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obophenotype / zebrafish-phenotype-ontology

A vocabulary for describing Zebrafish Phenotypes
https://obophenotype.github.io/zebrafish-phenotype-ontology/
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Remove single CARO dependency from ZFIN annotations? #63

Open matentzn opened 7 months ago

matentzn commented 7 months ago

CARO has been retired now in favour of Uberon. There is a single CARO annotation in ZFIN, CARO:0000010 (anatomical boundary). Can we replace this by Uberon, or ZFA?

./curation/zp_zfin_phenoGeneCleanData_fish.tsv:540715519       ZDB-GENE-091116-9       abnormal        ZDB-FISH-200305-1       ZDB-STAGE-010723-48   ZDB-STAGE-010723-48     ZDB-GENOX-200305-2      ZDB-PUB-190509-2        ZDB-FIG-190723-877      http://purl.obolibrary.org/obo/ZP_0137765CARO:0000010-BFO:0000050-ZFA:0009111-PATO:0001332-0-0-0
../curation/zp_zfin_phenoGeneCleanData_fish.tsv:540591612       ZDB-GENE-020507-3       abnormal        ZDB-FISH-210128-21      ZDB-STAGE-010723-12   ZDB-STAGE-010723-12     ZDB-GENOX-210128-10     ZDB-PUB-191202-3        ZDB-FIG-191230-1574     http://purl.obolibrary.org/obo/ZP_0141352CARO:0000010-BFO:0000050-ZFA:0000135-PATO:0002180-0-0-0
../curation/zp_zfin_phenotype_fish.tsv:ZDB-FISH-150901-21477    dlc<sup>tw212b/tw212b</sup>; zf523Tg    ZDB-STAGE-010723-9      Hatching:Long-pecZDB-STAGE-010723-9       Hatching:Long-pec       CARO:0000010    anatomical boundary     BFO:0000050     part_of ZFA:0000155     somite  PATO:0000051      morphology      abnormal                                                        ZDB-PUB-140513-175      ZDB-EXP-041102-1        CARO:0000010-BFO:0000050-ZFA:0000155-PATO:0000051-abnormal-0-0-0
../curation/zp_zfin_phenotype_fish.tsv:ZDB-FISH-150901-3161     dlc<sup>tw212b/tw212b</sup>     ZDB-STAGE-010723-9      Hatching:Long-pec       ZDB-STAGE-010723-9        Hatching:Long-pec       CARO:0000010    anatomical boundary     BFO:0000050     part_of ZFA:0000155     somite  PATO:0000051      morphology      abnormal                                                        ZDB-PUB-140513-175      ZDB-EXP-150410-1        CARO:0000010-BFO:0000050-ZFA:0000155-PATO:0000051-abnormal-0-0-0
../curation/zp_zfin_phenotype_fish.tsv:ZDB-FISH-170523-19       WT + MO1-myo18aa + MO1-myo18ab  ZDB-STAGE-010723-10     Pharyngula:Prim-5       ZDB-STAGE-010723-10       Pharyngula:Prim-5       CARO:0000010    anatomical boundary     BFO:0000050     part_of ZFA:0001056     myotome PATO:0000060      spatial pattern abnormal                                                        ZDB-PUB-140828-5        ZDB-EXP-041102-1        CARO:0000010-BFO:0000050-ZFA:0001056-PATO:0000060-abnormal-0-0-0
../curation/zp_zfin_phenotype_fish.tsv:ZDB-FISH-200305-1        asxl1<sup>zdf34/zdf34</sup>     ZDB-STAGE-010723-48     Larval:Days 14-20       ZDB-STAGE-010723-48       Larval:Days 14-20       CARO:0000010    anatomical boundary     BFO:0000050     part_of ZFA:0009111     hepatocyte      PATO:0001332      amorphous       abnormal                                                        ZDB-PUB-190509-2        ZDB-EXP-041102-1        CARO:0000010-BFO:0000050-ZFA:0009111-PATO:0001332-abnormal-0-0-0
../curation/zp_zfin_phenotype_fish.tsv:ZDB-FISH-210128-21       ml1Tg/ml1Tg + MO4-vangl2        ZDB-STAGE-010723-12     Gastrula:Bud    ZDB-STAGE-010723-12       Gastrula:Bud    CARO:0000010    anatomical boundary     BFO:0000050     part_of ZFA:0000135     notochord       PATO:0002180    straight  abnormal                                                        ZDB-PUB-191202-3        ZDB-EXP-070511-5        CARO:0000010-BFO:0000050-ZFA:0000135-PATO:0002180-abnormal-0-0-0