diff --git a/components/content/ArticleDoiList.vue b/components/content/ArticleDoiList.vue
index fe7727a672fbe67a3741e520b42d97b36550dc03..357e90ee40bc9dc5a3ac068918d372e8a3091926 100644
--- a/components/content/ArticleDoiList.vue
+++ b/components/content/ArticleDoiList.vue
@@ -1,11 +1,25 @@
<script setup lang="ts">
-const props = defineProps<{
- items: { doi: string, title?: string, divider: boolean, abstract?: string }[];
-}>();
+import ProseH2 from '~/components/content/ProseH2'
+// const props = defineProps<{
+// items: { doi: string; title?: string; divider: boolean; abstract?: string }[];
+// }>();
+
+const { page } = useContent();
+const computedDois = computed(() => {
+ if (page.value?.relevantAbstracts) {
+ return page.value.relevantAbstracts;
+ } else {
+ return [];
+ }
+});
</script>
<template>
+ <div v-if="computedDois?.length > 0">
+ <ProseH2 id="relevant-abstracts">Relevant abstracts</ProseH2>
+
<v-list density="compact">
- <ArticleDoi v-for="item, index in props.items" :key="item.doi" :index="index + 1" :doi="item.doi"
- :title="item?.title" :divider="item.divider" :abstract="item?.abstract" />
+ <ArticleDoi v-for="(item, index) in computedDois" :key="item.doi" :index="index + 1" :doi="item.doi"
+ :title="item?.title" :divider="item.divider" :abstract="item?.abstract" />
</v-list>
+ </div>
</template>
\ No newline at end of file
diff --git a/components/content/Contributors.vue b/components/content/Contributors.vue
index 5c173d624212826b6e80db4755ee37639d1178ae..e79060863111661627017e26de255e35f3a2cc70 100644
--- a/components/content/Contributors.vue
+++ b/components/content/Contributors.vue
@@ -9,6 +9,6 @@ const contributorsString = computed(() => {
</script>
<template>
- <div v-if="contributorsString" class="mt-n6 mb-6 text-subtitle-1 text-info">Contributors: {{ contributorsString }}
+ <div v-if="contributorsString" class="mt-n5 mb-6 text-subtitle-1 text-info">Contributors: {{ contributorsString }}
</div>
</template>
\ No newline at end of file
diff --git a/components/content/Ref.vue b/components/content/Ref.vue
index 7031d3aefea6ec7d43376f37a1ddc9f92be269e3..006afc08445f05b49419d17bac3dc15f0df40cac 100644
--- a/components/content/Ref.vue
+++ b/components/content/Ref.vue
@@ -1,13 +1,17 @@
<script setup lang="ts">
-
export interface Props {
- doi: string;
+ doi: string;
}
const props = withDefaults(defineProps<Props>(), {});
const { article } = useFetchArticle(props.doi);
</script>
<template>
- <v-chip variant="text" :href="`#${props.doi}`" class="pa-0 text-caption font-italic">({{ article?.author[0]?.family ?? 'test' }} et al, {{
- article.year
- }})</v-chip>
+ <v-chip
+ v-if="article"
+ variant="text"
+ :href="`#${props.doi}`"
+ class="pa-0 text-caption font-italic"
+ >({{ article?.author[0]?.family ?? "test" }} et al,
+ {{ article?.year }})</v-chip
+ >
</template>
\ No newline at end of file
diff --git a/content/3.defense-systems/abi2.md b/content/3.defense-systems/abi2.md
index 808a7367c8c6f20bb252a410e57a5cec2b8d6a54..ee06af707f5751426dea7d9d69e2e96560ee7f21 100644
--- a/content/3.defense-systems/abi2.md
+++ b/content/3.defense-systems/abi2.md
@@ -9,6 +9,8 @@ tableColumns:
Activator: ''
Effector: ''
PFAM: PF07751
+relevantAbstracts:
+ - doi: 10.1016/j.mib.2005.06.006
---
# Abi2
@@ -31,6 +33,3 @@ Among the 22k complete genomes of RefSeq, this system is present in 1210 genomes
*Proportion of genome encoding the Abi2 system for the 14 phyla with more than 50 genomes in the RefSeq database.*
-## Relevant abstracts
-
-
diff --git a/content/3.defense-systems/abia.md b/content/3.defense-systems/abia.md
index 912ea20db0b48724cc3d72306c6071bd0671ad41..3de86ab7e5ceebfb8521761e72cdbcdba832ccd7 100644
--- a/content/3.defense-systems/abia.md
+++ b/content/3.defense-systems/abia.md
@@ -9,9 +9,14 @@ tableColumns:
Activator: Unknown
Effector: Unknown
PFAM: PF00078, PF18160, PF18732
+relevantAbstracts:
+ - doi: 10.1023/A:1002027321171
+ - doi: 10.1016/j.mib.2005.06.006
+ - doi: 10.1093/nar/gkac467
---
# AbiA
+
The AbiA system have been describe in a total of 2 subsystems.
Here is some example found in the RefSeq database:
@@ -69,14 +74,5 @@ 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)
-## Relevant abstracts
-::article-doi-list
----
-items:
- - doi: 10.1023/A:1002027321171
- - doi: 10.1016/j.mib.2005.06.006
- - doi: 10.1093/nar/gkac467
----
-::
diff --git a/content/3.defense-systems/detocs.md b/content/3.defense-systems/detocs.md
index b715ca6408329a016b39d8cb29c7cd92d0152a84..40a0c168a451db0bf9fc1a75943956c544594c46 100644
--- a/content/3.defense-systems/detocs.md
+++ b/content/3.defense-systems/detocs.md
@@ -6,6 +6,8 @@ tableColumns:
abstract: |
During viral infection, cells can deploy immune strategies that deprive viruses of molecules essential for their replication. Here, we report a family of immune effectors in bacteria that, upon phage infection, degrade cellular adenosine triphosphate (ATP) and deoxyadenosine triphosphate (dATP) by cleaving the N-glycosidic bond between the adenine and sugar moieties. These ATP nucleosidase effectors are widely distributed within multiple bacterial defense systems, including cyclic oligonucleotide-based antiviral signaling systems (CBASS), prokaryotic argonautes, and nucleotide-binding leucine-rich repeat (NLR)-like proteins, and we show that ATP and dATP degradation during infection halts phage propagation. By analyzing homologs of the immune ATP nucleosidase domain, we discover and characterize Detocs, a family of bacterial defense systems with a two-component phosphotransfer-signaling architecture. The immune ATP nucleosidase domain is also encoded within diverse eukaryotic proteins with immune-like architectures, and we show biochemically that eukaryotic homologs preserve the ATP nucleosidase activity. Our findings suggest that ATP and dATP degradation is a cell-autonomous innate immune strategy conserved across the tree of life.
PFAM: PF01048, PF18742
+relevantAbstracts:
+ - doi: 10.1016/j.cell.2023.07.020
contributors:
- François Rousset
---
@@ -14,6 +16,7 @@ contributors:
# Detocs
## Description
+
Detocs (**De**fensive **T**w**o**-**C**omponent **S**ystem) is a family of 3-gene defense systems that mediate anti-phage activity by abortive infection.
## Molecular mechanism
@@ -83,16 +86,3 @@ dataUrl: /detocs/Detocs_hydrolase__dtcC-plddts_89.47253.pdb
---
::
-## Relevant abstract
-::article-doi-list
----
-items:
- - doi: 10.1016/j.cell.2023.07.020
-
----
-::
-
-
-## References
-
-Rousset et al., A conserved family of immune effectors cleaves cellular ATP upon viral infection. Cell 186, 1–13 (2023). https://doi.org/10.1016/j.cell.2023.07.020
diff --git a/server/plugins/content.ts b/server/plugins/content.ts
index 0f843c65913eb850e528d7653738a8deb4ca9e55..19dad94f6b91ee1e41275d3b50c32c772861a4b7 100644
--- a/server/plugins/content.ts
+++ b/server/plugins/content.ts
@@ -4,34 +4,44 @@ export default defineNitroPlugin((nitroApp) => {
nitroApp.hooks.hook('content:file:beforeParse',
(file) => {
if (file?._id?.startsWith('content:3.defense-systems:') && file?._id?.endsWith('.md')) {
- const regexp = /(?<=---\n).*?(?=\n---)/sg;
- const match = file.body.match(regexp);
- const frontMatter = match[0]
- const parsedFrontMatter = YAML.parse(frontMatter)
- if (parsedFrontMatter?.contributors?.length > 0) {
- file.body = file.body.replace(/(^#[\s+]\w*[\s\S])/gm, "$1:contributors\n\n")
+ const frontMatterRegex = /(?<=---\n).*?(?=\n---)/sg;
+
+ const fontMatterMatch = file.body.match(frontMatterRegex);
+ if (fontMatterMatch?.length > 0) {
+ const frontMatter = fontMatterMatch[0]
+ const parsedFrontMatter = YAML.parse(frontMatter)
+ if (parsedFrontMatter?.contributors?.length > 0) {
+ file.body = file.body.replace(/(^#[\s+]\w*[\s\S])/gm, "$1\n:contributors\n\n")
+ }
+ // try to look at :ref{doi=xxxx}
+ const matchRef = file.body.match(/(?<=:ref{doi=).*(?=})/gm)
+ if (matchRef?.length > 0) {
+ if (parsedFrontMatter?.relevantAbstracts) {
+ const relevantAbstractsSet = new Set(parsedFrontMatter.relevantAbstracts.map(({ doi }: { doi: string }) => doi))
+ const filteredMatchRef = matchRef.filter((doi: string) => !relevantAbstractsSet.has(doi))
+ parsedFrontMatter.relevantAbstracts = [...parsedFrontMatter.relevantAbstracts, ...filteredMatchRef.map((doi: string) => ({ doi }))]
+ } else {
+ parsedFrontMatter.relevantAbstracts = matchRef.map((doi: string) => ({ doi }))
+ }
+ const newFrontMatterStr = YAML.stringify(parsedFrontMatter)
+ file.body = file.body.replace(/---\n(.*?)\n---/gs, `---\n${newFrontMatterStr}\n---`)
+ }
}
}
})
- // nitroApp.hooks.hook(
- // 'content:file:afterParse',
- // (file) => {
- // if (file._id.endsWith('.md')) {
-
- // file.body.children.push({
- // type: "element",
- // tag: 'article-doi-list',
- // props: {
- // items: [
- // { doi: '10.1016/j.mib.2005.06.006' },
- // { doi: '10.1016/j.mib.2005.06.006' }]
- // },
- // children: []
- // })
-
- // }
- // })
+ nitroApp.hooks.hook(
+ 'content:file:afterParse',
+ (file) => {
+ if (file?._id?.startsWith('content:3.defense-systems:') && file._id.endsWith('.md')) {
+ file.body.children.push({
+ type: "element",
+ tag: 'article-doi-list',
+ props: {},
+ children: []
+ })
+ }
+ })
})
\ No newline at end of file