tgbugs / pyontutils

python utilities for working with ontologies
MIT License
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Why are genes classified under sequence feature #59

Closed memartone closed 2 years ago

memartone commented 5 years ago

http://purl.obolibrary.org/obo/SO_0000110

memartone commented 5 years ago

Huang uses Sst that is a sequence feature which is why I suspect that it is not coming back with the query.

tgbugs commented 5 years ago

I looked into how genes were modelled in other ontologies with an eye toward unifying their modelling with epigenetic modifications. Sequence feature is what others use and from a discussion with Marga Behrens it seemed that that was also how the epi folks are thinking about what they are measuring.

memartone commented 5 years ago

But it is not used consistently. So it is causing our query to fail. So pick one or the other.

On May 16, 2019, at 9:21 AM, Tom Gillespie notifications@github.com wrote:

I looked into how genes were modelled in other ontologies with an eye toward unifying their modelling with epigenetic modifications. Sequence feature is what others use and from a discussion with Marga Behrens it seemed that that was also how the epi folks are thinking about what they are measuring.

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tgbugs commented 2 years ago

Query issue resolved via phenotype indicators.