uPheno 2: Alpha review

[matentzn]

• Floating terms
  • FIXED anterior_to posterior_to (ZP) and dorsal_to, in left_side_of, in_right_side_of,
    • FIXED http://purl.obolibrary.org/obo/BSPO_0000096
    • FIXED http://purl.obolibrary.org/obo/BSPO_0000098
    • FIXED http://purl.obolibrary.org/obo/BSPO_0000120
    • FIXED http://purl.obolibrary.org/obo/BSPO_0000121
  • FIXED http://purl.obolibrary.org/obo/CARO_0010004 (missing import)
  • FIXED http://purl.obolibrary.org/obo/CHEBI_316698 (bug in FYPO, fixed)
  • FIXED http://purl.obolibrary.org/obo/ENVO_01001784 (seems to come from ENVO? No term exists with that id..)
  • FIXED http://purl.obolibrary.org/obo/GO_00000236 (bug in FYPO, fixed)
  • FIXED http://purl.obolibrary.org/obo/ZP_0103989 floating? - definitely should not
  • TODO http://purl.obolibrary.org/obo/UPHENO_0031759 (-> floating because it is only defined, and the bearer is not in the ontology!)
  • TODO http://purl.obolibrary.org/obo/NCIT_C3824 (the missing class from the above case)
  • FIXED NCBI taxon terms:
    • FIXED http://purl.obolibrary.org/obo/NCBITaxon_40151
    • FIXED http://purl.obolibrary.org/obo/NCBITaxon_63221
    • FIXED http://purl.obolibrary.org/obo/NCBITaxon_51337
  • TODO All Species specific phenotypes are rendered under owl:Thing, but that is a bug I have now reported to Protege.
    • Maybe I could simply remove those restrictions in a post processing script
  • PLANA terms (reported to sofia)
    • FIXED http://purl.obolibrary.org/obo/PLANA_0007501
    • FIXED http://purl.obolibrary.org/obo/PLANA_0000077
• Obsolete terms with references:
  • http://purl.obolibrary.org/obo/BTO_0000316
    • Lots of FYPO references
  • http://purl.obolibrary.org/obo/GO_0008003
    • http://purl.obolibrary.org/obo/UBERON_0005787
  • http://purl.obolibrary.org/obo/GO_0031513
    • http://purl.obolibrary.org/obo/OBA_0005774
    • http://purl.obolibrary.org/obo/OBA_0005768
  • http://purl.obolibrary.org/obo/GO_0016265
    • http://purl.obolibrary.org/obo/OBA_0002455
    • http://purl.obolibrary.org/obo/UBERON_0000071
  • http://purl.obolibrary.org/obo/GO_0072372
    • http://purl.obolibrary.org/obo/OBA_0005773
    • http://purl.obolibrary.org/obo/OBA_0005767
  • A bunch of obsolete PLANA references (send to Sofia in slack)
  • http://purl.obolibrary.org/obo/GO_0035636
    • http://purl.obolibrary.org/obo/UBERON_0011252
  • http://purl.obolibrary.org/obo/UBERON_0004355
    • http://purl.obolibrary.org/obo/OBA_0004312
    • http://purl.obolibrary.org/obo/OBA_0004288
• Weird labels
  • TODO http://purl.obolibrary.org/obo/UPHENO_0075938
    • “owl: Thing in label"
      • Pattern domains should be changed.
• Missing axioms
  • TODO Upheno phenotypes should probably get the ‘has phenotype affecting` axioms as well.
  • TODO DPO EQs are not preserved
  • TODO PHIPO EQs are not preserved
• REVIEW are only anatomy and biological process or all vars instantiated?
  • if all, remove option from config
• TODO There is an abnormal anatomical entity (II and IIPO) version!

[matentzn]

Ameded:

• Need to remove "has phenotype affecting OWL:thing" assertions (fix in relation module)
• There are some unconnected classes in the final artefact, like
  • http://purl.obolibrary.org/obo/CHEBI_1086440
  • http://purl.obolibrary.org/obo/UBERON_0004355
• the NBO behavior phenotype branch is pulled in because of HPO classes inhering in them.
• All lesion terms are floating.. Need to be careful not to destroy the classification with the blacklist!
• We need the phenotype root annotation for OLS
• uPheno has now a whooping 8 cell classes:

• There are still a significant number of references to obsolete classes

[matentzn]

Should there be reasoning after the SS components are merged in - this may confuse users of them.

[matentzn]

Need to be carefully with the assumption that root phenotypes are abnormal - in the case of MP, they are not!

[matentzn]

Why does http://purl.obolibrary.org/obo/PHIPO_0000274 have no valid EQ?
-- because I did not yet dare to overwrite the matches! Should do that!

[matentzn]

upheno:phenotype and upheno:phenotype by species should be unqualified phenotypes. We only care about abnormal phenotypes