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comparison lexmapr/definitions.py @ 0:f5c39d0447be

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"planemo upload"
author kkonganti
date Wed, 31 Aug 2022 14:32:07 -0400
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-1:000000000000 0:f5c39d0447be
1 """Static definitions"""
2
3 import os
4
5
6 # root path
7 ROOT = os.path.dirname(__file__)
8
9 # URL to list of OLS ontologies where download link is given
10 embl_ontologies = 'https://www.ebi.ac.uk/ols/ontologies'
11
12 # beginning of URL to ontology PURL
13 purl_link = 'http://purl.obolibrary.org/obo/'
14
15 # directory for downloaded OWL files
16 owl_dir = 'lexmapr/owl_files'
17
18 # path to database with synonyms from predefined resources and from OWL files
19 synonym_db = 'lexmapr/owl_files/label_synonyms.db'
20
21 # path to database with all ontologies of interest
22 ontol_db = 'lexmapr/owl_files/ontol_table.db'
23
24
25 # ontologies of interest
26 ontol_interest = [#'BFO',
27 #'CHEBI',
28 #'ENVO',
29 'FOODON',
30 #'GENEPIO',
31 'NCBITAXON', # NCBITaxon is not valid as of April 2022
32 #'OGMS',
33 #'PATO',
34 #'PCO',
35 #'UBERON',
36 ]
37
38 # ontology accessions that do not have labels or are placeholders as of April 2022
39 # will skip in database building
40 missing_ontol_labels = ['GENEPIO_0001367','GENEPIO_0001368','GENEPIO_0001369','GENEPIO_0001370',
41 'GENEPIO_0001372','GENEPIO_0001373','_MIAA_0000021',
42 ]
43
44 # terms indicating that the metadata was not given/collected; will output empty results
45 not_provided = ['not applicable','unknown','n a','not provided','not available','miscellaneous',
46 'not collected','missing','unidentified','unknown','none','unamed','other',
47 'undetermined','not known','no history given','no source specified','null',
48 'unspecified','not reported','not available not collected','not isolated',
49 'not available','not provided','xxx','mising','misng','other','unidentified',
50 'not determined other','reported later','intact unknown','not determined',
51 'not ascertained','unk','nd','nd others','nd other','etc','na','',' ',
52 'not supplied','not specified',
53 ]
54
55 # below are bin definitions
56 # TODO: food consumer group:FOODON_03510136 changed, formatted as '* as food consumer'
57 # can collect as 'for *' in text?
58 #fo_consumer = []
59
60 fo_product = ['algal food product:FOODON_00001184',
61 'amphibian:FOODON_03411624',
62 'amphibian or reptile food product:FOODON_00002200',
63 'animal based refined or partially-refined food product:FOODON_00001595',
64 'avian egg food product:FOODON_00001105',
65 'avian food product:FOODON_001251',
66 'bakery food product:FOODON_00001626',
67 'cell-based technology food product:FOODON_00003376',
68 'dairy food product:FOODON_00001256',
69 'dietary supplement:FOODON_03401298',
70 'fish egg food product:FOODON_00001250',
71 'fish food product:FOODON_00001248',
72 'food product analog:FOODON_00001871',
73 'food product component:FOODON_00001714',
74 'fungus food product:FOODON_00001143',
75 'game animal food product:FOODON_00002477',
76 'insect food product:FOODON_00001177',
77 'meat food product:FOODON_00002477',
78 'microbial food product:FOODON_00001145',
79 'plant food product:FOODON_00001015',
80 'poultry food product:FOODON_00001283',
81 'prepared food product:FOODON_00001180',
82 'processed food product:FOODON_03311737',
83 'reptile egg food product:FOODON_00002199',
84 'seafood product:FOODON_00001046',
85 'shellfish food product:FOODON_00001293',
86 'soup food product:FOODON_00002257',
87 'sustainable agriculture food product:FOODON_00003375',
88 'vegetarian food product:FOODON_00003194',
89 'vertebrate animal food product:FOODON_00001092',
90 ]
91
92 fo_quality = ['food (acidified):FOODON_03301625',
93 'food (adulterated):FOODON_00003367',
94 'food (baked):FOODON_00002456',
95 'food (batter-coated):FOODON_00002662',
96 'food (blanched):FOODON_00002767',
97 'food (blend):FOODON_00003889',
98 'food (boiled):FOODON_00002688',
99 'food (breaded):FOODON_00002661',
100 'food (broiled or grilled):FOODON_00002647',
101 'food (canned):FOODON_00002418',
102 'food (chilled):FOODON_00002642',
103 'food (chopped):FOODON_00002777',
104 'food (cleaned):FOODON_00002708',
105 'food (colored):FOODON_00002650',
106 'food (comminuted):FOODON_00002754',
107 'food (cooked):FOODON_00001181',
108 'food (deep-fried):FOODON_03307052',
109 'food (dehydrated):FOODON_00002643',
110 'food (dried):FOODON_03307539',
111 'food (fat or oil coated):FOODON_03460233',
112 'food (fermented):FOODON_00001258',
113 'food (filled):FOODON_00002644',
114 'food (flavored):FOODON_00002646',
115 'food (freeze-dried):FOODON_03301752',
116 'food (fresh):FOODON_00002457',
117 'food (fried):FOODON_00002660',
118 'food (frozen):FOODON_03302148',
119 'food (genetically-modified):FOODON_03530251',
120 'food (ground):FOODON_00002713',
121 'food (harvested):FOODON_00003398',
122 'food (heat treated):FOODON_03316043',
123 'food (hulled):FOODON_00002720',
124 'food (hydrolized):FOODON_00002653',
125 'food (irradiated):FOODON_03305364',
126 'food (juiced):FOODON_00003499',
127 'food (liquid):FOODON_03430130',
128 'food (milled):FOODON_00002649',
129 'food (not genetically-modified):FOODON_00003379',
130 'food (organically grown):FOODON_03306690',
131 'food (packaged):FOODON_00002739',
132 'food (packed in high pressurised containers):FOODON_03317139',
133 'food (pan-fried):FOODON_00002463',
134 'food (paste):FOODON_00003887',
135 'food (pasteurized):FOODON_00002654',
136 'food (peeled):FOODON_00002655',
137 'food (pickled):FOODON_00001079',
138 'food (powdered):FOODON_00002976',
139 'food (precooked):FOODON_00002971',
140 'food (precooked, frozen):FOODON_03305323',
141 'food (preserved):FOODON_00002158',
142 'food (puffed):FOODON_00002656',
143 'food (raw):FOODON_03311126',
144 'food (rehydrated):FOODON_00002755',
145 'food (roasted):FOODON_00002744',
146 'food (salted):FOODON_03460173',
147 'food (seasoned):FOODON_00002733',
148 'fruit (seedless):FOODON_00003461',
149 'food (semiliquid):FOODON_03430103',
150 'food (semisolid):FOODON_03430144',
151 'food (sliced):FOODON_00002455',
152 'food (smoked or smoke-flavored):FOODON_03460172',
153 'food (solid):FOODON_03430151',
154 'food (spoiled):FOODON_00003366',
155 'food (starch or flour thickened):FOODON_03315268',
156 'food (steamed):FOODON_00002657',
157 'food (sugar-free):FOODON_03315838',
158 'food (textured):FOODON_00002658',
159 'food (toasted):FOODON_00002659',
160 'food (unprocessed):FOODON_03316056',
161 'food (unstandardized):FOODON_03315636',
162 ]
163
164 fo_organism = ['algae:FOODON_03411301',
165 'animal:FOODON_00003004',
166 'fungus:FOODON_03411261',
167 'lichen:FOODON_03412345',
168 'whole plant:PO_0000003',
169 ]
170
171 ncbi_taxon = ['Actinopterygii:NCBITaxon_7898', #mix of taxon types
172 'Ecdysozoa:NCBITaxon_1206794',
173 'Echinodermata:NCBITaxon_7586',
174 'Fungi:NCBITaxon_4751',
175 'Spiralia:NCBITaxon_2697495',
176 'Viridiplantae:NCBITaxon_33090',
177 'Amphibia:NCBITaxon_8292',
178 #'Sauropsida:NCBITaxon_8457',
179 'Aves:NCBITaxon_8782',
180 'Crocodylia:NCBITaxon_1294634',
181 'Testudinata:NCBITaxon_2841271',
182 'Lepidosauria:NCBITaxon_8504',
183 #'Mammalia:NCBITaxon_40674',
184 'Artiodactyla:NCBITaxon_91561',
185 'Carnivora:NCBITaxon_33554',
186 'Chiroptera:NCBITaxon_9397',
187 'Chrysochloridae:NCBITaxon_9389',
188 'Eulipotyphla:NCBITaxon_9362',
189 'Hyracoidea:NCBITaxon_9810',
190 'Macroscelidea:NCBITaxon_28734',
191 'Metatheria:NCBITaxon_9263',
192 'Ornithorhynchidae:NCBITaxon_9256',
193 'Perissodactyla:NCBITaxon_9787',
194 'Pholidota:NCBITaxon_9971',
195 'Primates:NCBITaxon_9443',
196 'Proboscidea:NCBITaxon_9779',
197 'Rodentia:NCBITaxon_9989',
198 'Sirenia:NCBITaxon_9774',
199 'Tachyglossidae:NCBITaxon_9259',
200 'Tenrecidae:NCBITaxon_9369',
201 'Tubulidentata:NCBITaxon_9815',
202 'Xenarthra:NCBITaxon_9348',
203 ]
204
205 arg_bins = {#'fo_consumer':fo_consumer,
206 'fo_product':fo_product,
207 'fo_quality':fo_quality,
208 'fo_organism':fo_organism,
209 'ncbi_taxon':ncbi_taxon,
210 }