylococcus epidermidis* in *Staphylococcus epidermidis* has an anti-phage effect against CNPx (Depardieu et al., 2016)
-
-A system from *Staphylococcus epidermidis* in *Staphylococcus aureus* has an anti-phage effect against phage 80alpha, phage 85, phiNM1, phiNM2, phiNM4 (Depardieu et al., 2016)
-
+<mermaid>
+graph LR;
+ Depardieu_2016[<a href='https://doi.org/10.1016/j.chom.2016.08.010'>Depardieu et al., 2016</a>] --> Origin_0
+ Origin_0[Staphylococcus epidermidis
+<a href='https://ncbi.nlm.nih.gov/protein/WP_001001347.1'>WP_001001347.1</a>] --> Expressed_0[Staphylococcus epidermidis]
+ Expressed_0[Staphylococcus epidermidis] ----> CNPx
+ Depardieu_2016[<a href='https://doi.org/10.1016/j.chom.2016.08.010'>Depardieu et al., 2016</a>] --> Origin_0
+ Origin_0[Staphylococcus epidermidis
+<a href='https://ncbi.nlm.nih.gov/protein/WP_001001347.1'>WP_001001347.1</a>] --> Expressed_1[Staphylococcus aureus]
+ Expressed_1[Staphylococcus aureus] ----> phage80alpha & phage85 & phiNM1 & phiNM2 & phiNM4
+ subgraph Title1[Reference]
+ Depardieu_2016
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_1
+end
+ subgraph Title4[Phage infected]
+ CNPx
+ phage80alpha
+ phage85
+ phiNM1
+ phiNM2
+ phiNM4
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/thoeris.md b/content/3.defense-systems/thoeris.md
index 66b69abe..8efc7114 100644
--- a/content/3.defense-systems/thoeris.md
+++ b/content/3.defense-systems/thoeris.md
@@ -72,15 +72,64 @@ dataUrl: /thoeris/Thoeris_II,Thoeris__ThsB_Global,0,V-plddts_93.32159.pdb
::
## Experimental validation
-
-Thoeris systems were experimentally validated using:
-
-A system from *Bacillus amyloliquefaciens* in *Bacillus subtilis* has an anti-phage effect against SPO1, SBSphiJ, SBSphiC (Doron et al., 2018)
-
-A system from *Bacillus cereus* in *Bacillus subtilis* has an anti-phage effect against phi29, SBSphiC, SPO1, SBSphiJ (Doron et al., 2018; Ofir et al., 2021)
-
-A system from *Bacillus dafuensis* in *Bacillus subtilis* has an anti-phage effect against phi3T, SPBeta, SPR, SBSphi11, SBSphi13, phi29, SBSphiJ, SPO1 (Ofir et al., 2021)
-
+<mermaid>
+graph LR;
+ Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_0
+ Origin_0[Bacillus amyloliquefaciens
+<a href='https://ncbi.nlm.nih.gov/protein/AFJ62118.1'>AFJ62118.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/AFJ62119.1'>AFJ62119.1</a>] --> Expressed_0[Bacillus subtilis]
+ Expressed_0[Bacillus subtilis] ----> SPO1 & SBSphiJ & SBSphiC
+ Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_1
+ Ofir_2021[<a href='https://doi.org/10.1038/s41586-021-04098-7'>Ofir et al., 2021</a>] --> Origin_1
+ Origin_1[Bacillus cereus
+<a href='https://ncbi.nlm.nih.gov/protein/EJR09241.1'>EJR09241.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/EJR09240.1'>EJR09240.1</a>] --> Expressed_1[Bacillus subtilis]
+ Expressed_1[Bacillus subtilis] ----> phi29 & SBSphiC & SPO1 & SBSphiJ
+ Ofir_2021[<a href='https://doi.org/10.1038/s41586-021-04098-7'>Ofir et al., 2021</a>] --> Origin_2
+ Origin_2[Bacillus dafuensis
+<a href='https://ncbi.nlm.nih.gov/protein/WP_057775117.1'>WP_057775117.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_057775115.1'>WP_057775115.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/WP_057775113.1'>WP_057775113.1</a>] --> Expressed_2[Bacillus subtilis]
+ Expressed_2[Bacillus subtilis] ----> phi3T & SPBeta & SPR & SBSphi11 & SBSphi13 & phi29 & SBSphiJ & SPO1
+ subgraph Title1[Reference]
+ Doron_2018
+ Ofir_2021
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_1
+ Origin_1
+ Origin_2
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_1
+ Expressed_1
+ Expressed_2
+end
+ subgraph Title4[Phage infected]
+ SPO1
+ SBSphiJ
+ SBSphiC
+ phi29
+ SBSphiC
+ SPO1
+ SBSphiJ
+ phi29
+ SBSphiC
+ SPO1
+ SBSphiJ
+ phi3T
+ SPBeta
+ SPR
+ SBSphi11
+ SBSphi13
+ phi29
+ SBSphiJ
+ SPO1
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/tiamat.md b/content/3.defense-systems/tiamat.md
index 0324f6c6..5728b62d 100644
--- a/content/3.defense-systems/tiamat.md
+++ b/content/3.defense-systems/tiamat.md
@@ -45,11 +45,30 @@ dataUrl: /tiamat/Tiamat__TmtA-plddts_86.46392.pdb
::
## Experimental validation
-
-Tiamat systems were experimentally validated using:
-
-A system from *Bacillus cereus* in *Escherichia coli* has an anti-phage effect against T6, T5 (Millman et al., 2022)
-
+<mermaid>
+graph LR;
+ Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
+ Origin_0[Bacillus cereus
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2641244160'>2641244160</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T6 & T5
+ subgraph Title1[Reference]
+ Millman_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ T6
+ T5
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/uzume.md b/content/3.defense-systems/uzume.md
index c8f0aabf..8bdb173c 100644
--- a/content/3.defense-systems/uzume.md
+++ b/content/3.defense-systems/uzume.md
@@ -44,11 +44,31 @@ dataUrl: /uzume/Uzume__UzmA-plddts_94.2491.pdb
::
## Experimental validation
-
-Uzume systems were experimentally validated using:
-
-A system from *Bacillus sp. FJAT-27231* in *Bacillus subtilis* has an anti-phage effect against SPO1, SP82G, SBSphiC (Millman et al., 2022)
-
+<mermaid>
+graph LR;
+ Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
+ Origin_0[Bacillus sp. FJAT-27231
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2638179248'>2638179248</a>] --> Expressed_0[Bacillus subtilis]
+ Expressed_0[Bacillus subtilis] ----> SPO1 & SP82G & SBSphiC
+ subgraph Title1[Reference]
+ Millman_2022
+end
+ subgraph Title2[System origin]
+ Origin_0
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+end
+ subgraph Title4[Phage infected]
+ SPO1
+ SP82G
+ SBSphiC
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/viperin.md b/content/3.defense-systems/viperin.md
index b2cf1ae9..a371b6e4 100644
--- a/content/3.defense-systems/viperin.md
+++ b/content/3.defense-systems/viperin.md
@@ -62,45 +62,166 @@ dataUrl: /viperin/Viperin__pVip-plddts_95.08271.pdb
::
## Experimental validation
-
-Viperin systems were experimentally validated using:
-
-Subsystem pVip6 with a system from *Selenomonas ruminatium* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
-
-Subsystem pVip7 with a system from *Fibrobacter sp. UWT3* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
-
-Subsystem pVip9 with a system from *Vibrio porteresiae* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
-
-Subsystem pVip12 with a system from *Ruegeria intermedia* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
-
-Subsystem pVip15 with a system from *Coraliomargarita akajimensis* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
-
-Subsystem pVip21 with a system from *Lewinella persica* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
-
-Subsystem pVip32 with a system from *Phormidium sp. OSCR GFM* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
-
-Subsystem pVip34 with a system from *Cryomorphaceae bacterium* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
-
-Subsystem pVip37 with a system from *Shewanella sp. cp20* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
-
-Subsystem pVip39 with a system from *Burkholderiales-76 (UID4002)* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
-
-Subsystem pVip44 with a system from *Chondromyces crocatus* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
-
-Subsystem pVip46 with a system from *Photobacterium swingsii* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
-
-Subsystem pVip57 with a system from *Flavobacterium lacus* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
-
-Subsystem pVip58 with a system from *Pseudoalteromonas ulvae* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
-
-Subsystem pVip60 with a system from *Lacinutrix sp. JCM 13824* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
-
-Subsystem pVip61 with a system from *Euryarchaeota archaeon SCGC AG-487_M08* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
-
-Subsystem pVip62 with a system from *Fibrobacteria bacterium* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
-
-Subsystem pVip63 with a system from *Pseudoalteromonas sp. XI10* in *Escherichia coli* has an anti-phage effect against T7 (Bernheim et al., 2020)
-
+<mermaid>
+graph LR;
+ Bernheim_2020[<a href='https://doi.org/10.1038/s41586-020-2762-2'>Bernheim et al., 2020</a>] --> Origin_0
+ Origin_0[ pVip6
+Selenomonas ruminatium
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2624749465'>2624749465</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> T7
+ Bernheim_2020[<a href='https://doi.org/10.1038/s41586-020-2762-2'>Bernheim et al., 2020</a>] --> Origin_1
+ Origin_1[ pVip7
+Fibrobacter sp. UWT3
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2739066738'>2739066738</a>] --> Expressed_1[Escherichia coli]
+ Expressed_1[Escherichia coli] ----> T7
+ Bernheim_2020[<a href='https://doi.org/10.1038/s41586-020-2762-2'>Bernheim et al., 2020</a>] --> Origin_2
+ Origin_2[ pVip9
+Vibrio porteresiae
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2574301464'>2574301464</a>] --> Expressed_2[Escherichia coli]
+ Expressed_2[Escherichia coli] ----> T7
+ Bernheim_2020[<a href='https://doi.org/10.1038/s41586-020-2762-2'>Bernheim et al., 2020</a>] --> Origin_3
+ Origin_3[ pVip12
+Ruegeria intermedia
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2698137626'>2698137626</a>] --> Expressed_3[Escherichia coli]
+ Expressed_3[Escherichia coli] ----> T7
+ Bernheim_2020[<a href='https://doi.org/10.1038/s41586-020-2762-2'>Bernheim et al., 2020</a>] --> Origin_4
+ Origin_4[ pVip15
+Coraliomargarita akajimensis
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=646713396'>646713396</a>] --> Expressed_4[Escherichia coli]
+ Expressed_4[Escherichia coli] ----> T7
+ Bernheim_2020[<a href='https://doi.org/10.1038/s41586-020-2762-2'>Bernheim et al., 2020</a>] --> Origin_5
+ Origin_5[ pVip21
+Lewinella persica
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2515428782'>2515428782</a>] --> Expressed_5[Escherichia coli]
+ Expressed_5[Escherichia coli] ----> T7
+ Bernheim_2020[<a href='https://doi.org/10.1038/s41586-020-2762-2'>Bernheim et al., 2020</a>] --> Origin_6
+ Origin_6[ pVip32
+Phormidium sp. OSCR GFM
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2609132705'>2609132705</a>] --> Expressed_6[Escherichia coli]
+ Expressed_6[Escherichia coli] ----> T7
+ Bernheim_2020[<a href='https://doi.org/10.1038/s41586-020-2762-2'>Bernheim et al., 2020</a>] --> Origin_7
+ Origin_7[ pVip34
+Cryomorphaceae bacterium
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2619892213'>2619892213</a>] --> Expressed_7[Escherichia coli]
+ Expressed_7[Escherichia coli] ----> T7
+ Bernheim_2020[<a href='https://doi.org/10.1038/s41586-020-2762-2'>Bernheim et al., 2020</a>] --> Origin_8
+ Origin_8[ pVip37
+Shewanella sp. cp20
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2632937107'>2632937107</a>] --> Expressed_8[Escherichia coli]
+ Expressed_8[Escherichia coli] ----> T7
+ Bernheim_2020[<a href='https://doi.org/10.1038/s41586-020-2762-2'>Bernheim et al., 2020</a>] --> Origin_9
+ Origin_9[ pVip39
+Burkholderiales-76 UID4002
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2634960437'>2634960437</a>] --> Expressed_9[Escherichia coli]
+ Expressed_9[Escherichia coli] ----> T7
+ Bernheim_2020[<a href='https://doi.org/10.1038/s41586-020-2762-2'>Bernheim et al., 2020</a>] --> Origin_10
+ Origin_10[ pVip44
+Chondromyces crocatus
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2648875132'>2648875132</a>] --> Expressed_10[Escherichia coli]
+ Expressed_10[Escherichia coli] ----> T7
+ Bernheim_2020[<a href='https://doi.org/10.1038/s41586-020-2762-2'>Bernheim et al., 2020</a>] --> Origin_11
+ Origin_11[ pVip46
+Photobacterium swingsii
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2649993803'>2649993803</a>] --> Expressed_11[Escherichia coli]
+ Expressed_11[Escherichia coli] ----> T7
+ Bernheim_2020[<a href='https://doi.org/10.1038/s41586-020-2762-2'>Bernheim et al., 2020</a>] --> Origin_12
+ Origin_12[ pVip57
+Flavobacterium lacus
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2718503187'>2718503187</a>] --> Expressed_12[Escherichia coli]
+ Expressed_12[Escherichia coli] ----> T7
+ Bernheim_2020[<a href='https://doi.org/10.1038/s41586-020-2762-2'>Bernheim et al., 2020</a>] --> Origin_13
+ Origin_13[ pVip58
+Pseudoalteromonas ulvae
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2721736750'>2721736750</a>] --> Expressed_13[Escherichia coli]
+ Expressed_13[Escherichia coli] ----> T7
+ Bernheim_2020[<a href='https://doi.org/10.1038/s41586-020-2762-2'>Bernheim et al., 2020</a>] --> Origin_14
+ Origin_14[ pVip60
+Lacinutrix sp. JCM 13824
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2733913669'>2733913669</a>] --> Expressed_14[Escherichia coli]
+ Expressed_14[Escherichia coli] ----> T7
+ Bernheim_2020[<a href='https://doi.org/10.1038/s41586-020-2762-2'>Bernheim et al., 2020</a>] --> Origin_15
+ Origin_15[ pVip61
+Euryarchaeota archaeon SCGC AG-487_M08
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2741341560'>2741341560</a>] --> Expressed_15[Escherichia coli]
+ Expressed_15[Escherichia coli] ----> T7
+ Bernheim_2020[<a href='https://doi.org/10.1038/s41586-020-2762-2'>Bernheim et al., 2020</a>] --> Origin_16
+ Origin_16[ pVip62
+Fibrobacteria bacterium
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2743907592'>2743907592</a>] --> Expressed_16[Escherichia coli]
+ Expressed_16[Escherichia coli] ----> T7
+ Bernheim_2020[<a href='https://doi.org/10.1038/s41586-020-2762-2'>Bernheim et al., 2020</a>] --> Origin_17
+ Origin_17[ pVip63
+Pseudoalteromonas sp. XI10
+<a href='https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2744633848'>2744633848</a>] --> Expressed_17[Escherichia coli]
+ Expressed_17[Escherichia coli] ----> T7
+ subgraph Title1[Reference]
+ Bernheim_2020
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_1
+ Origin_2
+ Origin_3
+ Origin_4
+ Origin_5
+ Origin_6
+ Origin_7
+ Origin_8
+ Origin_9
+ Origin_10
+ Origin_11
+ Origin_12
+ Origin_13
+ Origin_14
+ Origin_15
+ Origin_16
+ Origin_17
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_1
+ Expressed_2
+ Expressed_3
+ Expressed_4
+ Expressed_5
+ Expressed_6
+ Expressed_7
+ Expressed_8
+ Expressed_9
+ Expressed_10
+ Expressed_11
+ Expressed_12
+ Expressed_13
+ Expressed_14
+ Expressed_15
+ Expressed_16
+ Expressed_17
+end
+ subgraph Title4[Phage infected]
+ T7
+ T7
+ T7
+ T7
+ T7
+ T7
+ T7
+ T7
+ T7
+ T7
+ T7
+ T7
+ T7
+ T7
+ T7
+ T7
+ T7
+ T7
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/content/3.defense-systems/zorya.md b/content/3.defense-systems/zorya.md
index 77310bbe..c83b7c26 100644
--- a/content/3.defense-systems/zorya.md
+++ b/content/3.defense-systems/zorya.md
@@ -93,15 +93,57 @@ dataUrl: /zorya/Zorya_TypeII,Zorya__ZorB,0,V-plddts_91.39341.pdb
::
## Experimental validation
-
-Zorya systems were experimentally validated using:
-
-Subsystem Type I with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against LambdaVir, SECphi27, T7 (Doron et al., 2018)
-
-Subsystem Type II with a system from *Escherichia coli* in *Escherichia coli* has an anti-phage effect against T7, SECphi17 (Doron et al., 2018)
-
-Subsystem Type III with a system from *Stenotrophomonas nitritireducens* in *Escherichia coli* has an anti-phage effect against T1, T4, T7, LambdaVir, PVP-SE1 (Payne et al., 2021)
-
+<mermaid>
+graph LR;
+ Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_0
+ Origin_0[ Type I
+Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/ABV17222.1'>ABV17222.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/ABV17786.1'>ABV17786.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/ABV16709.1'>ABV16709.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/ABV17208.1'>ABV17208.1</a>] --> Expressed_0[Escherichia coli]
+ Expressed_0[Escherichia coli] ----> LambdaVir & SECphi27 & T7
+ Doron_2018[<a href='https://doi.org/10.1126/science.aar4120'>Doron et al., 2018</a>] --> Origin_1
+ Origin_1[ Type II
+Escherichia coli
+<a href='https://ncbi.nlm.nih.gov/protein/ACA79490.1'>ACA79490.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/ACA79491.1'>ACA79491.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/ACA79492.1'>ACA79492.1</a>] --> Expressed_1[Escherichia coli]
+ Expressed_1[Escherichia coli] ----> T7 & SECphi17
+ Payne_2021[<a href='https://doi.org/10.1093/nar/gkab883'>Payne et al., 2021</a>] --> Origin_2
+ Origin_2[ Type III
+Stenotrophomonas nitritireducens
+<a href='https://ncbi.nlm.nih.gov/protein/WP_055768786.1'>WP_055768786.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_055768783.1'>WP_055768783.1</a>,
+<a href='https://ncbi.nlm.nih.gov/protein/WP_055768781.1'>WP_055768781.1</a>, <a href='https://ncbi.nlm.nih.gov/protein/WP_055768778.1'>WP_055768778.1</a>] --> Expressed_2[Escherichia coli]
+ Expressed_2[Escherichia coli] ----> T1 & T4 & T7 & LambdaVir & PVP-SE1
+ subgraph Title1[Reference]
+ Doron_2018
+ Payne_2021
+end
+ subgraph Title2[System origin]
+ Origin_0
+ Origin_1
+ Origin_2
+end
+ subgraph Title3[Expression species]
+ Expressed_0
+ Expressed_1
+ Expressed_2
+end
+ subgraph Title4[Phage infected]
+ LambdaVir
+ SECphi27
+ T7
+ T7
+ SECphi17
+ T1
+ T4
+ T7
+ LambdaVir
+ PVP-SE1
+end
+ style Title1 fill:none,stroke:none,stroke-width:none
+ style Title2 fill:none,stroke:none,stroke-width:none
+ style Title3 fill:none,stroke:none,stroke-width:none
+ style Title4 fill:none,stroke:none,stroke-width:none
+</mermaid>
## Relevant abstracts
::relevant-abstracts
diff --git a/package-lock.json b/package-lock.json
index cdc4b6c2..fdcc1366 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -9,6 +9,7 @@
"@pinia/nuxt": "^0.4.11",
"d3": "^7.8.5",
"meilisearch": "^0.35.0",
+ "mermaid": "^10.6.1",
"pinia": "^2.1.6",
"vue-json-csv": "^2.1.0",
"yaml": "^2.3.3"
@@ -42,10 +43,10 @@
}
},
"node_modules/@babel/code-frame": {
- "version": "7.22.13",
+ "version": "7.23.4",
"license": "MIT",
"dependencies": {
- "@babel/highlight": "^7.22.13",
+ "@babel/highlight": "^7.23.4",
"chalk": "^2.4.2"
},
"engines": {
@@ -95,10 +96,10 @@
}
},
"node_modules/@babel/generator": {
- "version": "7.23.3",
+ "version": "7.23.4",
"license": "MIT",
"dependencies": {
- "@babel/types": "^7.23.3",
+ "@babel/types": "^7.23.4",
"@jridgewell/gen-mapping": "^0.3.2",
"@jridgewell/trace-mapping": "^0.3.17",
"jsesc": "^2.5.1"
@@ -302,7 +303,7 @@
}
},
"node_modules/@babel/helper-string-parser": {
- "version": "7.22.5",
+ "version": "7.23.4",
"license": "MIT",
"engines": {
"node": ">=6.9.0"
@@ -323,19 +324,19 @@
}
},
"node_modules/@babel/helpers": {
- "version": "7.23.2",
+ "version": "7.23.4",
"license": "MIT",
"dependencies": {
"@babel/template": "^7.22.15",
- "@babel/traverse": "^7.23.2",
- "@babel/types": "^7.23.0"
+ "@babel/traverse": "^7.23.4",
+ "@babel/types": "^7.23.4"
},
"engines": {
"node": ">=6.9.0"
}
},
"node_modules/@babel/highlight": {
- "version": "7.22.20",
+ "version": "7.23.4",
"license": "MIT",
"dependencies": {
"@babel/helper-validator-identifier": "^7.22.20",
@@ -347,7 +348,7 @@
}
},
"node_modules/@babel/parser": {
- "version": "7.23.3",
+ "version": "7.23.4",
"license": "MIT",
"bin": {
"parser": "bin/babel-parser.js"
@@ -442,7 +443,7 @@
}
},
"node_modules/@babel/plugin-transform-typescript": {
- "version": "7.23.3",
+ "version": "7.23.4",
"dev": true,
"license": "MIT",
"dependencies": {
@@ -459,7 +460,7 @@
}
},
"node_modules/@babel/standalone": {
- "version": "7.23.3",
+ "version": "7.23.4",
"license": "MIT",
"engines": {
"node": ">=6.9.0"
@@ -478,17 +479,17 @@
}
},
"node_modules/@babel/traverse": {
- "version": "7.23.3",
+ "version": "7.23.4",
"license": "MIT",
"dependencies": {
- "@babel/code-frame": "^7.22.13",
- "@babel/generator": "^7.23.3",
+ "@babel/code-frame": "^7.23.4",
+ "@babel/generator": "^7.23.4",
"@babel/helper-environment-visitor": "^7.22.20",
"@babel/helper-function-name": "^7.23.0",
"@babel/helper-hoist-variables": "^7.22.5",
"@babel/helper-split-export-declaration": "^7.22.6",
- "@babel/parser": "^7.23.3",
- "@babel/types": "^7.23.3",
+ "@babel/parser": "^7.23.4",
+ "@babel/types": "^7.23.4",
"debug": "^4.1.0",
"globals": "^11.1.0"
},
@@ -497,10 +498,10 @@
}
},
"node_modules/@babel/types": {
- "version": "7.23.3",
+ "version": "7.23.4",
"license": "MIT",
"dependencies": {
- "@babel/helper-string-parser": "^7.22.5",
+ "@babel/helper-string-parser": "^7.23.4",
"@babel/helper-validator-identifier": "^7.22.20",
"to-fast-properties": "^2.0.0"
},
@@ -508,6 +509,10 @@
"node": ">=6.9.0"
}
},
+ "node_modules/@braintree/sanitize-url": {
+ "version": "6.0.4",
+ "license": "MIT"
+ },
"node_modules/@cloudflare/kv-asset-handler": {
"version": "0.3.0",
"dev": true,
@@ -517,7 +522,7 @@
}
},
"node_modules/@esbuild/linux-x64": {
- "version": "0.19.5",
+ "version": "0.19.6",
"cpu": [
"x64"
],
@@ -820,12 +825,9 @@
}
},
"node_modules/@npmcli/agent/node_modules/lru-cache": {
- "version": "10.0.2",
+ "version": "10.0.3",
"dev": true,
"license": "ISC",
- "dependencies": {
- "semver": "^7.3.5"
- },
"engines": {
"node": "14 || >=16.14"
}
@@ -868,12 +870,9 @@
}
},
"node_modules/@npmcli/git/node_modules/lru-cache": {
- "version": "10.0.2",
+ "version": "10.0.3",
"dev": true,
"license": "ISC",
- "dependencies": {
- "semver": "^7.3.5"
- },
"engines": {
"node": "14 || >=16.14"
}
@@ -1025,13 +1024,13 @@
"license": "MIT"
},
"node_modules/@nuxt/devtools": {
- "version": "1.0.2",
+ "version": "1.0.3",
"dev": true,
"license": "MIT",
"dependencies": {
"@antfu/utils": "^0.7.6",
- "@nuxt/devtools-kit": "1.0.2",
- "@nuxt/devtools-wizard": "1.0.2",
+ "@nuxt/devtools-kit": "1.0.3",
+ "@nuxt/devtools-wizard": "1.0.3",
"@nuxt/kit": "^3.8.1",
"birpc": "^0.2.14",
"consola": "^3.2.3",
@@ -1041,7 +1040,7 @@
"fast-glob": "^3.3.2",
"flatted": "^3.2.9",
"get-port-please": "^3.1.1",
- "h3": "^1.8.2",
+ "h3": "^1.9.0",
"hookable": "^5.5.3",
"image-meta": "^0.2.0",
"is-installed-globally": "^1.0.0",
@@ -1057,9 +1056,9 @@
"perfect-debounce": "^1.0.0",
"pkg-types": "^1.0.3",
"rc9": "^2.1.1",
- "scule": "^1.0.0",
+ "scule": "^1.1.0",
"semver": "^7.5.4",
- "simple-git": "^3.20.0",
+ "simple-git": "^3.21.0",
"sirv": "^2.0.3",
"unimport": "^3.5.0",
"vite-plugin-inspect": "^0.7.42",
@@ -1076,7 +1075,7 @@
}
},
"node_modules/@nuxt/devtools-kit": {
- "version": "1.0.2",
+ "version": "1.0.3",
"dev": true,
"license": "MIT",
"dependencies": {
@@ -1192,7 +1191,7 @@
}
},
"node_modules/@nuxt/devtools-wizard": {
- "version": "1.0.2",
+ "version": "1.0.3",
"dev": true,
"license": "MIT",
"dependencies": {
@@ -1976,11 +1975,11 @@
}
},
"node_modules/@sindresorhus/is": {
- "version": "3.1.2",
+ "version": "6.1.0",
"dev": true,
"license": "MIT",
"engines": {
- "node": ">=10"
+ "node": ">=16"
},
"funding": {
"url": "https://github.com/sindresorhus/is?sponsor=1"
@@ -2033,9 +2032,23 @@
"url": "https://github.com/sponsors/isaacs"
}
},
+ "node_modules/@types/d3-scale": {
+ "version": "4.0.8",
+ "license": "MIT",
+ "dependencies": {
+ "@types/d3-time": "*"
+ }
+ },
+ "node_modules/@types/d3-scale-chromatic": {
+ "version": "3.0.2",
+ "license": "MIT"
+ },
+ "node_modules/@types/d3-time": {
+ "version": "3.0.3",
+ "license": "MIT"
+ },
"node_modules/@types/debug": {
"version": "4.1.12",
- "dev": true,
"license": "MIT",
"dependencies": {
"@types/ms": "*"
@@ -2071,11 +2084,10 @@
},
"node_modules/@types/ms": {
"version": "0.7.34",
- "dev": true,
"license": "MIT"
},
"node_modules/@types/node": {
- "version": "18.18.9",
+ "version": "18.18.10",
"dev": true,
"license": "MIT",
"dependencies": {
@@ -2247,44 +2259,44 @@
}
},
"node_modules/@vitejs/plugin-vue": {
- "version": "4.4.1",
+ "version": "4.5.0",
"dev": true,
"license": "MIT",
"engines": {
"node": "^14.18.0 || >=16.0.0"
},
"peerDependencies": {
- "vite": "^4.0.0",
+ "vite": "^4.0.0 || ^5.0.0",
"vue": "^3.2.25"
}
},
"node_modules/@vitejs/plugin-vue-jsx": {
- "version": "3.0.2",
+ "version": "3.1.0",
"dev": true,
"license": "MIT",
"dependencies": {
- "@babel/core": "^7.22.10",
- "@babel/plugin-transform-typescript": "^7.22.10",
+ "@babel/core": "^7.23.3",
+ "@babel/plugin-transform-typescript": "^7.23.3",
"@vue/babel-plugin-jsx": "^1.1.5"
},
"engines": {
"node": "^14.18.0 || >=16.0.0"
},
"peerDependencies": {
- "vite": "^4.0.0",
+ "vite": "^4.0.0 || ^5.0.0",
"vue": "^3.0.0"
}
},
"node_modules/@vue-macros/common": {
- "version": "1.8.0",
+ "version": "1.9.0",
"dev": true,
"license": "MIT",
"dependencies": {
- "@babel/types": "^7.22.17",
- "@rollup/pluginutils": "^5.0.4",
- "@vue/compiler-sfc": "^3.3.4",
+ "@babel/types": "^7.23.3",
+ "@rollup/pluginutils": "^5.0.5",
+ "@vue/compiler-sfc": "^3.3.8",
"ast-kit": "^0.11.2",
- "local-pkg": "^0.4.3",
+ "local-pkg": "^0.5.0",
"magic-string-ast": "^0.3.0"
},
"engines": {
@@ -2299,17 +2311,6 @@
}
}
},
- "node_modules/@vue-macros/common/node_modules/local-pkg": {
- "version": "0.4.3",
- "dev": true,
- "license": "MIT",
- "engines": {
- "node": ">=14"
- },
- "funding": {
- "url": "https://github.com/sponsors/antfu"
- }
- },
"node_modules/@vue/babel-helper-vue-transform-on": {
"version": "1.1.5",
"dev": true,
@@ -2999,12 +3000,9 @@
}
},
"node_modules/cacache/node_modules/lru-cache": {
- "version": "10.0.2",
+ "version": "10.0.3",
"dev": true,
"license": "ISC",
- "dependencies": {
- "semver": "^7.3.5"
- },
"engines": {
"node": "14 || >=16.14"
}
@@ -3046,7 +3044,7 @@
}
},
"node_modules/caniuse-lite": {
- "version": "1.0.30001562",
+ "version": "1.0.30001563",
"funding": [
{
"type": "opencollective",
@@ -3101,7 +3099,6 @@
},
"node_modules/character-entities": {
"version": "2.0.2",
- "dev": true,
"license": "MIT",
"funding": {
"type": "github",
@@ -3335,6 +3332,13 @@
"dev": true,
"license": "MIT"
},
+ "node_modules/cose-base": {
+ "version": "1.0.3",
+ "license": "MIT",
+ "dependencies": {
+ "layout-base": "^1.0.0"
+ }
+ },
"node_modules/crc-32": {
"version": "1.2.2",
"dev": true,
@@ -3549,6 +3553,48 @@
"version": "3.1.2",
"license": "MIT"
},
+ "node_modules/cytoscape": {
+ "version": "3.27.0",
+ "license": "MIT",
+ "dependencies": {
+ "heap": "^0.2.6",
+ "lodash": "^4.17.21"
+ },
+ "engines": {
+ "node": ">=0.10"
+ }
+ },
+ "node_modules/cytoscape-cose-bilkent": {
+ "version": "4.1.0",
+ "license": "MIT",
+ "dependencies": {
+ "cose-base": "^1.0.0"
+ },
+ "peerDependencies": {
+ "cytoscape": "^3.2.0"
+ }
+ },
+ "node_modules/cytoscape-fcose": {
+ "version": "2.2.0",
+ "license": "MIT",
+ "dependencies": {
+ "cose-base": "^2.2.0"
+ },
+ "peerDependencies": {
+ "cytoscape": "^3.2.0"
+ }
+ },
+ "node_modules/cytoscape-fcose/node_modules/cose-base": {
+ "version": "2.2.0",
+ "license": "MIT",
+ "dependencies": {
+ "layout-base": "^2.0.0"
+ }
+ },
+ "node_modules/cytoscape-fcose/node_modules/layout-base": {
+ "version": "2.0.1",
+ "license": "MIT"
+ },
"node_modules/d3": {
"version": "7.8.5",
"license": "ISC",
@@ -3788,6 +3834,36 @@
"node": ">=12"
}
},
+ "node_modules/d3-sankey": {
+ "version": "0.12.3",
+ "license": "BSD-3-Clause",
+ "dependencies": {
+ "d3-array": "1 - 2",
+ "d3-shape": "^1.2.0"
+ }
+ },
+ "node_modules/d3-sankey/node_modules/d3-array": {
+ "version": "2.12.1",
+ "license": "BSD-3-Clause",
+ "dependencies": {
+ "internmap": "^1.0.0"
+ }
+ },
+ "node_modules/d3-sankey/node_modules/d3-path": {
+ "version": "1.0.9",
+ "license": "BSD-3-Clause"
+ },
+ "node_modules/d3-sankey/node_modules/d3-shape": {
+ "version": "1.3.7",
+ "license": "BSD-3-Clause",
+ "dependencies": {
+ "d3-path": "1"
+ }
+ },
+ "node_modules/d3-sankey/node_modules/internmap": {
+ "version": "1.0.1",
+ "license": "ISC"
+ },
"node_modules/d3-scale": {
"version": "4.0.2",
"license": "ISC",
@@ -3888,6 +3964,18 @@
"node": ">=12"
}
},
+ "node_modules/dagre-d3-es": {
+ "version": "7.0.10",
+ "license": "MIT",
+ "dependencies": {
+ "d3": "^7.8.2",
+ "lodash-es": "^4.17.21"
+ }
+ },
+ "node_modules/dayjs": {
+ "version": "1.11.10",
+ "license": "MIT"
+ },
"node_modules/debug": {
"version": "4.3.4",
"license": "MIT",
@@ -3905,7 +3993,6 @@
},
"node_modules/decode-named-character-reference": {
"version": "1.0.2",
- "dev": true,
"license": "MIT",
"dependencies": {
"character-entities": "^2.0.0"
@@ -4099,7 +4186,6 @@
},
"node_modules/dequal": {
"version": "2.0.3",
- "dev": true,
"license": "MIT",
"engines": {
"node": ">=6"
@@ -4157,7 +4243,6 @@
},
"node_modules/diff": {
"version": "5.1.0",
- "dev": true,
"license": "BSD-3-Clause",
"engines": {
"node": ">=0.3.1"
@@ -4211,6 +4296,10 @@
"url": "https://github.com/fb55/domhandler?sponsor=1"
}
},
+ "node_modules/dompurify": {
+ "version": "3.0.6",
+ "license": "(MPL-2.0 OR Apache-2.0)"
+ },
"node_modules/domutils": {
"version": "3.1.0",
"dev": true,
@@ -4264,9 +4353,13 @@
"license": "MIT"
},
"node_modules/electron-to-chromium": {
- "version": "1.4.585",
+ "version": "1.4.588",
"license": "ISC"
},
+ "node_modules/elkjs": {
+ "version": "0.8.2",
+ "license": "EPL-2.0"
+ },
"node_modules/emoji-regex": {
"version": "8.0.0",
"dev": true,
@@ -4387,7 +4480,7 @@
}
},
"node_modules/esbuild": {
- "version": "0.19.5",
+ "version": "0.19.6",
"dev": true,
"hasInstallScript": true,
"license": "MIT",
@@ -4398,28 +4491,28 @@
"node": ">=12"
},
"optionalDependencies": {
- "@esbuild/android-arm": "0.19.5",
- "@esbuild/android-arm64": "0.19.5",
- "@esbuild/android-x64": "0.19.5",
- "@esbuild/darwin-arm64": "0.19.5",
- "@esbuild/darwin-x64": "0.19.5",
- "@esbuild/freebsd-arm64": "0.19.5",
- "@esbuild/freebsd-x64": "0.19.5",
- "@esbuild/linux-arm": "0.19.5",
- "@esbuild/linux-arm64": "0.19.5",
- "@esbuild/linux-ia32": "0.19.5",
- "@esbuild/linux-loong64": "0.19.5",
- "@esbuild/linux-mips64el": "0.19.5",
- "@esbuild/linux-ppc64": "0.19.5",
- "@esbuild/linux-riscv64": "0.19.5",
- "@esbuild/linux-s390x": "0.19.5",
- "@esbuild/linux-x64": "0.19.5",
- "@esbuild/netbsd-x64": "0.19.5",
- "@esbuild/openbsd-x64": "0.19.5",
- "@esbuild/sunos-x64": "0.19.5",
- "@esbuild/win32-arm64": "0.19.5",
- "@esbuild/win32-ia32": "0.19.5",
- "@esbuild/win32-x64": "0.19.5"
+ "@esbuild/android-arm": "0.19.6",
+ "@esbuild/android-arm64": "0.19.6",
+ "@esbuild/android-x64": "0.19.6",
+ "@esbuild/darwin-arm64": "0.19.6",
+ "@esbuild/darwin-x64": "0.19.6",
+ "@esbuild/freebsd-arm64": "0.19.6",
+ "@esbuild/freebsd-x64": "0.19.6",
+ "@esbuild/linux-arm": "0.19.6",
+ "@esbuild/linux-arm64": "0.19.6",
+ "@esbuild/linux-ia32": "0.19.6",
+ "@esbuild/linux-loong64": "0.19.6",
+ "@esbuild/linux-mips64el": "0.19.6",
+ "@esbuild/linux-ppc64": "0.19.6",
+ "@esbuild/linux-riscv64": "0.19.6",
+ "@esbuild/linux-s390x": "0.19.6",
+ "@esbuild/linux-x64": "0.19.6",
+ "@esbuild/netbsd-x64": "0.19.6",
+ "@esbuild/openbsd-x64": "0.19.6",
+ "@esbuild/sunos-x64": "0.19.6",
+ "@esbuild/win32-arm64": "0.19.6",
+ "@esbuild/win32-ia32": "0.19.6",
+ "@esbuild/win32-x64": "0.19.6"
}
},
"node_modules/escalade": {
@@ -4849,16 +4942,16 @@
}
},
"node_modules/h3": {
- "version": "1.8.2",
+ "version": "1.9.0",
"dev": true,
"license": "MIT",
"dependencies": {
"cookie-es": "^1.0.0",
- "defu": "^6.1.2",
- "destr": "^2.0.1",
- "iron-webcrypto": "^0.10.1",
+ "defu": "^6.1.3",
+ "destr": "^2.0.2",
+ "iron-webcrypto": "^1.0.0",
"radix3": "^1.1.0",
- "ufo": "^1.3.0",
+ "ufo": "^1.3.2",
"uncrypto": "^0.1.3",
"unenv": "^1.7.4"
}
@@ -5311,6 +5404,10 @@
"dev": true,
"license": "MIT"
},
+ "node_modules/heap": {
+ "version": "0.2.7",
+ "license": "MIT"
+ },
"node_modules/hookable": {
"version": "5.5.3",
"license": "MIT"
@@ -5327,12 +5424,9 @@
}
},
"node_modules/hosted-git-info/node_modules/lru-cache": {
- "version": "10.0.2",
+ "version": "10.0.3",
"dev": true,
"license": "ISC",
- "dependencies": {
- "semver": "^7.3.5"
- },
"engines": {
"node": "14 || >=16.14"
}
@@ -5550,7 +5644,7 @@
"license": "MIT"
},
"node_modules/iron-webcrypto": {
- "version": "0.10.1",
+ "version": "1.0.0",
"dev": true,
"license": "MIT",
"funding": {
@@ -5944,6 +6038,9 @@
],
"license": "MIT"
},
+ "node_modules/khroma": {
+ "version": "2.1.0"
+ },
"node_modules/kleur": {
"version": "3.0.3",
"dev": true,
@@ -5978,6 +6075,10 @@
"shell-quote": "^1.8.1"
}
},
+ "node_modules/layout-base": {
+ "version": "1.0.2",
+ "license": "MIT"
+ },
"node_modules/lazystream": {
"version": "1.0.1",
"dev": true,
@@ -6079,7 +6180,10 @@
},
"node_modules/lodash": {
"version": "4.17.21",
- "dev": true,
+ "license": "MIT"
+ },
+ "node_modules/lodash-es": {
+ "version": "4.17.21",
"license": "MIT"
},
"node_modules/lodash.debounce": {
@@ -6301,7 +6405,6 @@
},
"node_modules/mdast-util-from-markdown": {
"version": "1.3.1",
- "dev": true,
"license": "MIT",
"dependencies": {
"@types/mdast": "^3.0.0",
@@ -6324,7 +6427,6 @@
},
"node_modules/mdast-util-from-markdown/node_modules/@types/mdast": {
"version": "3.0.15",
- "dev": true,
"license": "MIT",
"dependencies": {
"@types/unist": "^2"
@@ -6332,12 +6434,10 @@
},
"node_modules/mdast-util-from-markdown/node_modules/@types/unist": {
"version": "2.0.10",
- "dev": true,
"license": "MIT"
},
"node_modules/mdast-util-from-markdown/node_modules/mdast-util-to-string": {
"version": "3.2.0",
- "dev": true,
"license": "MIT",
"dependencies": {
"@types/mdast": "^3.0.0"
@@ -6349,7 +6449,6 @@
},
"node_modules/mdast-util-from-markdown/node_modules/micromark": {
"version": "3.2.0",
- "dev": true,
"funding": [
{
"type": "GitHub Sponsors",
@@ -6383,7 +6482,6 @@
},
"node_modules/mdast-util-from-markdown/node_modules/micromark-core-commonmark": {
"version": "1.1.0",
- "dev": true,
"funding": [
{
"type": "GitHub Sponsors",
@@ -6416,7 +6514,6 @@
},
"node_modules/mdast-util-from-markdown/node_modules/micromark-factory-destination": {
"version": "1.1.0",
- "dev": true,
"funding": [
{
"type": "GitHub Sponsors",
@@ -6436,7 +6533,6 @@
},
"node_modules/mdast-util-from-markdown/node_modules/micromark-factory-label": {
"version": "1.1.0",
- "dev": true,
"funding": [
{
"type": "GitHub Sponsors",
@@ -6457,7 +6553,6 @@
},
"node_modules/mdast-util-from-markdown/node_modules/micromark-factory-space": {
"version": "1.1.0",
- "dev": true,
"funding": [
{
"type": "GitHub Sponsors",
@@ -6476,7 +6571,6 @@
},
"node_modules/mdast-util-from-markdown/node_modules/micromark-factory-title": {
"version": "1.1.0",
- "dev": true,
"funding": [
{
"type": "GitHub Sponsors",
@@ -6497,7 +6591,6 @@
},
"node_modules/mdast-util-from-markdown/node_modules/micromark-factory-whitespace": {
"version": "1.1.0",
- "dev": true,
"funding": [
{
"type": "GitHub Sponsors",
@@ -6518,7 +6611,6 @@
},
"node_modules/mdast-util-from-markdown/node_modules/micromark-util-character": {
"version": "1.2.0",
- "dev": true,
"funding": [
{
"type": "GitHub Sponsors",
@@ -6537,7 +6629,6 @@
},
"node_modules/mdast-util-from-markdown/node_modules/micromark-util-chunked": {
"version": "1.1.0",
- "dev": true,
"funding": [
{
"type": "GitHub Sponsors",
@@ -6555,7 +6646,6 @@
},
"node_modules/mdast-util-from-markdown/node_modules/micromark-util-classify-character": {
"version": "1.1.0",
- "dev": true,
"funding": [
{
"type": "GitHub Sponsors",
@@ -6575,7 +6665,6 @@
},
"node_modules/mdast-util-from-markdown/node_modules/micromark-util-combine-extensions": {
"version": "1.1.0",
- "dev": true,
"funding": [
{
"type": "GitHub Sponsors",
@@ -6592,27 +6681,8 @@
"micromark-util-types": "^1.0.0"
}
},
- "node_modules/mdast-util-from-markdown/node_modules/micromark-util-decode-numeric-character-reference": {
- "version": "1.1.0",
- "dev": true,
- "funding": [
- {
- "type": "GitHub Sponsors",
- "url": "https://github.com/sponsors/unifiedjs"
- },
- {
- "type": "OpenCollective",
- "url": "https://opencollective.com/unified"
- }
- ],
- "license": "MIT",
- "dependencies": {
- "micromark-util-symbol": "^1.0.0"
- }
- },
"node_modules/mdast-util-from-markdown/node_modules/micromark-util-encode": {
"version": "1.1.0",
- "dev": true,
"funding": [
{
"type": "GitHub Sponsors",
@@ -6627,7 +6697,6 @@
},
"node_modules/mdast-util-from-markdown/node_modules/micromark-util-html-tag-name": {
"version": "1.2.0",
- "dev": true,
"funding": [
{
"type": "GitHub Sponsors",
@@ -6640,27 +6709,8 @@
],
"license": "MIT"
},
- "node_modules/mdast-util-from-markdown/node_modules/micromark-util-normalize-identifier": {
- "version": "1.1.0",
- "dev": true,
- "funding": [
- {
- "type": "GitHub Sponsors",
- "url": "https://github.com/sponsors/unifiedjs"
- },
- {
- "type": "OpenCollective",
- "url": "https://opencollective.com/unified"
- }
- ],
- "license": "MIT",
- "dependencies": {
- "micromark-util-symbol": "^1.0.0"
- }
- },
"node_modules/mdast-util-from-markdown/node_modules/micromark-util-resolve-all": {
"version": "1.1.0",
- "dev": true,
"funding": [
{
"type": "GitHub Sponsors",
@@ -6678,7 +6728,6 @@
},
"node_modules/mdast-util-from-markdown/node_modules/micromark-util-sanitize-uri": {
"version": "1.2.0",
- "dev": true,
"funding": [
{
"type": "GitHub Sponsors",
@@ -6698,7 +6747,6 @@
},
"node_modules/mdast-util-from-markdown/node_modules/micromark-util-subtokenize": {
"version": "1.1.0",
- "dev": true,
"funding": [
{
"type": "GitHub Sponsors",
@@ -6717,24 +6765,8 @@
"uvu": "^0.5.0"
}
},
- "node_modules/mdast-util-from-markdown/node_modules/micromark-util-symbol": {
- "version": "1.1.0",
- "dev": true,
- "funding": [
- {
- "type": "GitHub Sponsors",
- "url": "https://github.com/sponsors/unifiedjs"
- },
- {
- "type": "OpenCollective",
- "url": "https://opencollective.com/unified"
- }
- ],
- "license": "MIT"
- },
"node_modules/mdast-util-from-markdown/node_modules/micromark-util-types": {
"version": "1.1.0",
- "dev": true,
"funding": [
{
"type": "GitHub Sponsors",
@@ -6749,7 +6781,6 @@
},
"node_modules/mdast-util-from-markdown/node_modules/unist-util-stringify-position": {
"version": "3.0.3",
- "dev": true,
"license": "MIT",
"dependencies": {
"@types/unist": "^2.0.0"
@@ -6839,21 +6870,6 @@
"micromark-util-types": "^1.0.0"
}
},
- "node_modules/mdast-util-gfm-autolink-literal/node_modules/micromark-util-symbol": {
- "version": "1.1.0",
- "dev": true,
- "funding": [
- {
- "type": "GitHub Sponsors",
- "url": "https://github.com/sponsors/unifiedjs"
- },
- {
- "type": "OpenCollective",
- "url": "https://opencollective.com/unified"
- }
- ],
- "license": "MIT"
- },
"node_modules/mdast-util-gfm-autolink-literal/node_modules/micromark-util-types": {
"version": "1.1.0",
"dev": true,
@@ -6921,41 +6937,8 @@
"dev": true,
"license": "MIT"
},
- "node_modules/mdast-util-gfm-footnote/node_modules/micromark-util-normalize-identifier": {
- "version": "1.1.0",
- "dev": true,
- "funding": [
- {
- "type": "GitHub Sponsors",
- "url": "https://github.com/sponsors/unifiedjs"
- },
- {
- "type": "OpenCollective",
- "url": "https://opencollective.com/unified"
- }
- ],
- "license": "MIT",
- "dependencies": {
- "micromark-util-symbol": "^1.0.0"
- }
- },
- "node_modules/mdast-util-gfm-footnote/node_modules/micromark-util-symbol": {
- "version": "1.1.0",
- "dev": true,
- "funding": [
- {
- "type": "GitHub Sponsors",
- "url": "https://github.com/sponsors/unifiedjs"
- },
- {
- "type": "OpenCollective",
- "url": "https://opencollective.com/unified"
- }
- ],
- "license": "MIT"
- },
- "node_modules/mdast-util-gfm-strikethrough": {
- "version": "1.0.3",
+ "node_modules/mdast-util-gfm-strikethrough": {
+ "version": "1.0.3",
"dev": true,
"license": "MIT",
"dependencies": {
@@ -7215,6 +7198,32 @@
"node": ">= 8"
}
},
+ "node_modules/mermaid": {
+ "version": "10.6.1",
+ "license": "MIT",
+ "dependencies": {
+ "@braintree/sanitize-url": "^6.0.1",
+ "@types/d3-scale": "^4.0.3",
+ "@types/d3-scale-chromatic": "^3.0.0",
+ "cytoscape": "^3.23.0",
+ "cytoscape-cose-bilkent": "^4.1.0",
+ "cytoscape-fcose": "^2.1.0",
+ "d3": "^7.4.0",
+ "d3-sankey": "^0.12.3",
+ "dagre-d3-es": "7.0.10",
+ "dayjs": "^1.11.7",
+ "dompurify": "^3.0.5",
+ "elkjs": "^0.8.2",
+ "khroma": "^2.0.0",
+ "lodash-es": "^4.17.21",
+ "mdast-util-from-markdown": "^1.3.0",
+ "non-layered-tidy-tree-layout": "^2.0.2",
+ "stylis": "^4.1.3",
+ "ts-dedent": "^2.2.0",
+ "uuid": "^9.0.0",
+ "web-worker": "^1.2.0"
+ }
+ },
"node_modules/micromark": {
"version": "4.0.0",
"dev": true,
@@ -7282,6 +7291,39 @@
"micromark-util-types": "^2.0.0"
}
},
+ "node_modules/micromark-core-commonmark/node_modules/micromark-util-normalize-identifier": {
+ "version": "2.0.0",
+ "dev": true,
+ "funding": [
+ {
+ "type": "GitHub Sponsors",
+ "url": "https://github.com/sponsors/unifiedjs"
+ },
+ {
+ "type": "OpenCollective",
+ "url": "https://opencollective.com/unified"
+ }
+ ],
+ "license": "MIT",
+ "dependencies": {
+ "micromark-util-symbol": "^2.0.0"
+ }
+ },
+ "node_modules/micromark-core-commonmark/node_modules/micromark-util-symbol": {
+ "version": "2.0.0",
+ "dev": true,
+ "funding": [
+ {
+ "type": "GitHub Sponsors",
+ "url": "https://github.com/sponsors/unifiedjs"
+ },
+ {
+ "type": "OpenCollective",
+ "url": "https://opencollective.com/unified"
+ }
+ ],
+ "license": "MIT"
+ },
"node_modules/micromark-extension-gfm": {
"version": "2.0.3",
"dev": true,
@@ -7370,21 +7412,6 @@
"micromark-util-symbol": "^1.0.0"
}
},
- "node_modules/micromark-extension-gfm-autolink-literal/node_modules/micromark-util-symbol": {
- "version": "1.1.0",
- "dev": true,
- "funding": [
- {
- "type": "GitHub Sponsors",
- "url": "https://github.com/sponsors/unifiedjs"
- },
- {
- "type": "OpenCollective",
- "url": "https://opencollective.com/unified"
- }
- ],
- "license": "MIT"
- },
"node_modules/micromark-extension-gfm-autolink-literal/node_modules/micromark-util-types": {
"version": "1.1.0",
"dev": true,
@@ -7641,24 +7668,6 @@
],
"license": "MIT"
},
- "node_modules/micromark-extension-gfm-footnote/node_modules/micromark-util-normalize-identifier": {
- "version": "1.1.0",
- "dev": true,
- "funding": [
- {
- "type": "GitHub Sponsors",
- "url": "https://github.com/sponsors/unifiedjs"
- },
- {
- "type": "OpenCollective",
- "url": "https://opencollective.com/unified"
- }
- ],
- "license": "MIT",
- "dependencies": {
- "micromark-util-symbol": "^1.0.0"
- }
- },
"node_modules/micromark-extension-gfm-footnote/node_modules/micromark-util-resolve-all": {
"version": "1.1.0",
"dev": true,
@@ -7718,21 +7727,6 @@
"uvu": "^0.5.0"
}
},
- "node_modules/micromark-extension-gfm-footnote/node_modules/micromark-util-symbol": {
- "version": "1.1.0",
- "dev": true,
- "funding": [
- {
- "type": "GitHub Sponsors",
- "url": "https://github.com/sponsors/unifiedjs"
- },
- {
- "type": "OpenCollective",
- "url": "https://opencollective.com/unified"
- }
- ],
- "license": "MIT"
- },
"node_modules/micromark-extension-gfm-footnote/node_modules/micromark-util-types": {
"version": "1.1.0",
"dev": true,
@@ -7840,21 +7834,6 @@
"micromark-util-types": "^1.0.0"
}
},
- "node_modules/micromark-extension-gfm-strikethrough/node_modules/micromark-util-symbol": {
- "version": "1.1.0",
- "dev": true,
- "funding": [
- {
- "type": "GitHub Sponsors",
- "url": "https://github.com/sponsors/unifiedjs"
- },
- {
- "type": "OpenCollective",
- "url": "https://opencollective.com/unified"
- }
- ],
- "license": "MIT"
- },
"node_modules/micromark-extension-gfm-strikethrough/node_modules/micromark-util-types": {
"version": "1.1.0",
"dev": true,
@@ -7924,21 +7903,6 @@
"micromark-util-types": "^1.0.0"
}
},
- "node_modules/micromark-extension-gfm-table/node_modules/micromark-util-symbol": {
- "version": "1.1.0",
- "dev": true,
- "funding": [
- {
- "type": "GitHub Sponsors",
- "url": "https://github.com/sponsors/unifiedjs"
- },
- {
- "type": "OpenCollective",
- "url": "https://opencollective.com/unified"
- }
- ],
- "license": "MIT"
- },
"node_modules/micromark-extension-gfm-table/node_modules/micromark-util-types": {
"version": "1.1.0",
"dev": true,
@@ -8035,7 +7999,7 @@
"micromark-util-types": "^1.0.0"
}
},
- "node_modules/micromark-extension-gfm-task-list-item/node_modules/micromark-util-symbol": {
+ "node_modules/micromark-extension-gfm-task-list-item/node_modules/micromark-util-types": {
"version": "1.1.0",
"dev": true,
"funding": [
@@ -8050,7 +8014,7 @@
],
"license": "MIT"
},
- "node_modules/micromark-extension-gfm-task-list-item/node_modules/micromark-util-types": {
+ "node_modules/micromark-extension-gfm/node_modules/micromark-util-chunked": {
"version": "1.1.0",
"dev": true,
"funding": [
@@ -8063,9 +8027,12 @@
"url": "https://opencollective.com/unified"
}
],
- "license": "MIT"
+ "license": "MIT",
+ "dependencies": {
+ "micromark-util-symbol": "^1.0.0"
+ }
},
- "node_modules/micromark-extension-gfm/node_modules/micromark-util-chunked": {
+ "node_modules/micromark-extension-gfm/node_modules/micromark-util-combine-extensions": {
"version": "1.1.0",
"dev": true,
"funding": [
@@ -8080,10 +8047,11 @@
],
"license": "MIT",
"dependencies": {
- "micromark-util-symbol": "^1.0.0"
+ "micromark-util-chunked": "^1.0.0",
+ "micromark-util-types": "^1.0.0"
}
},
- "node_modules/micromark-extension-gfm/node_modules/micromark-util-combine-extensions": {
+ "node_modules/micromark-extension-gfm/node_modules/micromark-util-types": {
"version": "1.1.0",
"dev": true,
"funding": [
@@ -8096,14 +8064,10 @@
"url": "https://opencollective.com/unified"
}
],
- "license": "MIT",
- "dependencies": {
- "micromark-util-chunked": "^1.0.0",
- "micromark-util-types": "^1.0.0"
- }
+ "license": "MIT"
},
- "node_modules/micromark-extension-gfm/node_modules/micromark-util-symbol": {
- "version": "1.1.0",
+ "node_modules/micromark-factory-destination": {
+ "version": "2.0.0",
"dev": true,
"funding": [
{
@@ -8115,10 +8079,15 @@
"url": "https://opencollective.com/unified"
}
],
- "license": "MIT"
+ "license": "MIT",
+ "dependencies": {
+ "micromark-util-character": "^2.0.0",
+ "micromark-util-symbol": "^2.0.0",
+ "micromark-util-types": "^2.0.0"
+ }
},
- "node_modules/micromark-extension-gfm/node_modules/micromark-util-types": {
- "version": "1.1.0",
+ "node_modules/micromark-factory-destination/node_modules/micromark-util-symbol": {
+ "version": "2.0.0",
"dev": true,
"funding": [
{
@@ -8132,7 +8101,7 @@
],
"license": "MIT"
},
- "node_modules/micromark-factory-destination": {
+ "node_modules/micromark-factory-label": {
"version": "2.0.0",
"dev": true,
"funding": [
@@ -8147,12 +8116,13 @@
],
"license": "MIT",
"dependencies": {
+ "devlop": "^1.0.0",
"micromark-util-character": "^2.0.0",
"micromark-util-symbol": "^2.0.0",
"micromark-util-types": "^2.0.0"
}
},
- "node_modules/micromark-factory-label": {
+ "node_modules/micromark-factory-label/node_modules/micromark-util-symbol": {
"version": "2.0.0",
"dev": true,
"funding": [
@@ -8165,13 +8135,7 @@
"url": "https://opencollective.com/unified"
}
],
- "license": "MIT",
- "dependencies": {
- "devlop": "^1.0.0",
- "micromark-util-character": "^2.0.0",
- "micromark-util-symbol": "^2.0.0",
- "micromark-util-types": "^2.0.0"
- }
+ "license": "MIT"
},
"node_modules/micromark-factory-space": {
"version": "2.0.0",
@@ -8213,6 +8177,21 @@
"micromark-util-types": "^2.0.0"
}
},
+ "node_modules/micromark-factory-title/node_modules/micromark-util-symbol": {
+ "version": "2.0.0",
+ "dev": true,
+ "funding": [
+ {
+ "type": "GitHub Sponsors",
+ "url": "https://github.com/sponsors/unifiedjs"
+ },
+ {
+ "type": "OpenCollective",
+ "url": "https://opencollective.com/unified"
+ }
+ ],
+ "license": "MIT"
+ },
"node_modules/micromark-factory-whitespace": {
"version": "2.0.0",
"dev": true,
@@ -8234,6 +8213,21 @@
"micromark-util-types": "^2.0.0"
}
},
+ "node_modules/micromark-factory-whitespace/node_modules/micromark-util-symbol": {
+ "version": "2.0.0",
+ "dev": true,
+ "funding": [
+ {
+ "type": "GitHub Sponsors",
+ "url": "https://github.com/sponsors/unifiedjs"
+ },
+ {
+ "type": "OpenCollective",
+ "url": "https://opencollective.com/unified"
+ }
+ ],
+ "license": "MIT"
+ },
"node_modules/micromark-util-character": {
"version": "2.0.1",
"dev": true,
@@ -8253,6 +8247,21 @@
"micromark-util-types": "^2.0.0"
}
},
+ "node_modules/micromark-util-character/node_modules/micromark-util-symbol": {
+ "version": "2.0.0",
+ "dev": true,
+ "funding": [
+ {
+ "type": "GitHub Sponsors",
+ "url": "https://github.com/sponsors/unifiedjs"
+ },
+ {
+ "type": "OpenCollective",
+ "url": "https://opencollective.com/unified"
+ }
+ ],
+ "license": "MIT"
+ },
"node_modules/micromark-util-chunked": {
"version": "2.0.0",
"dev": true,
@@ -8271,7 +8280,7 @@
"micromark-util-symbol": "^2.0.0"
}
},
- "node_modules/micromark-util-classify-character": {
+ "node_modules/micromark-util-chunked/node_modules/micromark-util-symbol": {
"version": "2.0.0",
"dev": true,
"funding": [
@@ -8284,14 +8293,9 @@
"url": "https://opencollective.com/unified"
}
],
- "license": "MIT",
- "dependencies": {
- "micromark-util-character": "^2.0.0",
- "micromark-util-symbol": "^2.0.0",
- "micromark-util-types": "^2.0.0"
- }
+ "license": "MIT"
},
- "node_modules/micromark-util-combine-extensions": {
+ "node_modules/micromark-util-classify-character": {
"version": "2.0.0",
"dev": true,
"funding": [
@@ -8306,12 +8310,13 @@
],
"license": "MIT",
"dependencies": {
- "micromark-util-chunked": "^2.0.0",
+ "micromark-util-character": "^2.0.0",
+ "micromark-util-symbol": "^2.0.0",
"micromark-util-types": "^2.0.0"
}
},
- "node_modules/micromark-util-decode-numeric-character-reference": {
- "version": "2.0.1",
+ "node_modules/micromark-util-classify-character/node_modules/micromark-util-symbol": {
+ "version": "2.0.0",
"dev": true,
"funding": [
{
@@ -8323,13 +8328,10 @@
"url": "https://opencollective.com/unified"
}
],
- "license": "MIT",
- "dependencies": {
- "micromark-util-symbol": "^2.0.0"
- }
+ "license": "MIT"
},
- "node_modules/micromark-util-decode-string": {
- "version": "1.1.0",
+ "node_modules/micromark-util-combine-extensions": {
+ "version": "2.0.0",
"dev": true,
"funding": [
{
@@ -8343,15 +8345,12 @@
],
"license": "MIT",
"dependencies": {
- "decode-named-character-reference": "^1.0.0",
- "micromark-util-character": "^1.0.0",
- "micromark-util-decode-numeric-character-reference": "^1.0.0",
- "micromark-util-symbol": "^1.0.0"
+ "micromark-util-chunked": "^2.0.0",
+ "micromark-util-types": "^2.0.0"
}
},
- "node_modules/micromark-util-decode-string/node_modules/micromark-util-character": {
- "version": "1.2.0",
- "dev": true,
+ "node_modules/micromark-util-decode-numeric-character-reference": {
+ "version": "1.1.0",
"funding": [
{
"type": "GitHub Sponsors",
@@ -8364,13 +8363,11 @@
],
"license": "MIT",
"dependencies": {
- "micromark-util-symbol": "^1.0.0",
- "micromark-util-types": "^1.0.0"
+ "micromark-util-symbol": "^1.0.0"
}
},
- "node_modules/micromark-util-decode-string/node_modules/micromark-util-decode-numeric-character-reference": {
+ "node_modules/micromark-util-decode-string": {
"version": "1.1.0",
- "dev": true,
"funding": [
{
"type": "GitHub Sponsors",
@@ -8383,12 +8380,14 @@
],
"license": "MIT",
"dependencies": {
+ "decode-named-character-reference": "^1.0.0",
+ "micromark-util-character": "^1.0.0",
+ "micromark-util-decode-numeric-character-reference": "^1.0.0",
"micromark-util-symbol": "^1.0.0"
}
},
- "node_modules/micromark-util-decode-string/node_modules/micromark-util-symbol": {
- "version": "1.1.0",
- "dev": true,
+ "node_modules/micromark-util-decode-string/node_modules/micromark-util-character": {
+ "version": "1.2.0",
"funding": [
{
"type": "GitHub Sponsors",
@@ -8399,11 +8398,14 @@
"url": "https://opencollective.com/unified"
}
],
- "license": "MIT"
+ "license": "MIT",
+ "dependencies": {
+ "micromark-util-symbol": "^1.0.0",
+ "micromark-util-types": "^1.0.0"
+ }
},
"node_modules/micromark-util-decode-string/node_modules/micromark-util-types": {
"version": "1.1.0",
- "dev": true,
"funding": [
{
"type": "GitHub Sponsors",
@@ -8447,8 +8449,7 @@
"license": "MIT"
},
"node_modules/micromark-util-normalize-identifier": {
- "version": "2.0.0",
- "dev": true,
+ "version": "1.1.0",
"funding": [
{
"type": "GitHub Sponsors",
@@ -8461,7 +8462,7 @@
],
"license": "MIT",
"dependencies": {
- "micromark-util-symbol": "^2.0.0"
+ "micromark-util-symbol": "^1.0.0"
}
},
"node_modules/micromark-util-resolve-all": {
@@ -8502,6 +8503,21 @@
"micromark-util-symbol": "^2.0.0"
}
},
+ "node_modules/micromark-util-sanitize-uri/node_modules/micromark-util-symbol": {
+ "version": "2.0.0",
+ "dev": true,
+ "funding": [
+ {
+ "type": "GitHub Sponsors",
+ "url": "https://github.com/sponsors/unifiedjs"
+ },
+ {
+ "type": "OpenCollective",
+ "url": "https://opencollective.com/unified"
+ }
+ ],
+ "license": "MIT"
+ },
"node_modules/micromark-util-subtokenize": {
"version": "2.0.0",
"dev": true,
@@ -8523,7 +8539,7 @@
"micromark-util-types": "^2.0.0"
}
},
- "node_modules/micromark-util-symbol": {
+ "node_modules/micromark-util-subtokenize/node_modules/micromark-util-symbol": {
"version": "2.0.0",
"dev": true,
"funding": [
@@ -8538,6 +8554,20 @@
],
"license": "MIT"
},
+ "node_modules/micromark-util-symbol": {
+ "version": "1.1.0",
+ "funding": [
+ {
+ "type": "GitHub Sponsors",
+ "url": "https://github.com/sponsors/unifiedjs"
+ },
+ {
+ "type": "OpenCollective",
+ "url": "https://opencollective.com/unified"
+ }
+ ],
+ "license": "MIT"
+ },
"node_modules/micromark-util-types": {
"version": "2.0.0",
"dev": true,
@@ -8553,6 +8583,57 @@
],
"license": "MIT"
},
+ "node_modules/micromark/node_modules/micromark-util-decode-numeric-character-reference": {
+ "version": "2.0.1",
+ "dev": true,
+ "funding": [
+ {
+ "type": "GitHub Sponsors",
+ "url": "https://github.com/sponsors/unifiedjs"
+ },
+ {
+ "type": "OpenCollective",
+ "url": "https://opencollective.com/unified"
+ }
+ ],
+ "license": "MIT",
+ "dependencies": {
+ "micromark-util-symbol": "^2.0.0"
+ }
+ },
+ "node_modules/micromark/node_modules/micromark-util-normalize-identifier": {
+ "version": "2.0.0",
+ "dev": true,
+ "funding": [
+ {
+ "type": "GitHub Sponsors",
+ "url": "https://github.com/sponsors/unifiedjs"
+ },
+ {
+ "type": "OpenCollective",
+ "url": "https://opencollective.com/unified"
+ }
+ ],
+ "license": "MIT",
+ "dependencies": {
+ "micromark-util-symbol": "^2.0.0"
+ }
+ },
+ "node_modules/micromark/node_modules/micromark-util-symbol": {
+ "version": "2.0.0",
+ "dev": true,
+ "funding": [
+ {
+ "type": "GitHub Sponsors",
+ "url": "https://github.com/sponsors/unifiedjs"
+ },
+ {
+ "type": "OpenCollective",
+ "url": "https://opencollective.com/unified"
+ }
+ ],
+ "license": "MIT"
+ },
"node_modules/micromatch": {
"version": "4.0.5",
"license": "MIT",
@@ -8947,14 +9028,17 @@
"license": "MIT"
},
"node_modules/node-emoji": {
- "version": "2.1.0",
+ "version": "2.1.1",
"dev": true,
"license": "MIT",
"dependencies": {
- "@sindresorhus/is": "^3.1.2",
+ "@sindresorhus/is": "^6.0.0",
"char-regex": "^1.0.2",
"emojilib": "^2.4.0",
"skin-tone": "^2.0.0"
+ },
+ "engines": {
+ "node": ">=18"
}
},
"node_modules/node-fetch": {
@@ -9011,7 +9095,7 @@
}
},
"node_modules/node-gyp-build": {
- "version": "4.6.1",
+ "version": "4.7.0",
"dev": true,
"license": "MIT",
"bin": {
@@ -9103,6 +9187,10 @@
"version": "2.0.13",
"license": "MIT"
},
+ "node_modules/non-layered-tidy-tree-layout": {
+ "version": "2.0.2",
+ "license": "MIT"
+ },
"node_modules/nopt": {
"version": "5.0.0",
"dev": true,
@@ -9807,12 +9895,9 @@
}
},
"node_modules/path-scurry/node_modules/lru-cache": {
- "version": "10.0.2",
+ "version": "10.0.3",
"dev": true,
"license": "ISC",
- "dependencies": {
- "semver": "^7.3.5"
- },
"engines": {
"node": "14 || >=16.14"
}
@@ -10806,6 +10891,24 @@
"url": "https://opencollective.com/unified"
}
},
+ "node_modules/remark-mdc/node_modules/micromark-util-decode-numeric-character-reference": {
+ "version": "2.0.1",
+ "dev": true,
+ "funding": [
+ {
+ "type": "GitHub Sponsors",
+ "url": "https://github.com/sponsors/unifiedjs"
+ },
+ {
+ "type": "OpenCollective",
+ "url": "https://opencollective.com/unified"
+ }
+ ],
+ "license": "MIT",
+ "dependencies": {
+ "micromark-util-symbol": "^2.0.0"
+ }
+ },
"node_modules/remark-mdc/node_modules/micromark-util-decode-string": {
"version": "2.0.0",
"dev": true,
@@ -10827,6 +10930,39 @@
"micromark-util-symbol": "^2.0.0"
}
},
+ "node_modules/remark-mdc/node_modules/micromark-util-normalize-identifier": {
+ "version": "2.0.0",
+ "dev": true,
+ "funding": [
+ {
+ "type": "GitHub Sponsors",
+ "url": "https://github.com/sponsors/unifiedjs"
+ },
+ {
+ "type": "OpenCollective",
+ "url": "https://opencollective.com/unified"
+ }
+ ],
+ "license": "MIT",
+ "dependencies": {
+ "micromark-util-symbol": "^2.0.0"
+ }
+ },
+ "node_modules/remark-mdc/node_modules/micromark-util-symbol": {
+ "version": "2.0.0",
+ "dev": true,
+ "funding": [
+ {
+ "type": "GitHub Sponsors",
+ "url": "https://github.com/sponsors/unifiedjs"
+ },
+ {
+ "type": "OpenCollective",
+ "url": "https://opencollective.com/unified"
+ }
+ ],
+ "license": "MIT"
+ },
"node_modules/remark-parse": {
"version": "10.0.2",
"dev": true,
@@ -10981,21 +11117,6 @@
"micromark-util-symbol": "^1.0.0"
}
},
- "node_modules/remark-rehype/node_modules/micromark-util-symbol": {
- "version": "1.1.0",
- "dev": true,
- "funding": [
- {
- "type": "GitHub Sponsors",
- "url": "https://github.com/sponsors/unifiedjs"
- },
- {
- "type": "OpenCollective",
- "url": "https://opencollective.com/unified"
- }
- ],
- "license": "MIT"
- },
"node_modules/remark-rehype/node_modules/micromark-util-types": {
"version": "1.1.0",
"dev": true,
@@ -11266,7 +11387,6 @@
},
"node_modules/sade": {
"version": "1.8.1",
- "dev": true,
"license": "MIT",
"dependencies": {
"mri": "^1.1.0"
@@ -11481,7 +11601,7 @@
}
},
"node_modules/simple-git": {
- "version": "3.20.0",
+ "version": "3.21.0",
"dev": true,
"license": "MIT",
"dependencies": {
@@ -11817,6 +11937,10 @@
"postcss": "^8.2.15"
}
},
+ "node_modules/stylis": {
+ "version": "4.3.0",
+ "license": "MIT"
+ },
"node_modules/supports-color": {
"version": "5.5.0",
"license": "MIT",
@@ -11843,7 +11967,7 @@
"dev": true
},
"node_modules/svgo": {
- "version": "3.0.3",
+ "version": "3.0.4",
"dev": true,
"license": "MIT",
"dependencies": {
@@ -11851,6 +11975,7 @@
"commander": "^7.2.0",
"css-select": "^5.1.0",
"css-tree": "^2.2.1",
+ "css-what": "^6.1.0",
"csso": "5.0.5",
"picocolors": "^1.0.0"
},
@@ -12022,6 +12147,13 @@
"url": "https://github.com/sponsors/wooorm"
}
},
+ "node_modules/ts-dedent": {
+ "version": "2.2.0",
+ "license": "MIT",
+ "engines": {
+ "node": ">=6.10"
+ }
+ },
"node_modules/tuf-js": {
"version": "2.1.0",
"dev": true,
@@ -12318,13 +12450,13 @@
}
},
"node_modules/unplugin": {
- "version": "1.5.0",
+ "version": "1.5.1",
"license": "MIT",
"dependencies": {
- "acorn": "^8.10.0",
+ "acorn": "^8.11.2",
"chokidar": "^3.5.3",
"webpack-sources": "^3.2.3",
- "webpack-virtual-modules": "^0.5.0"
+ "webpack-virtual-modules": "^0.6.0"
}
},
"node_modules/unplugin-vue-router": {
@@ -12437,12 +12569,9 @@
}
},
"node_modules/unstorage/node_modules/lru-cache": {
- "version": "10.0.2",
+ "version": "10.0.3",
"dev": true,
"license": "ISC",
- "dependencies": {
- "semver": "^7.3.5"
- },
"engines": {
"node": "14 || >=16.14"
}
@@ -12536,9 +12665,19 @@
"dev": true,
"license": "MIT"
},
+ "node_modules/uuid": {
+ "version": "9.0.1",
+ "funding": [
+ "https://github.com/sponsors/broofa",
+ "https://github.com/sponsors/ctavan"
+ ],
+ "license": "MIT",
+ "bin": {
+ "uuid": "dist/bin/uuid"
+ }
+ },
"node_modules/uvu": {
"version": "0.5.6",
- "dev": true,
"license": "MIT",
"dependencies": {
"dequal": "^2.0.0",
@@ -12555,7 +12694,6 @@
},
"node_modules/uvu/node_modules/kleur": {
"version": "4.1.5",
- "dev": true,
"license": "MIT",
"engines": {
"node": ">=6"
@@ -13176,7 +13314,7 @@
}
},
"node_modules/vuetify": {
- "version": "3.4.1",
+ "version": "3.4.2",
"dev": true,
"license": "MIT",
"engines": {
@@ -13234,6 +13372,10 @@
"url": "https://github.com/sponsors/wooorm"
}
},
+ "node_modules/web-worker": {
+ "version": "1.2.0",
+ "license": "Apache-2.0"
+ },
"node_modules/webidl-conversions": {
"version": "3.0.1",
"license": "BSD-2-Clause"
@@ -13246,7 +13388,7 @@
}
},
"node_modules/webpack-virtual-modules": {
- "version": "0.5.0",
+ "version": "0.6.0",
"license": "MIT"
},
"node_modules/whatwg-url": {
diff --git a/package.json b/package.json
index bd57ac87..5e3a703f 100644
--- a/package.json
+++ b/package.json
@@ -22,6 +22,7 @@
"@pinia/nuxt": "^0.4.11",
"d3": "^7.8.5",
"meilisearch": "^0.35.0",
+ "mermaid": "^10.6.1",
"pinia": "^2.1.6",
"vue-json-csv": "^2.1.0",
"yaml": "^2.3.3"
diff --git a/plugins/mermaid.client.js b/plugins/mermaid.client.js
new file mode 100644
index 00000000..3139ad42
--- /dev/null
+++ b/plugins/mermaid.client.js
@@ -0,0 +1,11 @@
+// this code is from : https://gitlab.com/dokos/documentation/-/blob/132cce8c6e2126d8dba8ad09b7c7dd6d08a7c461/mermaid.client.js
+
+import mermaid from "mermaid"
+
+export default defineNuxtPlugin((nuxtApp) => {
+ mermaid.initialize({
+ startOnLoad: false,
+ securityLevel: 'loose',
+ })
+ nuxtApp.provide('mermaid', () => mermaid)
+})
diff --git a/public/pfam-a-hmm.csv b/public/pfam-a-hmm.csv
new file mode 100644
index 00000000..473f4577
--- /dev/null
+++ b/public/pfam-a-hmm.csv
@@ -0,0 +1,15 @@
+ID,AC,DE,GA,TP,ML,CL,NE
+1-cysPrx_C,PF10417.13,C-terminal domain of 1-Cys peroxiredoxin,21.1; 21.1;,Domain,40,,
+10_blade,PF21734.1,10-bladed beta propeller domain,27; 27;,Repeat,345,CL0186,
+117-like_vir,PF21578.1,"Virus, 117-like",27; 27;,Family,101,CL0070,
+120_Rick_ant,PF12574.12,120 KDa Rickettsia surface antigen,25; 25;,Family,240,,
+12TM_1,PF09847.13,Membrane protein of 12 TMs,33.2; 33.2;,Family,449,CL0181,
+14-3-3,PF00244.24,14-3-3 protein,33.2; 33.2;,Repeat,223,CL0020,
+17kDa_Anti_2,PF16998.9,17 kDa outer membrane surface antigen,26.6; 26.6;,Family,115,CL0500,
+2-Hacid_dh,PF00389.34,"D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain",24.6; 24.6;,Domain,134,CL0063,2-Hacid_dh_C
+2-Hacid_dh_C,PF02826.23,"D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain",25.1; 25.1;,Domain,178,CL0063,
+2-oxoacid_dh,PF00198.27,2-oxoacid dehydrogenases acyltransferase (catalytic domain),23; 23;,Domain,232,CL0149,
+2-oxogl_dehyd_N,PF16078.9,2-oxoglutarate dehydrogenase N-terminus,27; 27;,Family,41,,
+2-ph_phosp,PF04029.18,2-phosphosulpholactate phosphatase,26.4; 26.4;,Family,226,,
+2-thiour_desulf,PF04463.16,2-thiouracil desulfurase,34.7; 34.7;,Family,139,,
+23ISL,PF16620.9,Unstructured linker between I-set domains 2 and 3 on MYLCK,25; 25;,Disordered,146,,
diff --git a/server/plugins/content.ts b/server/plugins/content.ts
index 878a8d23..1e597d72 100644
--- a/server/plugins/content.ts
+++ b/server/plugins/content.ts
@@ -29,8 +29,6 @@ export default defineNitroPlugin((nitroApp) => {
if (file?.body?.children?.length > 0) {
// has contributors
if (file?.contributors?.length > 0) {
- console.log("has contributors")
- console.log(file.body.children.slice(0, 2))
const h1Index = file.body.children.findIndex(({ tag }) => tag === "h1")
if (h1Index >= 0) {
file.body.children.splice(h1Index + 1, 0, {
--
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