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UMLS 2020AB post processing issues #201

Closed alexskr closed 2 years ago

alexskr commented 3 years ago

document various issues associated with UMLS2020AB processing

alexskr commented 3 years ago
alexskr commented 3 years ago

a number of ontologies have problems with obsoleteParent. Looks like "Obsolete branch root" owl properly is used instead of the "Obsolete property". Perhaps UI needs to provide a better explanation to reduce this confusion. 

[logs]$ grep obsoleteParent umls2020ab_process_rdf_and_metrics | cut -d '"' -f 2
Submission http://data.bioontology.org/ontologies/AGRO/submissions/3 obsoleteParent http://www.geneontology.org/formats/oboInOwl#ObsoleteClass not found
Submission http://data.bioontology.org/ontologies/IDO/submissions/13 obsoleteParent http://www.geneontology.org/formats/oboInOwl#ObsoleteClass not found
Submission http://data.bioontology.org/ontologies/CHEAR/submissions/15 obsoleteParent http://www.geneontology.org/formats/oboInOwl#ObsoleteClass not found
Submission http://data.bioontology.org/ontologies/ONTONEO-CORE/submissions/1 obsoleteParent local:true not found
Submission http://data.bioontology.org/ontologies/HAKMSVU/submissions/2 obsoleteParent local:University not found
Submission http://data.bioontology.org/ontologies/COGPO/submissions/1 obsoleteParent http://www.geneontology.org/formats/oboInOwl#ObsoleteClass not found
Submission http://data.bioontology.org/ontologies/CCONT/submissions/3 obsoleteParent http://www.geneontology.org/formats/oboInOwl#ObsoleteClass not found
Submission http://data.bioontology.org/ontologies/EFO/submissions/212 obsoleteParent http://www.geneontology.org/formats/oboInOwl#ObsoleteClass not found
Submission http://data.bioontology.org/ontologies/GWAS_EFO_SKOS/submissions/1 obsoleteParent http://www.geneontology.org/formats/oboInOwl#ObsoleteClass not found
Submission http://data.bioontology.org/ontologies/GLYCO/submissions/1 obsoleteParent http://www.geneontology.org/formats/oboInOwl#ObsoleteClass not found
Submission http://data.bioontology.org/ontologies/MWLA/submissions/1 obsoleteParent local:measurement not found
Submission http://data.bioontology.org/ontologies/NMR/submissions/12 obsoleteParent local:_obsolete not found
Submission http://data.bioontology.org/ontologies/RBO/submissions/10 obsoleteParent http://www.geneontology.org/formats/oboInOwl#ObsoleteClass not found
Submission http://data.bioontology.org/ontologies/PTSDO/submissions/2 obsoleteParent local:ObsoleteClass not found
Submission http://data.bioontology.org/ontologies/BDO/submissions/9 obsoleteParent http://www.geneontology.org/formats/oboInOwl#ObsoleteClass not found
Submission http://data.bioontology.org/ontologies/ANCESTRO/submissions/10 obsoleteParent http://www.ebi.ac.uk/ancestro/obsolete_class not found
Submission http://data.bioontology.org/ontologies/BMT/submissions/1 obsoleteParent http://www.geneontology.org/formats/oboInOwl#ObsoleteClass not found
Submission http://data.bioontology.org/ontologies/GENO/submissions/26 obsoleteParent http://www.geneontology.org/formats/oboInOwl#ObsoleteClass not found
Submission http://data.bioontology.org/ontologies/ICD10INFR/submissions/1 obsoleteParent local:true not found
Submission http://data.bioontology.org/ontologies/FOODON/submissions/69 obsoleteParent http://www.geneontology.org/formats/oboInOwl#ObsoleteClass not found
Submission http://data.bioontology.org/ontologies/TYPON/submissions/11 obsoleteParent http://www.geneontology.org/formats/oboInOwl#ObsoleteClass not found
Submission http://data.bioontology.org/ontologies/NGSONTO/submissions/32 obsoleteParent http://www.geneontology.org/formats/oboInOwl#ObsoleteClass not found
Submission http://data.bioontology.org/ontologies/HPCHTEST/submissions/1 obsoleteParent local:true not found
Submission http://data.bioontology.org/ontologies/MP/submissions/393 obsoleteParent http://www.geneontology.org/formats/oboInOwl#ObsoleteClass not found
Submission http://data.bioontology.org/ontologies/ITO/submissions/6 obsoleteParent http://www.geneontology.org/formats/oboInOwl#ObsoleteClass not found
Submission http://data.bioontology.org/ontologies/RAD/submissions/16 obsoleteParent http://purl.bioontology.org/ontology/RID/RID15849 not found
Submission http://data.bioontology.org/ontologies/COVIDCRFRAPID/submissions/12 obsoleteParent http://www.geneontology.org/formats/oboInOwl#ObsoleteClass not found
Submission http://data.bioontology.org/ontologies/LOINCCH/submissions/1 obsoleteParent local:true not found
Submission http://data.bioontology.org/ontologies/OLAM/submissions/5 obsoleteParent http://www.geneontology.org/formats/oboInOwl#ObsoleteClass not found
Submission http://data.bioontology.org/ontologies/ENVO/submissions/55 obsoleteParent http://www.geneontology.org/formats/oboInOwl#ObsoleteClass not found
Submission http://data.bioontology.org/ontologies/NIFSUBCELL/submissions/1 obsoleteParent http://www.geneontology.org/formats/oboInOwl#ObsoleteClass not found
Submission http://data.bioontology.org/ontologies/RADLEX/submissions/41 obsoleteParent http://purl.bioontology.org/ontology/RID/RID15849 not found
Submission http://data.bioontology.org/ontologies/ECSO/submissions/64 obsoleteParent http://www.geneontology.org/formats/oboInOwl#ObsoleteClass not found
Submission http://data.bioontology.org/ontologies/IDOBRU/submissions/61 obsoleteParent http://www.geneontology.org/formats/oboInOwl#ObsoleteClass not found
Submission http://data.bioontology.org/ontologies/ODNAE/submissions/3 obsoleteParent http://www.geneontology.org/formats/oboInOwl#ObsoleteClass not found
Submission http://data.bioontology.org/ontologies/OHMI/submissions/26 obsoleteParent http://www.geneontology.org/formats/oboInOwl#ObsoleteClass not found
Submission http://data.bioontology.org/ontologies/MERA/submissions/1 obsoleteParent local:object not found
Submission http://data.bioontology.org/ontologies/ORTHO/submissions/18 obsoleteParent http://www.geneontology.org/formats/oboInOwl#ObsoleteClass not found
Submission http://data.bioontology.org/ontologies/MONO/submissions/2 obsoleteParent local:Organism not found
Submission http://data.bioontology.org/ontologies/ONTONEO/submissions/11 obsoleteParent local:true not found
Submission http://data.bioontology.org/ontologies/EP/submissions/2 obsoleteParent http://www.geneontology.org/formats/oboInOwl#ObsoleteClass not found
Submission http://data.bioontology.org/ontologies/DOCCC/submissions/3 obsoleteParent local:20131231 not found
Submission http://data.bioontology.org/ontologies/LEGALAPA/submissions/1 obsoleteParent local:true not found
Submission http://data.bioontology.org/ontologies/ORDO/submissions/21 obsoleteParent http://www.geneontology.org/formats/oboInOwl#ObsoleteClass not found
Submission http://data.bioontology.org/ontologies/COMODI/submissions/6 obsoleteParent local:_obsolete not found
Submission http://data.bioontology.org/ontologies/SNPO/submissions/4 obsoleteParent http://www.geneontology.org/formats/oboInOwl#ObsoleteClass not found
Submission http://data.bioontology.org/ontologies/HPIO/submissions/2 obsoleteParent http://www.geneontology.org/formats/oboInOwl#ObsoleteClass not found
Submission http://data.bioontology.org/ontologies/HPCH/submissions/14 obsoleteParent local:true not found
Submission http://data.bioontology.org/ontologies/HANCESTRO/submissions/8 obsoleteParent http://www.geneontology.org/formats/oboInOwl#ObsoleteClass not found
Submission http://data.bioontology.org/ontologies/NIFCELL/submissions/15 obsoleteParent http://www.geneontology.org/formats/oboInOwl#ObsoleteClass not found
Submission http://data.bioontology.org/ontologies/ECP/submissions/2 obsoleteParent http://iris.med.duth.gr/research/ecp/ontology/eCP.owl not found
Submission http://data.bioontology.org/ontologies/SOPHARM/submissions/18 obsoleteParent http://www.geneontology.org/formats/oboInOwl#ObsoleteClass not found
Submission http://data.bioontology.org/ontologies/MIZZOU_CCO/submissions/8 obsoleteParent local:true not found
Submission http://data.bioontology.org/ontologies/PDO_CAS/submissions/1 obsoleteParent local:false not found
Submission http://data.bioontology.org/ontologies/BMTO/submissions/5 obsoleteParent http://www.geneontology.org/formats/oboInOwl#ObsoleteClass not found
Submission http://data.bioontology.org/ontologies/OCVDAE/submissions/2 obsoleteParent http://www.geneontology.org/formats/oboInOwl#ObsoleteClass not found
alexskr commented 3 years ago

delete spam ontology http://bioportal.bioontology.org/ontologies/VPS

alexskr commented 3 years ago

added creator of VPS ontology to the spam list

alexskr commented 3 years ago 
ERROR -- : Failed, exception: RuntimeError: Empty page 1 of 1 persisted after retrying 10 times. Missing Labels Generation of 13 aborted...

for a bunch of SKOS ontologies: FAST-CHRONO, LC-SUBJSCHEMES,SKOSPLAY-EX7,SKOSTEST,LCGFT,DCTERMS, etc

alexskr commented 3 years ago

RADLEX: Obsolete parent term is fixed

alexskr commented 3 years ago

MedDRA German is added.