Some normal phenotypes snug into ZFIN?

[matentzn]

'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]

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]

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

[matentzn]

@ybradford "Phenotype is not inherently abnormal"