--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lexmapr/definitions.py	Wed Aug 31 14:32:07 2022 -0400
@@ -0,0 +1,210 @@
+"""Static definitions"""
+
+import os
+
+
+# root path
+ROOT = os.path.dirname(__file__)
+
+# URL to list of OLS ontologies where download link is given
+embl_ontologies = 'https://www.ebi.ac.uk/ols/ontologies'
+
+# beginning of URL to ontology PURL
+purl_link = 'http://purl.obolibrary.org/obo/'
+
+# directory for downloaded OWL files
+owl_dir = 'lexmapr/owl_files'
+
+# path to database with synonyms from predefined resources and from OWL files
+synonym_db = 'lexmapr/owl_files/label_synonyms.db'
+
+# path to database with all ontologies of interest
+ontol_db = 'lexmapr/owl_files/ontol_table.db'
+
+
+# ontologies of interest
+ontol_interest = [#'BFO',
+                  #'CHEBI',
+                  #'ENVO',
+                  'FOODON',
+                  #'GENEPIO',
+                  'NCBITAXON', # NCBITaxon is not valid as of April 2022
+                  #'OGMS',
+                  #'PATO',
+                  #'PCO',
+                  #'UBERON',
+                 ]
+
+# ontology accessions that do not have labels or are placeholders as of April 2022
+# will skip in database building
+missing_ontol_labels = ['GENEPIO_0001367','GENEPIO_0001368','GENEPIO_0001369','GENEPIO_0001370',
+                        'GENEPIO_0001372','GENEPIO_0001373','_MIAA_0000021',
+                       ]
+
+# terms indicating that the metadata was not given/collected; will output empty results
+not_provided = ['not applicable','unknown','n a','not provided','not available','miscellaneous',
+                'not collected','missing','unidentified','unknown','none','unamed','other',
+                'undetermined','not known','no history given','no source specified','null',
+                'unspecified','not reported','not available not collected','not isolated',
+                'not available','not provided','xxx','mising','misng','other','unidentified',
+                'not determined other','reported later','intact unknown','not determined',
+                'not ascertained','unk','nd','nd others','nd other','etc','na','',' ',
+                'not supplied','not specified',
+               ]
+
+# below are bin definitions
+# TODO: food consumer group:FOODON_03510136 changed, formatted as '* as food consumer'
+#       can collect as 'for *' in text?
+#fo_consumer = []
+
+fo_product = ['algal food product:FOODON_00001184',
+              'amphibian:FOODON_03411624',
+              'amphibian or reptile food product:FOODON_00002200',
+              'animal based refined or partially-refined food product:FOODON_00001595',
+              'avian egg food product:FOODON_00001105',
+              'avian food product:FOODON_001251',
+              'bakery food product:FOODON_00001626',
+              'cell-based technology food product:FOODON_00003376',
+              'dairy food product:FOODON_00001256',
+              'dietary supplement:FOODON_03401298',
+              'fish egg food product:FOODON_00001250',
+              'fish food product:FOODON_00001248',
+              'food product analog:FOODON_00001871',
+              'food product component:FOODON_00001714',
+              'fungus food product:FOODON_00001143',
+              'game animal food product:FOODON_00002477',
+              'insect food product:FOODON_00001177',
+              'meat food product:FOODON_00002477',
+              'microbial food product:FOODON_00001145',
+              'plant food product:FOODON_00001015',
+              'poultry food product:FOODON_00001283',
+              'prepared food product:FOODON_00001180',
+              'processed food product:FOODON_03311737',
+              'reptile egg food product:FOODON_00002199',
+              'seafood product:FOODON_00001046',
+              'shellfish food product:FOODON_00001293',
+              'soup food product:FOODON_00002257',
+              'sustainable agriculture food product:FOODON_00003375',
+              'vegetarian food product:FOODON_00003194',
+              'vertebrate animal food product:FOODON_00001092',
+             ]
+
+fo_quality = ['food (acidified):FOODON_03301625',
+              'food (adulterated):FOODON_00003367',
+              'food (baked):FOODON_00002456',
+              'food (batter-coated):FOODON_00002662',
+              'food (blanched):FOODON_00002767',
+              'food (blend):FOODON_00003889',
+              'food (boiled):FOODON_00002688',
+              'food (breaded):FOODON_00002661',
+              'food (broiled or grilled):FOODON_00002647',
+              'food (canned):FOODON_00002418',
+              'food (chilled):FOODON_00002642',
+              'food (chopped):FOODON_00002777',
+              'food (cleaned):FOODON_00002708',
+              'food (colored):FOODON_00002650',
+              'food (comminuted):FOODON_00002754',
+              'food (cooked):FOODON_00001181',
+              'food (deep-fried):FOODON_03307052',
+              'food (dehydrated):FOODON_00002643',
+              'food (dried):FOODON_03307539',
+              'food (fat or oil coated):FOODON_03460233',
+              'food (fermented):FOODON_00001258',
+              'food (filled):FOODON_00002644',
+              'food (flavored):FOODON_00002646',
+              'food (freeze-dried):FOODON_03301752',
+              'food (fresh):FOODON_00002457',
+              'food (fried):FOODON_00002660',
+              'food (frozen):FOODON_03302148',
+              'food (genetically-modified):FOODON_03530251',
+              'food (ground):FOODON_00002713',
+              'food (harvested):FOODON_00003398',
+              'food (heat treated):FOODON_03316043',
+              'food (hulled):FOODON_00002720',
+              'food (hydrolized):FOODON_00002653',
+              'food (irradiated):FOODON_03305364',
+              'food (juiced):FOODON_00003499',
+              'food (liquid):FOODON_03430130',
+              'food (milled):FOODON_00002649',
+              'food (not genetically-modified):FOODON_00003379',
+              'food (organically grown):FOODON_03306690',
+              'food (packaged):FOODON_00002739',
+              'food (packed in high pressurised containers):FOODON_03317139',
+              'food (pan-fried):FOODON_00002463',
+              'food (paste):FOODON_00003887',
+              'food (pasteurized):FOODON_00002654',
+              'food (peeled):FOODON_00002655',
+              'food (pickled):FOODON_00001079',
+              'food (powdered):FOODON_00002976',
+              'food (precooked):FOODON_00002971',
+              'food (precooked, frozen):FOODON_03305323',
+              'food (preserved):FOODON_00002158',
+              'food (puffed):FOODON_00002656',
+              'food (raw):FOODON_03311126',
+              'food (rehydrated):FOODON_00002755',
+              'food (roasted):FOODON_00002744',
+              'food (salted):FOODON_03460173',
+              'food (seasoned):FOODON_00002733',
+              'fruit (seedless):FOODON_00003461',
+              'food (semiliquid):FOODON_03430103',
+              'food (semisolid):FOODON_03430144',
+              'food (sliced):FOODON_00002455',
+              'food (smoked or smoke-flavored):FOODON_03460172',
+              'food (solid):FOODON_03430151',
+              'food (spoiled):FOODON_00003366',
+              'food (starch or flour thickened):FOODON_03315268',
+              'food (steamed):FOODON_00002657',
+              'food (sugar-free):FOODON_03315838',
+              'food (textured):FOODON_00002658',
+              'food (toasted):FOODON_00002659',
+              'food (unprocessed):FOODON_03316056',
+              'food (unstandardized):FOODON_03315636',
+             ]
+
+fo_organism = ['algae:FOODON_03411301',
+               'animal:FOODON_00003004',
+               'fungus:FOODON_03411261',
+               'lichen:FOODON_03412345',
+               'whole plant:PO_0000003',
+              ]
+
+ncbi_taxon = ['Actinopterygii:NCBITaxon_7898', #mix of taxon types
+              'Ecdysozoa:NCBITaxon_1206794',
+              'Echinodermata:NCBITaxon_7586',
+              'Fungi:NCBITaxon_4751',
+              'Spiralia:NCBITaxon_2697495',
+              'Viridiplantae:NCBITaxon_33090',
+              'Amphibia:NCBITaxon_8292',
+              #'Sauropsida:NCBITaxon_8457',
+              'Aves:NCBITaxon_8782',
+              'Crocodylia:NCBITaxon_1294634',
+              'Testudinata:NCBITaxon_2841271',
+              'Lepidosauria:NCBITaxon_8504',
+              #'Mammalia:NCBITaxon_40674',
+              'Artiodactyla:NCBITaxon_91561',
+              'Carnivora:NCBITaxon_33554',
+              'Chiroptera:NCBITaxon_9397',
+              'Chrysochloridae:NCBITaxon_9389',
+              'Eulipotyphla:NCBITaxon_9362',
+              'Hyracoidea:NCBITaxon_9810',
+              'Macroscelidea:NCBITaxon_28734',
+              'Metatheria:NCBITaxon_9263',
+              'Ornithorhynchidae:NCBITaxon_9256',
+              'Perissodactyla:NCBITaxon_9787',
+              'Pholidota:NCBITaxon_9971',
+              'Primates:NCBITaxon_9443',
+              'Proboscidea:NCBITaxon_9779',
+              'Rodentia:NCBITaxon_9989',
+              'Sirenia:NCBITaxon_9774',
+              'Tachyglossidae:NCBITaxon_9259',
+              'Tenrecidae:NCBITaxon_9369',
+              'Tubulidentata:NCBITaxon_9815',
+              'Xenarthra:NCBITaxon_9348',              
+             ]
+
+arg_bins = {#'fo_consumer':fo_consumer,
+            'fo_product':fo_product,
+            'fo_quality':fo_quality,
+            'fo_organism':fo_organism,
+            'ncbi_taxon':ncbi_taxon,
+           }