GENO-ontology

GENO-ontology copied to clipboard

A rich and diverse set of CQs related to genotype representation and G2P associations would be useful for a number of purposes: - inform model development - document utility of...

mbrush

We are generating an ontology of reference chromosomes and their parts (arms, regions, bands) from the UCSC chromosome band data ( see [dipper issue #42](https://github.com/monarch-initiative/dipper/issues/42) ). It is expected that...

mbrush

Reported by @TomConlin https://github.com/monarch-initiative/dipper/issues/379 geno-developer has: ``` formerly used http://purl.obolibrary.org/obo/GENO_0000532 ``` I recommend using the obsoletion plugin and not burying IRIs in comments TO manually repair, add back the IRI,...

cmungall

Document how gene interactions are modeled

1

A good question from @kyook (see the slides in Dropbox for background) ``` I don’t understand where gene interactions are accounted for. We separate genetic background - like in your...

cmungall

germline vs somatic variants

2

we will need to disambiguate between variants (and perhaps any geno partonomy) that are germline vs somatic. how should these be represented? should there be classes for "germline variant" "somatic...

nlwashington

reference and alternate base properties

1

We need some object and/or data properties for listing reference and alternate nucleotide (and/or amino acid) sequences. I could not find any other ontologies that have these. so to say...

nlwashington

genetic disease polygenic vs. monogenic

1

We need some classification of inheritance patterns, this should relate existing classes. Not sure which ontology or where this goes, but something like this: inheritance pattern --polygenic --monogenic ----dominant ----recessive...

mellybelly

epigenetic genotype (epitype?)

1

At some point we'll need to consider a person's epigenetic factors related to disease susceptibility, etc. This could include methylation patterns, histone modifications, etc. Should this be another subclass of...

nlwashington

Central Ticket for documenting all term requests for SO. 1. chromosome band staining intensity qualities presently implemented in GENO as placeholders. And then mireot to replace temp GENO classes. Also...

mbrush

i have been pointed to the documentation for chromosomal rearrangements: http://onlinelibrary.wiley.com/doi/10.1002/0471142905.hga04cs17/pdf this has a lot of good information about karyotypes, and all the kinds of things that can happen. here's...

nlwashington