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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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Some normal phenotypes snug into ZFIN? #23

Open matentzn opened 5 years ago

matentzn commented 5 years ago

'cilium multi-ciliated epithelial cell normal, abnormal' 'determination of left/right asymmetry in lateral mesoderm normal, abnormal' 'determination of pancreatic left/right asymmetry normal, abnormal' 'embryonic heart tube left/right pattern formation normal, abnormal' 'trunk normal neural crest cell development, abnormal' 'whole organism normal, abnormal'

Here are the ZFIN annotations I found:

phenotype_fish.txt:ZDB-FISH-150901-10141    WT + MO1-mir34b + MO2-myb   ZDB-STAGE-010723-13 Pharyngula:Prim-25  ZDB-STAGE-010723-13 Pharyngula:Prim-25  GO:0005929  cilium  BFO:0000050 part_of ZFA:0005242 multi-ciliated epithelial cell  PATO:0000461    normal  normal                          ZDB-PUB-130703-10   ZDB-EXP-140205-10
phenotype_fish.txt:ZDB-FISH-150901-12354    eif3ba<sup>la024215Tg/la024215Tg</sup>  ZDB-STAGE-010723-10 Pharyngula:Prim-5   ZDB-STAGE-010723-10 Pharyngula:Prim-5   GO:0014032  neural crest cell development   BFO:0000066 occurs_in   ZFA:0001115 trunk   PATO:0000461    normal  normal                          ZDB-PUB-130710-52   ZDB-EXP-041102-1
phenotype_fish.txt:ZDB-FISH-150901-16886    katnb1<sup>mh103/mh103</sup>    ZDB-STAGE-010723-2  Gastrula:Shield ZDB-STAGE-010723-2  Gastrula:Shield                 ZFA:0001094 whole organism  PATO:0000461    normal  normal                          ZDB-PUB-141219-3    ZDB-EXP-041102-1
phenotype_fish.txt:ZDB-FISH-150901-19627    kif6<sup>gw326/gw326</sup>  ZDB-STAGE-010723-30 Segmentation:14-19 somites  ZDB-STAGE-010723-30 Segmentation:14-19 somites      GO:0003140  determination of left/right asymmetry in lateral mesoderm   PATO:0000461    normal  normal                          ZDB-PUB-141007-7    ZDB-EXP-041102-1
phenotype_fish.txt:ZDB-FISH-150901-19627    kif6<sup>gw326/gw326</sup>  ZDB-STAGE-010723-30 Segmentation:14-19 somites  ZDB-STAGE-010723-8  Larval:Protruding-mouth         GO:0035469  determination of pancreatic left/right asymmetry    PATO:0000461    normal  normal                          ZDB-PUB-141007-7    ZDB-EXP-041102-1
phenotype_fish.txt:ZDB-FISH-150901-19627    kif6<sup>gw326/gw326</sup>  ZDB-STAGE-010723-32 Pharyngula:Prim-15  ZDB-STAGE-010723-32 Pharyngula:Prim-15              GO:0060971  embryonic heart tube left/right pattern formation   PATO:0000461    normal  normal                          ZDB-PUB-141007-7    ZDB-EXP-041102-1
phenotype_fish.txt:ZDB-FISH-150901-3309 katnb1<sup>mh101/mh101</sup>; katnb1<sup>mh102/mh102</sup>  ZDB-STAGE-010723-2  Gastrula:Shield ZDB-STAGE-010723-2  Gastrula:Shield         ZFA:0001094 whole organism  PATO:0000461    normal  normal

I thought phenotype fish only contained 'abnormal' now? We need to account for this soon, because we know have abnormally normal phenotypes which looks a bit funny. :P

matentzn commented 4 years ago

Also: in the metadata, like in the examples above, it clearly says "normal" for about 11K records in the ZFIN dataset.. @ybradford as far as I remember, you told me that phenotype_fish data only contains abnormal records; how then do I interpret when the columns:

Phenotype Keyword ID Phenotype Keyword Name Phenotype Tag
PATO:0002050 normal amount normal
PATO:0000461 normal normal

All of these are currently mapped to abnormal phenotypes; what do they really mean?

matentzn commented 4 years ago

We need to start collecting normal phenotypes; make sure that we have patterns for normal phenotypes!

matentzn commented 4 years ago

@ybradford "Phenotype is not inherently abnormal"