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sba1 / bio-ontology-zp

Automated construction of a phenotype ontology for zebrafish
BSD 3-Clause "New" or "Revised" License
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many zp id decomps missing #8

Closed nlwashington closed 9 years ago

nlwashington commented 9 years ago

i don't think the zp.annot_sourceinfo is quite right.

for example, i have an old version of the mapping file that defines:

ZP:0000028  abnormal(ly) disrupted endoderm development GO:0007492      PATO:0001507    PATO:0000460
ZP:0000123  abnormal(ly) absent mouth   ZFA:0000547     PATO:0000462    PATO:0000460

but these are completely missing in the new file zp.annot_sourceinfo

is that expected? there seem to be many missing.

i count ~5200 that are in both my old mapping file and the new one on hudson, ~1200 unique to the new file you've made, and 5563 only in my old one! can you bring these back @drseb ?

nlwashington commented 9 years ago

let me know if you need my old file for comparison.

drseb commented 9 years ago

You are right, but it seems that only the zp.annot_sourceinfo has an error. The annotation between ZDB-GENE-000201-18 and ZP:0000028 is present in zp.annot and the class ZP:0000028 is present in zp.owl. I am investigating. (Please note, that zp.owl has this information as OWL Annotation - maybe you want to use this instead.)