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GenEpiO / genepio

The Genomic Epidemiology Application Ontology describes the genomics, laboratory, clinical and epidemiological contextual information required to support data sharing and integration for foodborne infectious disease surveillance and outbreak investigations.
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Potential terms to move to GenEpiO from the Influenza Ontology #22

Open PhiBabs935 opened 3 years ago

PhiBabs935 commented 3 years ago

Hi, Shane here. I am looking for a new home for terms that were originally created with FLU IDs. They are more general than influenza, so I wanted to move and re-import them. I thought GenEpiO might be suitable for some of them. Note, term labels and definitions of FLU terms are based on an unreleased, updated version I am working on, not the 2015 release version found on Bioportal and Ontobee.

Term Request / Revision / Import Form

-ID: FLU:0000995 -Term: sequence received date -definition: Data item specifying the date that the laboratory received the sequence.

-ID: FLU:0000801 -Term: sequence submission date -definition: Data item specifying the date that the sequence was submitted to some repository (such as to GenBank).

Note: I thought the above two terms may fit in GenEpiO based on the existing subclasses of 'isolate history item' [http://purl.obolibrary.org/obo/GENEPIO_0000069].

-ID: FLU:0000815 -Term: specimen collection location - district -Definition: Datum specifying the district of the site of a given specimen collection event.

-ID: FLU:0000857 -Term: specimen collection location - sub-district -Definition: Datum specifying the sub-district of the site of a given specimen collection event.

Note: FLU had a variety of classes under the placeholder 'data about a collection location' [http://purl.obolibrary.org/obo/FLU_0000885]. I replaced most of these with the corresponding subclasses of GenEpiO's 'specimen collection site specification'. But I wasn't sure if the above two FLU terms were covered under the existing GenEpiO terms.

-ID: FLU:0000976 -Term: symptom onset date -Definition: A symptom onset date is a date-time entity that marks the start of one or more reported symptoms pertaining to an episode of human or animal illness

Of course, 'symptom onset date', is already imported to GenEpiO. My suggestion is that this term can be reintroduced with GenEpiO ID, as it is more general than influenza.

There are also a some FLU terms concerning GenBank submission metadata that I thought may find a home here [http://purl.obolibrary.org/obo/FLU_0001010], but I will save those for a later time.

ddooley commented 3 years ago

Hi Shane, So this is a little embarrassing that I didn't have a watch on all issues for GenEpiO and so didn't notice this one until now. I will have a look at your requests in the next week. Are they still current? I am also a curator for OBI and IAO, and OBI is collecting sequence related fields as well, which I am coordinating, so there is a possibility of OBI as a target too. I can help either way.

PhiBabs935 commented 3 years ago

Hi Damion, No worries. Yes, these are still current. I would be ok with the sequence related terms being moved to OBI instead. I already had other terms I suggested moving to OBI anyway in a separate tracker issue [https://github.com/obi-ontology/obi/issues/1286]. Thanks

ddooley commented 2 years ago

Update: we will be addressing these shortly. Note FLU can be found in BioPortal, e.g. sequence received date . A question about this particular term. It seems a bit odd that a lab would receive a sequence? Do they mean that a lab would be receiving sequencing results as a data set?