NTR: data items - sampling location

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The Ontology for Biomedical Investigations

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NTR: data items - sampling location #1578

Open cmrn-rhi opened 2 years ago

cmrn-rhi commented 2 years ago

Sampling Location Terms

ROBOT table new term requests (basic template, data item specific template unavailable at this time)
Terms with tan labels have already undergone an initial OBI review but need final review and to be entered into OBI.
GenEpiO ID (temporary) and Curation Notes annotations are for curation work and should be removed prior to ROBOT integration.

ROBOT table URL (I#1578 tab): https://docs.google.com/spreadsheets/d/1SiVgFDy9jOoFIhywvLjYLMBLqJsZ0B9An9170RYpQRM/edit#gid=2066156117

ontology ID	label
OBI:0002868	sampling location room
OBI:0002869	sampling location surface material
OBI:0002870	sampling location building level
OBI:0002871	sampling location condition
OBI:0002872	sampling location average daily occupancy
OBI:0002873	sampling location frequency of cleaning

@ddooley

ddooley commented 1 year ago

Discussed on call. OBI is shy of creating more data items as shadow hierarchies. Prefer to have models of material references like building locations/conditions described generally (ENVO?). GenEpiO could hang on to precomposed terms for "sampling location" x attribute. @zhengj2007 will add some content about how "sample/specimen location" currently is in OBO.

cmrn-rhi commented 1 year ago

@griffie could you provide "example of usage" annotations for these terms?

zhengj2007 commented 1 year ago

A couple of OBO ontologies have defined the sample collection location. In FLU, it is data about a collection location that has several subClasses, such as collection city, collection longitude GPS, collection location name, and collection state etc. In VEuPathDB ontology, it is defined as a site, location of specimen collection.

ddooley commented 1 year ago

@zhengj2007 do you want "location of specimen collection" moved into OBI?

Does anyone have an opinion about how it should be named? "specimen collection location"?

Also as I understand it, ENVO is moving away from having stuff under "site", since there is no axiomatization that seems to be useful beyond how material entities are defined anyways (i.e. both sites and material entities have fiat boundaries; beside that are there any features that distinguish the categories found under each? - this is an argument that Chris Mungall put forward). So is it ok to have "specimen collection location" under ME?