Merge pull request #1308 from biolink/infores_updates

deprecating sources via conversation in slack about biggim, bigclam, and clinical-profiles, also fixes #1291

infores_catalog_nodes.tsv

@@ -44,9 +44,9 @@ released	Automat Ubergraph Nonredundant	infores:automat-ubergraph-nonredundant	h
 released	Automat Viral Proteome	infores:automat-viral-protome	https://github.com/NCATSTranslator/Translator-All/wiki/Automat#viral-proteome		"A graph consisting of viral proteins from UniProt, connected by similarity edges from UniRef."
 released	Basic Formal Ontology	infores:bfo	http://www.obofoundry.org/ontology/bfo.html	BFO	
 released	Bgee	infores:bgee	https://bgee.org/	BGEE	
-released	Big Cell Line Association Miner	infores:bigclam	https://github.com/PriceLab/translator-bigquery-api	BigClam	
+deprecated	Big Cell Line Association Miner	infores:bigclam	https://github.com/PriceLab/translator-bigquery-api	BigClam	
 released	BiGG Models	infores:bigg-models	http://bigg.ucsd.edu/	BIGG	a knowledgebase of genome-scale metabolic network reconstructions
-released	Big Gene Interaction Miner	infores:biggim	https://github.com/PriceLab/translator-bigquery-api/	BigGIM	
+deprecated	Big Gene Interaction Miner	infores:biggim	https://github.com/PriceLab/translator-bigquery-api/	BigGIM	
 released	BindingDB	infores:bindingdb	https://www.bindingdb.org	The Binding Database	"BindingDB is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules. As of July 31, 2021, BindingDB contains 41,300 Entries, each with a DOI, containing 2,303,972 binding data for 8,561 protein targets and 995,797 small molecules."
 released	Bio2RDF	infores:bio2rdf	https://bio2rdf.org		
 released	BioCatalogue	infores:biocatalogue			
@@ -102,7 +102,7 @@ released	Chemotext	infores:chemotext	http://chemotext.mml.unc.edu/
 released	Clinital Interpretation of Variants in Cancer	infores:civic	https://civicdb.org/home	CIViC	
 released	Cell Ontology	infores:cl	https://obofoundry.org/ontology/cl.html	CL	
 released	Clinical Genome Resource (ClinGen) 	infores:clingen	https://clinicalgenome.org/		ClinGen is a NIH-funded resource dedicated to building a central resource that defines the clinical relevance of genes and variants for use in precision medicine and research
-released	Clinical Profiles	infores:clinical-profiles			
+deprecated	Clinical Profiles	infores:clinical-profiles			
 released	ClinicalTrials.gov	infores:clinicaltrials	https://clinicaltrials.gov		
 released	ClinVar	infores:clinvar	https://www.ncbi.nlm.nih.gov/clinvar/		"ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence."
 released	Connectivity Map	infores:cmap	https://clue.io/cmap	CMAP	"genome-scale library of cellular signatures that catalogs transcriptional responses to chemical, genetic, and disease perturbation"
@@ -273,6 +273,7 @@ released	PathWhiz	infores:pathwhiz	https://smpdb.ca/pathwhiz
 released	Phenotype and Trait Ontology	infores:pato	http://www.obofoundry.org/ontology/pato.html	PATO	
 released	Phenomics Integrated Ontology	infores:phenio	https://github.com/monarch-initiative/phenio	PHENIO	An ontology for accessing and comparing knowledge concerning phenotypes across species and genetic backgrounds.
 released	Pathosystems Resource Integration Center	infores:patric	https://ngdc.cncb.ac.cn/databasecommons/database/id/230	PATRIC	
+released	Text Mined pharmacogenomic polymorphisms	infores:pgxmine	https://pgxmine.pharmgkb.org/	PGxMine	Text mined pharmacogenomic polymorphisms to assist curation of PharmGKB.	
 released	Physician Data Query (PDQ) (from UMLS)	infores:pdq-umls	https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/PDQ/index.html		
 released	Pfam	infores:pfam	https://www.ebi.ac.uk/interpro		The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs).  Proteins are generally composed of one or more functional regions, commonly termed domains. Different combinations of domains give rise to the diverse range of proteins found in nature. The identification of domains that occur within proteins can therefore provide insights into their function.  Pfam also generates higher-level groupings of related entries, known as clans. A clan is a collection of Pfam entries which are related by similarity of sequence, structure or profile-HMM.  The data presented for each entry is based on the UniProt Reference Proteomes but information on individual UniProtKB sequences can still be found by entering the protein accession. Pfam full alignments are available from searching a variety of databases, either to provide different accessions (e.g. all UniProt and NCBI GI) or different levels of redundancy.
 released	Pharmacotherapy Database	infores:pharmacotherapydb	https://github.com/dhimmel/indications	PharmacotherapyDB	

scripts/verify_infores.py

@@ -3,7 +3,6 @@
 import requests
 import csv
 import time
-from typing import List
 
 INFORES_TSV = os.path.join('infores_catalog_nodes.tsv')
 
@@ -37,11 +36,14 @@ def validate(self):
         with open(INFORES_TSV, 'r') as tsv_file:
             reader = csv.reader(tsv_file, delimiter='\t')
             for line in reader:
-                if line[2] == 'id' or line[3] == '':
+                if len(line) < 5:
+                    raise ValueError("Invalid infores TSV: too few items in a line")
+                if line[2] == 'id' or line[3] == '' or line[0] == 'deprecated':
                     continue
+                # exceptions for resolvable URLs that don't return 200 response for some reason (e.g. require
+                # user to accept a popup before resolving):
                 if line[2] == 'infores:athena' \
                         or line[2] == 'infores:isb-wellness' \
-                        or line[0] == 'deprecated' \
                         or line[2] == 'infores:isb-incov' \
                         or line[2] == 'infores:preppi'  \
                         or line[2] == 'infores:ttd' \
@@ -57,7 +59,7 @@ def validate(self):
                 else:
                     print(line)
                     print("Invalid infores URL:" + line[3] + " for " + line[2])
-                    raise ValueError("Invalid infores URL")
+                    raise ValueError("invalid return code for URL" + line[3] + " for " + line[2])
 
 
 if __name__ == "__main__":