Some node expansion ontologies are not monoprefix #698
Comments
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Placing this one on the milestone, though it's uncertain if we'll be able to fix it in time, and it seems to happen only rarely. |
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Generating a list of prefixes for the files that use multiple prefixes: hp-parsed.json: PR, BFO, NCBITaxon, UBERON, SO, CL, RO, CHEBI, MAXO, OBI, MPATH, CARO, GO, NBO, HP, HsapDv, ENVO, PATO Looks like it's just these two that are non-monoprefix. Note: both contain mappings where the parent is not HP or MONDO, so we can't just check the original vs expanded to reason about which file it came from. |
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Hmm...based on the old posts, we only intended to support 6 ontologies at the time. Hence my post on provenance for subclass edges here. I'm not sure how the descendant-relationships were decided / parsed, and whether it's valid for all those other ontologies to be included. I agree with the discussion in the lab slack thread that for now, we could remove the non-mondo IDs from the mondo file and the non-hp IDs from the hp file... |
tokebe
added
On CI
Some of the ontologies used by present node expansion do not use purely the prefix for which they are named, which results in rare cases where BTE will fail a query with TypeError as the subclass edge-sourcing code is unable to handle this situation. Further, the subclassing code uses a base assumption that the ontology source will line up with the prefix, which clearly is not correct for these cases.
We need to figure out a better solution for subclass edge sourcing that avoids running into this problem.
The following (unfortunately long) query can replicate the error:
{ "message": { "query_graph": { "edges": { "edge_1": { "attribute_constraints": [], "object": "disease", "predicates": [ "biolink:ameliorates" ], "qualifier_constraints": [], "subject": "h" } }, "nodes": { "disease": { "categories": [ "biolink:DiseaseOrPhenotypicFeature" ], "constraints": [], "ids": [ "UMLS:C1847014", "UMLS:C2751329", "UMLS:C0001485", "UMLS:C0009450", "UMLS:C0020538", "UMLS:C0497247", "UMLS:C0007194", "UMLS:C4551472", "UMLS:C0020621", "UMLS:C0683388", "UMLS:C1514284", "UMLS:C1971021", "UMLS:C0019693", "UMLS:C0034186", "UMLS:C0020476", "UMLS:C0021400", "UMLS:C0029342", "UMLS:C0155871", "UMLS:C0042331", "UMLS:C0149931", "UMLS:C0744641", "UMLS:C0039503", "UMLS:C1568272", "UMLS:C0042384", "OMIM:MTHU037025", "UMLS:C0019080", "UMLS:C0041671", "UMLS:C0339002", "UMLS:C1263846", "UMLS:C1321905", "UMLS:C0155626", "UMLS:C0029827", "UMLS:C0036323", "UMLS:C0006261", "UMLS:C0006266", "UMLS:C0275524", "UMLS:C0729584", "UMLS:C0022658", "UMLS:C1408258", "UMLS:C0036983", "UMLS:C0600327", "UMLS:CN204669", "UMLS:C0003862", "UMLS:C0857177", "UMLS:C0262564", "UMLS:C0340293", "UMLS:C0003864", "UMLS:C0574941", "UMLS:C0010054", "UMLS:C0010068", "UMLS:C0264694", "UMLS:C1533195", "UMLS:C1956346", "UMLS:C0085111", "UMLS:C0205700", "UMLS:C0700053", "UMLS:C3495498", "UMLS:C0019572", "UMLS:C0031572", "UMLS:C0011881", "UMLS:C0006625", "UMLS:C0563273", "UMLS:C0038220", "UMLS:C1417172", "UMLS:C1144191", "UMLS:C3815188", "UMLS:C0038999", "MONDO:0021668", "UMLS:C1334180", "UMLS:C0342647", "UMLS:C2748783", "UMLS:C0034734", "UMLS:C0034735", "UMLS:C1282916", "GO:0006954", "UMLS:C0263854", "UMLS:C1384641", "UMLS:C0020445", "UMLS:C0549399", "UMLS:C0745103", "UMLS:C3276941", "UMLS:C0007222", "UMLS:C0243050", "UMLS:C0728936", "UMLS:C0042075", "UMLS:C1335051", "UMLS:C2675113", "MONDO:0016158", "UMLS:C3495801", "UMLS:C4050407", "UMLS:C0040820", "UMLS:C0678222", "UMLS:C0014118", "UMLS:C0375268", "UMLS:C0020649", "UMLS:C0032285", "MESH:C072778", "UMLS:C0009443", "GO:0000500", "UMLS:C0023772", "UMLS:C0154251", "UMLS:C0027796", "UMLS:C0751373", "UMLS:C1262477", "UMLS:C0001623", "UMLS:C0405580", "UMLS:C0376286", "UMLS:C1510471", "OMIM:MTHU027819", "UMLS:C1868649", "UMLS:C1868650", "UMLS:C1868651", "UMLS:C0024138", "UMLS:C5574816", "UMLS:C0006444", "UMLS:C0027051", "UMLS:C0003123", "UMLS:C1971624", "UMLS:C0024141", "UMLS:C1835309", "UMLS:C1366529", "UMLS:C3493221", "UMLS:C1836230", "UMLS:C1836231", "UMLS:C1836232", "UMLS:CN282826", "UMLS:C0730345", "UMLS:C1654921", "UMLS:C0236773", "UMLS:C0853193", "UMLS:C0011847", "UMLS:C0011849", "UMLS:C2347126", "UMLS:C0027404", "MONDO:0044684", "UMLS:C4553904", "UMLS:C0263666", "OMIM:MTHU039158", "OMIM:MTHU050872", "UMLS:C0039254", "UMLS:C0152073", "UMLS:C0003838", "UMLS:C0031115", "UMLS:C0085096", "UMLS:C0264995", "UMLS:C0750145", "UMLS:C1704436", "UMLS:C4025272", "UMLS:C4531019", "UMLS:C0029574", "UMLS:C0037268", "UMLS:C0037274", "UMLS:C0037277", "UMLS:C0002170", "UMLS:C0004096", "UMLS:C0085129", "UMLS:C0340062", "UMLS:C1833269", "UMLS:C1833270", "UMLS:C1869116", "UMLS:C3714497", "UBERON:0035938", "UMLS:C0020626", "UMLS:C0600139", "UMLS:C0016658", "MONDO_0004197", "UMLS:C0023467", "UMLS:C3275959", "UMLS:C0595948", "UMLS:C0162550", "UMLS:C0007820", "UMLS:C5203670", "UMLS:C0029877", "UMLS:C0699744", "UMLS:C0014130", "UMLS:C4025823", "UMLS:C0393735", "UMLS:C0018801", "UMLS:C0018802", "UMLS:C0264716", "UMLS:C0002103", "UMLS:C0847614", "UMLS:C2607914", "EFO:0003913", "UMLS:C0039103", "UMLS:C4521004", "UMLS:C1318485", "UMLS:C4520976", "UMLS:CN205145", "UMLS:C0023890", "UMLS:C0036690", "UMLS:C0243026", "UMLS:C0024117", "UMLS:C1527303", "UMLS:C0023646", "UMLS:C0149514", "UMLS:C0339289", "UMLS:C0349702", "UMLS:C1959583", "UMLS:CN236639", "UMLS:C0746102", "MESH:D003094", "UMLS:C0003851", "UMLS:C0003872", "UMLS:C0040021", "UMLS:C0009766", "UMLS:C0004238", "UMLS:C0149721", "UMLS:C0020517", "UMLS:C1527304", "UMLS:C3539909", "UMLS:C0001175", "UMLS:C0012242", "UMLS:C0017178", "UMLS:C4023588", "MONDO:0009410", "UBERON:0002185", "UMLS:C0018081", "UMLS:C0031046", "UMLS:C0033860", "UMLS:C0262985", "UMLS:C0004623", "UMLS:C0003873", "UMLS:C1306838", "UMLS:C1833448", "UMLS:C0085074", "UMLS:C0013604", "UMLS:C0268000", "UMLS:C0085605", "UMLS:C1306571", "UMLS:C0038013", "UMLS:C0038020", "UMLS:C0155877", "UMLS:C0013990", "UMLS:C0029607", "UMLS:C0034067", "UMLS:C0040460", "UMLS:C0038454", "UMLS:C0002965", "UMLS:C0086666", "UMLS:C0036341", "UMLS:C4538533", "UMLS:C0282687", "UMLS:C0008677", "UMLS:C0021603", "UMLS:C0917801", "UMLS:C4477058", "UMLS:C3277428", "UMLS:C0007193", "UMLS:C0029408", "UMLS:C0157946", "UMLS:C0013595" ], "is_set": false }, "h": { "categories": [ "biolink:ChemicalEntity" ], "constraints": [], "ids": [ "UMLS:C0032952", "UNII:ULS5I8J03O", "DRUGBANK:DB01234", "UMLS:C0069803", "UMLS:C0851344", "UMLS:C0025815", "UMLS:C0048306", "UMLS:C0076653", "UMLS:C0544368", "UNII:DJJ95FJP1H", "UMLS:C0016299", "DRUGBANK:DB00324", "UMLS:C0020268", "DRUGBANK:DB00823", "UMLS:C0022635", "UMLS:C0907850", "UMLS:C0058753", "UMLS:C4255884", "UMLS:C0014912", "UMLS:C0011689", "UMLS:C0065864", "DRUGBANK:DB00620", "UMLS:C0039601", "UMLS:C0304612", "UMLS:C0012228", "DRUGBANK:DB00896", "UMLS:C0065879", "UMLS:C0961209", "UMLS:C0006674", "UMLS:C0016280", "UMLS:C0068992", "UMLS:C0038149", "UMLS:C0068395", "UMLS:C0073983", "UMLS:C0065767", "UMLS:C0012319", "UMLS:C0044410", "DRUGBANK:DB01108", "UMLS:C0056391", "UMLS:C1135150", "UMLS:C0016374", "UMLS:C0008992", "UMLS:C0055895", "UMLS:C0249582", "UMLS:C0065865", "UMLS:C0073631", "UMLS:C0051556", "UMLS:C0013340", "UMLS:C4256093", "UMLS:C0031406", "UMLS:C0060389", "UMLS:C0036071", "UMLS:C0054201", "UMLS:C0039600", "UMLS:C0032950", "UMLS:C0025152", "DRUGBANK:DB00838", "UMLS:C0360534", "DRUGBANK:DB00663", "UMLS:C1948374", "UMLS:C1619629", "UMLS:C0004905", "UMLS:C0012258", "UMLS:C0006949", "DRUGBANK:DB00596", "UMLS:C0016301", "UMLS:C0030454", "UMLS:C0004057", "UMLS:C0033429", "UMLS:C0005308", "UMLS:C0022860", "UMLS:C0069751", "UMLS:C0068788", "UMLS:C0025826", "UMLS:C1449554", "UMLS:C0071836", "PUBCHEM.COMPOUND:54684589", "PUBCHEM.COMPOUND:101611440", "PUBCHEM.COMPOUND:54708862", "PUBCHEM.COMPOUND:64738", "UMLS:C0016366", "UMLS:C0016298", "DRUGBANK:DB00682", "UMLS:C0002238", "UMLS:C0520442", "DRUGBANK:DB08970", "UMLS:C0006657", "UMLS:C2713074", "DRUGBANK:DB00764", "UMLS:C0043822", "DRUGBANK:DB01420", "UMLS:C0025042", "UMLS:C1289957", "UMLS:C0033308", "UMLS:C4256086", "UMLS:C4256087", "UMLS:C0772364", "UMLS:C0060501", "UMLS:C1646276", "UMLS:C0053289", "UMLS:C0961485", "UMLS:C0060156", "UMLS:C0015837", "UMLS:C0068397", "UMLS:C0010961", "DRUGBANK:DB00712", "UMLS:C0002158", "UMLS:C0008024", "UMLS:C0117996", "UMLS:C0023566", "UMLS:C0006881", "UMLS:C1703665", "UMLS:C0056855", "UMLS:C0058004", "UMLS:C0011707", "UMLS:C0042105", "UMLS:C0011705", "UMLS:C0037982", "UMLS:C0014695", "UMLS:C0014696", "UMLS:C0042866", "UMLS:C0036079", "UMLS:C0029995", "UMLS:C0012265", "UMLS:C0028356" ], "is_set": false } } } }, "submitter": "infores:aragorn" }Tagging @colleenXu @ericz1803
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