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OBO release versions are not legal obo due to lack of declarations #21

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dosumis opened this issue Apr 11, 2019 · 0 comments
Open

OBO release versions are not legal obo due to lack of declarations #21

dosumis opened this issue Apr 11, 2019 · 0 comments
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@dosumis
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dosumis commented Apr 11, 2019

OBO format files should declare subsets and synonym types.

Merging imports into the OBO release file has led to OBO files that lack some of these declarations.

e.g. xpo.obo

has

[Term]
id: CHEBI:24431
name: chemical entity
namespace: chebi_ontology
def: "A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances." []
subset: 3_STAR
synonym: "chemical entity" EXACT [UniProt]

but the subset is not declared in the header

This prevents consumption by a number of legacy tools. I suspect this is a general ODK release issue, possibly stemming from ROBOT filtering. It may prevent adoption of complete ODK release pipeline by some resources using legacy OBO loaders.

CC @matentzn

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