PMIDs in KG2

[acevedol]

From AHM on 4/27, @edeutsch asked for information on PMIDs. How many of our sources are extracting PMID data and are they making it into KG2 edges?

I am looking into it, but also want to check with @saramsey if he might know.

[amykglen]

I ran a query in KG2c to get an idea of how many non-semmeddb sources we get PMIDs from:

match (n)-[e]->(m) where n.publications is not null and not "infores:semmeddb" in e.knowledge_source return distinct e.knowledge_source, count(distinct e) order by count(distinct e) desc

e.knowledge_source	count(distinct e)
["infores:pathwhiz"]	3975444
["infores:drugbank"]	2253707
["infores:ensembl-gene"]	1331738
["infores:hmdb"]	713751
["infores:hmdb", "infores:pathwhiz"]	682382
["infores:diseases"]	594581
["infores:intact"]	267449
["infores:disgenet"]	252930
["infores:goa"]	215042
["infores:pr"]	143262
["infores:ncit"]	119654
["infores:umls-metathesaurus"]	119355
["infores:reactome"]	86940
["infores:mesh"]	85789
["infores:chebi"]	66488
["infores:omim"]	64684
["infores:kegg"]	49562
["infores:diseases", "infores:disgenet"]	44476
["infores:dgidb"]	42807
["infores:uniprot"]	33991
["infores:chembl"]	30207
["infores:drugcentral"]	26789
["infores:go", "infores:go-plus"]	23698
["infores:go"]	23439
["infores:loinc-umls"]	22087
["infores:ncbi-gene", "infores:ensembl-gene", "infores:pr", "infores:uniprot"]	19511
["infores:chebi", "infores:go-plus"]	12105
["infores:go-plus"]	11756
["infores:ordo"]	10864
["infores:fma-umls"]	9626
["infores:disease-ontology"]	9163
["infores:uberon"]	9093
["infores:mondo"]	9020
["infores:mondo", "infores:efo"]	8762
["infores:rxnorm"]	7302
["infores:drugbank", "infores:drugcentral"]	6603
["infores:efo"]	6195
["infores:hpo"]	5075
["infores:fma-obo", "infores:fma-umls"]	4192
["infores:atc-codes-umls"]	2913

[acevedol]

Thank you, Amy!

[edeutsch]

Great! I'm surprised! I just did a query for pathways and got this: https://arax.ncats.io/?r=40441 and see publications associated with a non-SemMedDB edge, so this is great!

[saramsey]

Wow, that was more than I expected. Thank you for the analysis, @amykglen