models.py 17.9 KB
Newer Older
Hervé  MENAGER's avatar
Hervé MENAGER committed
1
2
3
4
from __future__ import unicode_literals

from django.db import models

5
from .ws import get_pubmed_info, get_epo_info, get_uniprot_info, get_taxonomy_info, get_go_info, get_pfam_info
6

Hervé  MENAGER's avatar
Hervé MENAGER committed
7
8
9
10
11
12
13
14
15
16
17
class Bibliography(models.Model):
    """
    Bibliography data table
    """
    SOURCES = (
        ('PM', 'PubMed article'),
        ('PT', 'Patent')
    )
    source = models.CharField('Bibliographic type', max_length=2, choices=SOURCES)
    id_source = models.CharField('Bibliographic ID', max_length=25)
    title = models.CharField('Title', max_length=300)
18
    journal_name = models.CharField('Journal name', max_length=50, null=True)
Hervé  MENAGER's avatar
Hervé MENAGER committed
19
20
    authors_list = models.CharField('Authors list', max_length=500)
    biblio_year = models.PositiveSmallIntegerField('Year')
21
22
23
24
25
26
27
    cytotox = models.BooleanField('Cytotoxicity data', default=False)
    in_silico = models.BooleanField('in silico study performed', default=False)
    in_vitro = models.BooleanField('in vitro study performed', default=False)
    in_vivo = models.BooleanField('in vivo study performed', default=False)
    in_cellulo = models.BooleanField('in cellulo study performed', default=False)
    pharmacokinetic = models.BooleanField('pharmacokinetic study performed', default=False)
    xray = models.BooleanField('contains xray data', default=False)
Hervé  MENAGER's avatar
Hervé MENAGER committed
28
29

    def save(self, *args, **kwargs):
30
31
32
33
34
35
36
37
        if self.source == 'PM':
            info = get_pubmed_info(self.id_source)
        else:
            info = get_epo_info(self.id_source)
        self.title = info['title']
        self.journal_name = info['journal_name']
        self.authors_list = info['authors_list']
        self.biblio_year = info['biblio_year']
Hervé  MENAGER's avatar
Hervé MENAGER committed
38
39
        super(Bibliography, self).save(*args, **kwargs)

Hervé  MENAGER's avatar
Hervé MENAGER committed
40
41
42
    class Meta:
        verbose_name_plural = "bibliographies"

43

Hervé  MENAGER's avatar
Hervé MENAGER committed
44
45

class Taxonomy(models.Model):
46
    taxonomy_id = models.DecimalField('NCBI TaxID', unique=True, max_digits=9, decimal_places=0)
Hervé  MENAGER's avatar
Hervé MENAGER committed
47
    name = models.CharField('Organism name', max_length=200)
48
49
50
51
52
53

    def save(self, *args, **kwargs):
        info = get_taxonomy_info(self.taxonomy_id)
        self.name = info['scientific_name']
        super(Taxonomy, self).save(*args, **kwargs)

54
55
56
    def __str__(self):
        return self.name

Hervé  MENAGER's avatar
Hervé MENAGER committed
57
58
    class Meta:
        verbose_name_plural = "taxonomies"
Hervé  MENAGER's avatar
Hervé MENAGER committed
59
60
61
62
63

class MolecularFunction(models.Model):
    go_id = models.CharField('Gene Ontology ID', unique=True, max_length=10) # GO term id format: 'GO:0000000' 
    description = models.CharField('description', max_length=500)

64
65
66
67
68
    def save(self, *args, **kwargs):
        info = get_go_info(self.go_id)
        self.description = info['label']
        super(MolecularFunction, self).save(*args, **kwargs)

69
70
71
    def __str__(self):
        return self.description

Hervé  MENAGER's avatar
Hervé MENAGER committed
72
73
74
75
76
77
78
79
80
class Protein(models.Model):
    uniprot_id = models.CharField('Uniprot ID', unique=True, max_length=10)
    recommended_name_long = models.CharField('Uniprot Recommended Name (long)', max_length=75)
    short_name = models.CharField('Short name', max_length=50)
    gene_name = models.CharField('Gene name', unique=True, max_length=30)
    entry_name = models.CharField('Entry name', max_length=30)
    organism = models.ForeignKey('Taxonomy')
    molecular_functions = models.ManyToManyField(MolecularFunction)

81
    def save(self, *args, **kwargs):
82
        info = get_uniprot_info(self.uniprot_id)
83
        self.recommended_name_long = info['recommended_name']
84
85
86
87
88
89
90
91
92
        self.gene_name = info['gene']
        self.entry_name = info['entry_name']
        try:
            taxonomy = Taxonomy.objects.get(taxonomy_id=info['organism'])
        except Taxonomy.DoesNotExist:
            taxonomy = Taxonomy()
            taxonomy.taxonomy_id = info['organism']
            taxonomy.save()
        self.organism = taxonomy
93
        super(Protein, self).save(*args, **kwargs)
94
95
96
97
98
99
100
101
        for go_id in info['molecular_functions']:
            try:
                mol_function = MolecularFunction.objects.get(go_id=go_id)
            except MolecularFunction.DoesNotExist:
                mol_function = MolecularFunction()
                mol_function.go_id = go_id
                mol_function.save()
            self.molecular_functions.add(mol_function)
102

103
104
105
    def __str__(self):
        return '{} ({})'.format(self.uniprot_id, self.recommended_name_long)

Hervé  MENAGER's avatar
Hervé MENAGER committed
106
107
108
109
class Domain(models.Model):
    pfam_acc = models.CharField('Pfam Accession', max_length=10, unique=True) 
    pfam_id = models.CharField('Pfam Family Identifier', max_length=20) 
    pfam_description = models.CharField('Pfam Description', max_length=100)
110
111
112
113
114
115
116
    domain_family = models.CharField('Domain family', max_length=25)  #TODO: what is this field? check database contents

    def save(self, *args, **kwargs):
        info = get_pfam_info(self.pfam_acc)
        self.pfam_id = info['id']
        self.pfam_description = info['description']
        super(Domain, self).save(*args, **kwargs)
Hervé  MENAGER's avatar
Hervé MENAGER committed
117

118
119
120
    def __str__(self):
        return '{} ({}-{})'.format(self.pfam_acc, self.pfam_id, self.pfam_description)

121
class ProteinDomainComplex(models.Model):
122
123
    protein = models.ForeignKey('Protein')
    domain = models.ForeignKey('Domain')
124
125
    ppc_copy_nb = models.IntegerField('Number of copies of the protein in the complex')
    
Hervé  MENAGER's avatar
Hervé MENAGER committed
126
127
    class Meta:
        verbose_name_plural = "complexes"
128

129
130
131
    def __str__(self):
        return '{}-{}'.format(self.protein_id, self.domain_id)

132
133
134
135
136
class ProteinDomainBoundComplex(ProteinDomainComplex):
    ppp_copy_nb_per_p = models.IntegerField('Number of copies of the protein in the pocket')
    pockets_nb = models.IntegerField('Total number of pockets in the complex')
    class Meta:
        verbose_name_plural = "bound complexes"
Hervé  MENAGER's avatar
Hervé MENAGER committed
137
    
138
139
140
class ProteinDomainPartnerComplex(ProteinDomainComplex):
    class Meta:
        verbose_name_plural = "partner complexes"
Hervé  MENAGER's avatar
Hervé MENAGER committed
141

142
143
144
class Symmetry(models.Model):
    code = models.CharField('Symmetry code', max_length=2)
    description = models.CharField('Description', max_length=300)
Hervé  MENAGER's avatar
Hervé MENAGER committed
145

146
147
148
    class Meta:
        verbose_name_plural = "symmetries"

149
150
151
    def __str__(self):
        return '{} ({})'.format(self.code, self.description)

152
class Ppi(models.Model):
153
    pdb_id = models.CharField('PDB ID', max_length=4, null=True)
154
    symmetry = models.ForeignKey(Symmetry)
Hervé  MENAGER's avatar
Hervé MENAGER committed
155

156
157
158
    def __str__(self):
        return '{} PPI, PDB:{}'.format(self.symmetry.description, self.pdb_id or 'unknown')

Hervé  MENAGER's avatar
Hervé MENAGER committed
159
160
161
162
163
164
165
166
class PpiComplex(models.Model):
    ppi = models.ForeignKey(Ppi)
    complex = models.ForeignKey(ProteinDomainComplex)
    cc_nb = models.IntegerField('Number of copies of the complex in the PPI', default=1)

    class Meta:
        verbose_name_plural = "Ppi complexes"

167
168
169
    def __str__(self):
        return 'PPI {}, Complex {} ({})'.format(self.ppi, self.complex, self.cc_nb)

170
class Disease(models.Model):
171
    ppi = models.ForeignKey(Ppi)
172
    disease_name = models.CharField('Disease', max_length=30) # is there any database/nomenclature for diseases?
Hervé  MENAGER's avatar
Hervé MENAGER committed
173
174


175
class Compound(models.Model):
Hervé  MENAGER's avatar
Hervé MENAGER committed
176
    canonical_smile = models.CharField('Canonical Smile', unique=True, max_length=500)
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
    #TODO index this table on canonical_smile
    is_macrocycle = models.BooleanField('Contains one or more macrocycles') 
    aromatic_ratio = models.DecimalField('Aromatic ratio', max_digits=3, decimal_places=2)
    balaban_index = models.DecimalField('Balaban index', max_digits=3, decimal_places=2)  
    fsp3 = models.DecimalField('Fsp3', max_digits=3, decimal_places=2)
    gc_molar_refractivity = models.DecimalField('GC Molar Refractivity', max_digits=5, decimal_places=2)
    log_d = models.DecimalField('LogD (Partition coefficient octanol-1/water, with pKa information)', max_digits=4, decimal_places=2)
    a_log_p = models.DecimalField('ALogP (Partition coefficient octanol-1/water)', max_digits=4, decimal_places=2)
    mean_atom_vol_vdw = models.DecimalField('Mean atom volume computed with VdW radii', max_digits=4, decimal_places=2)
    molecular_weight = models.DecimalField('Molecular weight', max_digits=6, decimal_places=2)
    nb_acceptor_h = models.IntegerField('Number of hydrogen bond acceptors')
    nb_aliphatic_amines = models.IntegerField('Number of aliphatics amines')
    nb_aromatic_bonds = models.IntegerField('Number of aromatic bonds')
    nb_aromatic_ether = models.IntegerField('Number of aromatic ethers')
    nb_aromatic_sssr = models.IntegerField('Number of aromatic Smallest Set of System Rings (SSSR)')
    nb_atom = models.IntegerField('Number of atoms') 
    nb_atom_non_h = models.IntegerField('Number of non hydrogen atoms') 
    nb_benzene_like_rings = models.IntegerField('Number of benzene-like rings')
    nb_bonds = models.IntegerField('Number of bonds')
    nb_bonds_non_h = models.IntegerField('Number of bonds not involving a hydrogen')  
    nb_br = models.IntegerField('Number of Bromine atoms')  
    nb_c = models.IntegerField('Number of Carbon atoms')  
    nb_chiral_centers = models.IntegerField('Number of chiral centers')  
    nb_circuits = models.IntegerField('Number of circuits')  
    nb_cl = models.IntegerField('Number of Chlorine atoms')  
    nb_csp2 = models.IntegerField('Number of sp2-hybridized carbon atoms')  
    nb_csp3 = models.IntegerField('Number of sp3-hybridized carbon atoms')  
    nb_donor_h = models.IntegerField('Number of hydrogen bond donors')  
    nb_double_bonds = models.IntegerField('Number of double bonds')  
    nb_f = models.IntegerField('Number of fluorine atoms')  
    nb_i = models.IntegerField('Number of iodine atoms')  
    nb_multiple_bonds = models.IntegerField('Number of multiple bonds')  
    nb_n = models.IntegerField('Number of nitrogen atoms')
    nb_o = models.IntegerField('Number of oxygen atoms')  
    nb_rings = models.IntegerField('Number of rings')  
    nb_rotatable_bonds = models.IntegerField('Number of rotatable bonds')  
    randic_index = models.DecimalField('Randic index', max_digits=4, decimal_places=2)  
    rdf070m = models.DecimalField('RDF070m, radial distribution function weighted by the atomic masses at 7Å', max_digits=5, decimal_places=2)  
    rotatable_bond_fraction = models.DecimalField('Fraction of rotatable bonds', max_digits=3, decimal_places=2)  
    sum_atom_polar = models.DecimalField('Sum of atomic polarizabilities', max_digits=5, decimal_places=2)  
    sum_atom_vol_vdw = models.DecimalField('Sum of atom volumes computed with VdW radii', max_digits=6, decimal_places=2)  
    tpsa = models.DecimalField('Topological Polar Surface Area (TPSA)', max_digits=5, decimal_places=2)  
    ui = models.DecimalField('Unsaturation index', max_digits=4, decimal_places=2)  
    wiener_index = models.IntegerField('Wiener index')  
    common_name = models.CharField('Common name', unique=True, max_length=20, blank=True, null=True)  
    pubchem_id = models.CharField('Pubchem ID', unique=True, max_length=10, blank=True, null=True)  
    chemspider_id = models.CharField('Chemspider ID', unique=True, max_length=10, blank=True, null=True)  
    chembl_id = models.CharField('Chembl ID', unique=True, max_length=30, blank=True, null=True)  
    iupac_name = models.CharField('IUPAC name', unique=True, max_length=255, blank=True, null=True)  
226
    mddr_compound = models.ForeignKey('MDDRCompoundImport', blank=True, null=True)  
227
228
229
230
231
232
233
234
235


class MDDRCompoundImport(models.Model):
    mddr_compound_id = models.IntegerField('MDDR compound ID')  
    mddr_name = models.CharField('MDDR name', max_length=40)  
    dvpmt_phase = models.CharField('Development phase', max_length=20)  
    canonical_smile = models.CharField('Canonical Smile', max_length=500, unique=True, blank=True, null=True)  
    #TODO index this table on canonical_smile
    db_import_date = models.DecimalField('MDDR release year/month', max_digits=6, decimal_places=0)  
Hervé  MENAGER's avatar
Hervé MENAGER committed
236

237
238
239
240
    class Meta:
        # over multiple releases of the MDDR database, the same compound can evolve in its development phase
        # the same compound can have different names and development phases in the same MDDR release
        unique_together = (('mddr_compound_id', 'mddr_name', 'dvpmt_phase'),)
Hervé  MENAGER's avatar
Hervé MENAGER committed
241
        verbose_name_plural = "MDDR compound imports"
Hervé  MENAGER's avatar
Hervé MENAGER committed
242
243


244
class MDDRCompoundActivityClass(models.Model):
245
    mddr_compound = models.ForeignKey(MDDRCompoundImport)  
246
    activity_class = models.CharField('Activity Class', max_length=100)  
Hervé  MENAGER's avatar
Hervé MENAGER committed
247
248

    class Meta:
249
        unique_together = (('mddr_compound', 'activity_class'),)
Hervé  MENAGER's avatar
Hervé MENAGER committed
250
        verbose_name_plural = "MDDR compound activity classes"
Hervé  MENAGER's avatar
Hervé MENAGER committed
251
252


253
254
255
256
class MDDRSimilarity(models.Model):
    canonical_smile_ippidb = models.CharField('Canonical Smile for IPPIDB compound', max_length=500, unique=True, blank=True, null=True)
    canonical_smile_mddr = models.CharField('Canonical Smile for MDDR Compound', max_length=500, unique=True, blank=True, null=True)
    tanimoto = models.DecimalField('Tanimoto', max_digits=6, decimal_places=5)  
Hervé  MENAGER's avatar
Hervé MENAGER committed
257
258

    class Meta:
259
        unique_together = (('canonical_smile_ippidb', 'canonical_smile_mddr'),)
Hervé  MENAGER's avatar
Hervé MENAGER committed
260
        verbose_name_plural = "MDDR similarities"
261

262
263
class CellLine(models.Model):
    name = models.CharField('Name', max_length=50, unique=True)
Hervé  MENAGER's avatar
Hervé MENAGER committed
264

265
266
267
268
269
270
271
272
273
274
class TestActivityDescription(models.Model):
    TEST_TYPES = (
        ('BIOCH', 'Biochemical assay'),
        ('CELL', 'Cellular assay')
    )
    TEST_MODULATION_TYPES = (
        ('B', 'Binding'),
        ('I', 'Inhibition'),
        ('S', 'Stabilization')
    )
275
276
    biblio = models.ForeignKey(Bibliography)
    ppi = models.ForeignKey(Ppi, blank=True, null=True)  
277
278
279
280
281
282
    test_name = models.CharField('Test name', max_length=100)  
    test_type = models.CharField('Test type', max_length=5, choices=TEST_TYPES)
    test_modulation_type = models.CharField('Test modulation type', max_length=1, choices=TEST_MODULATION_TYPES)
    nb_active_compounds = models.IntegerField('Total number of active compounds')  
    cell_line = models.ForeignKey(CellLine)

Hervé  MENAGER's avatar
Hervé MENAGER committed
283
284
285
286
287
288
    def get_complexes(self):
        return None
        # if test_modulation_type is Binding, return all bound complexes for the Ppi
        # if test_modulation_type is Inhibition, return all Ppi complexes
        # if test_modulation_type is Stabilization, return all bound complexes for the Ppi
        # this should be added to the Ppi class as well
289
290

class CompoundActivityResult(models.Model):
291
292
293
294
295
    MODULATION_TYPES = (
        ('B', 'Binding'),
        ('I', 'Inhibition'),
        ('S', 'Stabilization')
    )
Hervé  MENAGER's avatar
Hervé MENAGER committed
296
297
298
299
300
301
    ACTIVITY_TYPES = (
        ('pIC50','pIC50 (half maximal inhibitory concentration, -log10)'),
        ('pEC50','pEC50 (half maximal effective concentration, -log10)'),
        ('pKd','pKd (dissociation constant, -log10)'),
        ('pKi','pKi (inhibition constant, -log10)'),
    )
302
303
    compound = models.ForeignKey(Compound)  
    test_activity_description = models.ForeignKey(TestActivityDescription)  
Hervé  MENAGER's avatar
Hervé MENAGER committed
304
    activity_type = models.CharField('Activity type', max_length=5, choices=ACTIVITY_TYPES)
305
    activity = models.DecimalField('Activity', max_digits=12, decimal_places=10)  
306
    modulation_type = models.CharField('Modulation type', max_length=1, choices=MODULATION_TYPES)  
Hervé  MENAGER's avatar
Hervé MENAGER committed
307
308

    class Meta:
309
        unique_together = (('compound', 'test_activity_description', 'activity_type'),)
Hervé  MENAGER's avatar
Hervé MENAGER committed
310

311
class TestCytotoxDescription(models.Model):
312
    biblio = models.ForeignKey(Bibliography)  
313
314
315
    test_name = models.CharField('Cytotoxicity test name', max_length=100)  
    cell_line = models.ForeignKey(CellLine)
    compound_concentration = models.DecimalField('Compound concentration in μM', max_digits=7, decimal_places=3, blank=True, null=True)  
Hervé  MENAGER's avatar
Hervé MENAGER committed
316

317
class CompoundCytotoxicityResult(models.Model):
318
319
    compound = models.ForeignKey(Compound)  
    test_cytotoxicity_description = models.ForeignKey(TestCytotoxDescription)
320
    toxicity = models.BooleanField('Toxicity', default=False)
Hervé  MENAGER's avatar
Hervé MENAGER committed
321
322

    class Meta:
323
        unique_together = (('compound', 'test_cytotoxicity_description'),)
324
325
326
327
328

class AdministrationMode(models.Model):
    name = models.CharField('Administration mode', max_length=20, blank=True, null=True)

class TestPKDescription(models.Model):
329
    biblio = models.ForeignKey(Bibliography)  
330
331
332
333
334
335
336
    test_name = models.CharField('Pharmacokinetic test name', max_length=100)  
    organism = models.ForeignKey(Taxonomy)
    administration_mode = models.ForeignKey(AdministrationMode, blank=True, null=True)  
    dose = models.DecimalField('Dose in mg/kg', max_digits=7, decimal_places=4, blank=True, null=True)  
    dose_interval = models.IntegerField('Dose interval, in hours', blank=True, null=True)  

class CompoundPKResult(models.Model):
337
338
    compound = models.ForeignKey(Compound)  
    test_pk_description = models.ForeignKey(TestPKDescription)
339
340
341
342
343
344
345
346
    tolerated = models.NullBooleanField('Tolerated', null=True)
    auc = models.IntegerField('Area under curve (ng.mL-1.hr)', blank=True, null=True)  
    clearance = models.DecimalField('Clearance (mL/hr)', max_digits=7, decimal_places=3, blank=True, null=True)  
    cmax = models.DecimalField('Maximal concentration (ng/mL)', max_digits=7, decimal_places=3, blank=True, null=True)  
    oral_bioavailability = models.IntegerField('Oral Bioavailability (%F)', blank=True, null=True)  
    t_demi = models.IntegerField('t½', blank=True, null=True)  
    t_max = models.IntegerField('tmax', blank=True, null=True)  
    voldistribution = models.DecimalField('Volume distribution (Vd)', max_digits=5, decimal_places=2, blank=True, null=True)  
Hervé  MENAGER's avatar
Hervé MENAGER committed
347
348

    class Meta:
349
        unique_together = (('compound', 'test_pk_description'),)
Hervé  MENAGER's avatar
Hervé MENAGER committed
350
351


352
353
354
class CmpdAction(models.Model):
    ACTIVATION_MODES = (
        ('O', 'Orthosteric'),
355
        ('A', 'Allosteric')
356
    )
357
    compound = models.ForeignKey(Compound)  
358
    activation_mode = models.CharField('Activation mode', max_length=1, choices=ACTIVATION_MODES)  
359
    ppi = models.ForeignKey(Ppi)
360
361
    pdb_id = models.CharField('PDB ID', max_length=4)
    nb_copy_compounds = models.IntegerField('Number of copies for the compound')  
Hervé  MENAGER's avatar
Hervé MENAGER committed
362
363

    class Meta:
Hervé  MENAGER's avatar
Hervé MENAGER committed
364
365
366
367
368
369
        unique_together = (('ppi', 'compound', 'activation_mode', 'pdb_id'),)

    def get_complexes(self):
        return None
        # return all bound complexes for the Ppi
        # this should be added to the Ppi class as well
Hervé  MENAGER's avatar
Hervé MENAGER committed
370

371
class RefCompoundBiblio(models.Model):
372
373
    compound = models.ForeignKey(Compound)  
    bibliography = models.ForeignKey(Bibliography)  
374
    compound_name = models.CharField('Compound name in the publication', max_length=50)  
Hervé  MENAGER's avatar
Hervé MENAGER committed
375
376

    class Meta:
377
        unique_together = (('compound', 'bibliography'),)