Explorer: Pathways are not available for some compounds

[jakhag]

In many cases the pathways for compounds are not loading.
E.g. Lisinopril, Metformin, Coumarin, Aciclovir, ...
See here: http://alpha.openphacts.org:3001/compounds/pathways?uri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_43755

Sometimes they are available (but incomplete):
E.g. Caffeine, Menadione
http://alpha.openphacts.org:3001/compounds/pathways?uri=http%3A%2F%2Frdf.ebi.ac.uk%2Fresource%2Fchembl%2Fmolecule%2FCHEMBL113
(3 of 13 results loaded)

Probably related to this issue?
#373

[randykerber]

The search for CHEBI_4375 looks like it creates the following LDA calls:

http://alpha.openphacts.org:3002/compound?_format=json&app_key=cffc292726627ffc50ece1dccd15aeaf&app_id=161aeb7d&uri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_43755
http://alpha.openphacts.org:3002/pathways/byCompound/count?_format=json&app_key=cffc292726627ffc50ece1dccd15aeaf&app_id=161aeb7d&uri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_43755
http://alpha.openphacts.org:3002/pathways/byCompound?_format=json&app_key=cffc292726627ffc50ece1dccd15aeaf&app_id=161aeb7d&uri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_43755&_page=1&_pageSize=50
http://alpha.openphacts.org:3002/pathway?_format=json&app_key=cffc292726627ffc50ece1dccd15aeaf&app_id=161aeb7d&uri=http%3A%2F%2Fidentifiers.org%2Fwikipathways%2FWP2729

What's the first one who's results look wrong?

[randykerber]

Search for CHEMBL113 results in following LDA calls:

http://alpha.openphacts.org:3002/pathways/byCompound?_format=json&app_key=cffc292726627ffc50ece1dccd15aeaf&app_id=161aeb7d&uri=http%3A%2F%2Frdf.ebi.ac.uk%2Fresource%2Fchembl%2Fmolecule%2FCHEMBL113&_page=1&_pageSize=50
http://alpha.openphacts.org:3002/pathways/byCompound/count?_format=json&app_key=cffc292726627ffc50ece1dccd15aeaf&app_id=161aeb7d&uri=http%3A%2F%2Frdf.ebi.ac.uk%2Fresource%2Fchembl%2Fmolecule%2FCHEMBL113
http://alpha.openphacts.org:3002/pathway?_format=json&app_key=cffc292726627ffc50ece1dccd15aeaf&app_id=161aeb7d&uri=http%3A%2F%2Fidentifiers.org%2Fwikipathways%2FWP1825
http://alpha.openphacts.org:3002/pathway?_format=json&app_key=cffc292726627ffc50ece1dccd15aeaf&app_id=161aeb7d&uri=http%3A%2F%2Fidentifiers.org%2Fwikipathways%2FWP3119
http://alpha.openphacts.org:3002/pathway?_format=json&app_key=cffc292726627ffc50ece1dccd15aeaf&app_id=161aeb7d&uri=http%3A%2F%2Fidentifiers.org%2Fwikipathways%2FWP707
http://alpha.openphacts.org:3002/pathway?_format=json&app_key=cffc292726627ffc50ece1dccd15aeaf&app_id=161aeb7d&uri=http%3A%2F%2Fidentifiers.org%2Fwikipathways%2FWP3633
http://alpha.openphacts.org:3002/pathway?_format=json&app_key=cffc292726627ffc50ece1dccd15aeaf&app_id=161aeb7d&uri=http%3A%2F%2Fidentifiers.org%2Fwikipathways%2FWP3119
http://alpha.openphacts.org:3002/pathways/byCompound/count?_format=json&app_key=cffc292726627ffc50ece1dccd15aeaf&app_id=161aeb7d&uri=http%3A%2F%2Frdf.ebi.ac.uk%2Fresource%2Fchembl%2Fmolecule%2FCHEMBL113
http://alpha.openphacts.org:3002/pathway?_format=json&app_key=cffc292726627ffc50ece1dccd15aeaf&app_id=161aeb7d&uri=http%3A%2F%2Fidentifiers.org%2Fwikipathways%2FWP1825
http://alpha.openphacts.org:3002/pathways/byCompound?_format=json&app_key=cffc292726627ffc50ece1dccd15aeaf&app_id=161aeb7d&uri=http%3A%2F%2Frdf.ebi.ac.uk%2Fresource%2Fchembl%2Fmolecule%2FCHEMBL113&_page=1&_pageSize=50
http://alpha.openphacts.org:3002/pathway?_format=json&app_key=cffc292726627ffc50ece1dccd15aeaf&app_id=161aeb7d&uri=http%3A%2F%2Fidentifiers.org%2Fwikipathways%2FWP707
http://alpha.openphacts.org:3002/pathway?_format=json&app_key=cffc292726627ffc50ece1dccd15aeaf&app_id=161aeb7d&uri=http%3A%2F%2Fidentifiers.org%2Fwikipathways%2FWP3633
http://alpha.openphacts.org:3002/pathways/byCompound?_format=json&app_key=cffc292726627ffc50ece1dccd15aeaf&app_id=161aeb7d&uri=http%3A%2F%2Frdf.ebi.ac.uk%2Fresource%2Fchembl%2Fmolecule%2FCHEMBL113&_page=1&_pageSize=50
http://alpha.openphacts.org:3002/pathway?_format=json&app_key=cffc292726627ffc50ece1dccd15aeaf&app_id=161aeb7d&uri=http%3A%2F%2Fidentifiers.org%2Fwikipathways%2FWP1530
http://alpha.openphacts.org:3002/pathway?_format=json&app_key=cffc292726627ffc50ece1dccd15aeaf&app_id=161aeb7d&uri=http%3A%2F%2Fidentifiers.org%2Fwikipathways%2FWP2087
http://alpha.openphacts.org:3002/pathway?_format=json&app_key=cffc292726627ffc50ece1dccd15aeaf&app_id=161aeb7d&uri=http%3A%2F%2Fidentifiers.org%2Fwikipathways%2FWP1879
http://alpha.openphacts.org:3002/pathway?_format=json&app_key=cffc292726627ffc50ece1dccd15aeaf&app_id=161aeb7d&uri=http%3A%2F%2Fidentifiers.org%2Fwikipathways%2FWP1824
http://alpha.openphacts.org:3002/compound?_format=json&app_key=cffc292726627ffc50ece1dccd15aeaf&app_id=161aeb7d&uri=http%3A%2F%2Frdf.ebi.ac.uk%2Fresource%2Fchembl%2Fmolecule%2FCHEMBL113
http://alpha.openphacts.org:3002/pathway?_format=json&app_key=cffc292726627ffc50ece1dccd15aeaf&app_id=161aeb7d&uri=http%3A%2F%2Fidentifiers.org%2Fwikipathways%2FWP1824
http://alpha.openphacts.org:3002/pathway?_format=json&app_key=cffc292726627ffc50ece1dccd15aeaf&app_id=161aeb7d&uri=http%3A%2F%2Fidentifiers.org%2Fwikipathways%2FWP1879
http://alpha.openphacts.org:3002/pathway?_format=json&app_key=cffc292726627ffc50ece1dccd15aeaf&app_id=161aeb7d&uri=http%3A%2F%2Fidentifiers.org%2Fwikipathways%2FWP1530
http://alpha.openphacts.org:3002/pathway?_format=json&app_key=cffc292726627ffc50ece1dccd15aeaf&app_id=161aeb7d&uri=http%3A%2F%2Fidentifiers.org%2Fwikipathways%2FWP2087
http://alpha.openphacts.org:3002/patent/entities/count.rdfjson?uri=http%3A%2F%2Frdf.ebi.ac.uk%2Fresource%2Fsurechembl%2Fpatent%2FEP-1339685-A2&_metadata=all%2Cviews%2Cformats%2Cexecution%2Cbindings%2Csite

[Chris-Evelo]

Not really an answer to your question. But please note that while many pathways contain natural metabolites (e.g. amino acids) as compounds only very few of them contain drugs. So if you really want to find all pathways that contain targets for a drug you would normally first search the target (using ChEMBL) and then pathways that contain that target. Or... Did we actually include that in the pathway by compound call?