search

openphacts / GLOBAL

Global project issues [private for now. owner lee harland]
3 stars 0 forks source link

Explorer: Pathways are not available for some compounds #393

Open jakhag opened 7 years ago

jakhag commented 7 years ago

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? https://github.com/openphacts/GLOBAL/issues/373

randykerber commented 7 years ago

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 commented 7 years ago

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 commented 7 years ago

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?