Damion Dooley

multicellular organism and organism substance should be disjoint

10

It came up in discussion with @cmungall that currently there is no disjunction between multicellular organism and organism substance. Since NCBITaxon terms correspond to multicellular organisms, someone can define a...

Proper use of 'derives from' in referencing UBERON anatomical parts for FoodOn

5

In FoodOn we need to reference plant and animal parts and products derived from them without necessarily implying they are connected to the anatomy of whole organisms. Currently our pattern...

Could GenEpiO be refreshed?

1

It has a versionIRI genepio/releases/2022-02-06/genepio.owl so I'd have thought it would be updated by now, so I'm curious what the refresh rate is for OLS ontologies? Cheers, Damion

OLS isn't reporting IAO term: "has measurement value"

1

I was searching for that term but only got back the SIO entry. IAO's term is visible only by way of axiom in https://www.ebi.ac.uk/ols/ontologies/iao/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000032 (An exact match search doesn't return...

It would be great if a term's native ontology is listed as primary search result ontology e.g. 'has part'

1

For example, a search on 'has part' returns a BFO hit, but the "Ontology:" field tends to list some ontology that isn't BFO. I think it is safe to say...

NTR specimen collection device and subclasses

10

GenEpiO had been relying on NCIT terminology for a variety of specimen collection devices, but with some NTR requests via new MIxS specification for food sample collection, and more from...

Names of sequencing software

21

Does OBI want to take on lists of sequencing assembly software? If so, I can create NTRS for Unicycler, Shovil, Velvet, Canu, Spades. Its possible a "software template" could be...

OBI "device" should be renamed?

1

Right now "device" has very specific semantic: A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. Should this be renamed...

Dalia Alghamdi has a number of terms she'd like to move into OBI from her NGBO ontology. They are documented here: https://docs.google.com/spreadsheets/d/1QqPf57tA3OtJjof07DRxIiAiky3iy4qjfhVNY1o37xs/edit#gid=0 . Labels, parent terms and definitions can be...

NTR insulin concentration measurement assay and data item

2

For the new RO paper, a diagram indicating the relationship between diabetic retinopathy, insulin levels and vasoconstriction., needs a few insulin related terms.  We would add this term to...