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phenoscape / Phenex

Phenex is an application for annotating character matrix files with ontology terms using the Entity-Quality syntax for describing phenotypes.
http://phenex.phenoscape.org/
MIT License
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missing terms in quality field #15

Closed wdahdul closed 11 years ago

wdahdul commented 11 years ago

cartilaginous and ossified are in PATO but not available in Quality field in Phenex

balhoff commented 11 years ago

The terms have the wrong namespace in the ontology:

[Term] id: PATO:0001448 name: ossified namespace: vertebrate_skeletal_anatomy def: "A composition quality inhering in an bearer by virtue of the bearer's being hardened by the deposition of calcium into bone." [MAMMALOGY:MAMMALOGY] is_a: PATO:0000001 ! quality

[Term] id: PATO:0001449 name: cartilaginous namespace: vertebrate_skeletal_anatomy def: "A composition quality inhering in an bearer by virtue of the bearer's cartilage quantities." [Wikipedia:http://en.wikipedia.org/wiki/Cartilaginous] comment: Cartilage is a type of dense connective tissue. It is composed of specialized cells called chondrocytes (CL:0000138) that produce a large amount of extracellular matrix composed of collagen fibers, abundant ground substance rich in proteoglycan, and elastin fibers is_a: PATO:0000001 ! quality

balhoff commented 11 years ago

I think this was fixed in the ontology - no longer an issue.