Determine who is using GAZ and how it is being used #22
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IEDB uses GAZ to build a list of countries that we care about and organize them under a shallow hierarchy. The code is here: https://github.com/IEDB/GAZ |
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We're using GAZ in a few ontology projects: As a standard vocabulary for 1st order, 2nd order etc government: countries, provinces, states, territories and regions and municipalities. This is used in our Genomic Epidemiology Ontology (GenEpiO) to provide pick-lists for reporting outbreak cases; to describe patient nationalities, country of birth, and travel patterns, and eventually food traceability. In FoodOn, we have reused a 'hasCountryOfOrigin' annotation pointing to country, but would look to GAZ to describe region of origin as well. We developed a browser-based lookup function to navigate 'located in' hierarchies, but have discovered that the connection between 2nd/3rd order govt and municipalities is pretty spotty. Here's an example of a control that provides both 2nd and 3rd order branches separately. It comes with a lookup function so that a given application ontology doesn't have to list all of GAZ. Instead a user can select an app-provided GAZ entry, then press "lookup choices" to get further sub-class or 'located in' related items. I should also mention that GAZ is being proposed (with geonames as alternative) for locations related to Biosample collection in an ISO "TC 34/SC 9 working group 25 repository for draft ontology-driven specifications referenced in the draft working document ISO/TC 34/SC 9 N 000 "Microbiology of the Food Chain — Whole Genome Sequencing, Typing and Genomic Characterization of Foodborne Bacteria", visible at http://genepio.org/geem/form.html#GENEPIO:0002083
Pressing "lookup choices" fetches subordinate choices from OLS.
The final selection might not be contained in the local app ontology:
Having GAZ be refreshed in tandem with wikidata or geonames edits would be wonderful. A quick peek at municipality list:
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Action Item: Chris Mungall, -- will send email to the OBO Foundry. Action Item: Lynn - will examine BioSample - usage of GAZ |
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@lschriml any update on details on whether/how GAZ is used in BioSample (EBI or NCBI) |
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Yes,
GAZ has been used in BioSample since it was created.
GAZ is a core term in the MIxS standard.
County field, geographic location.
Also used in QIIME, QITTA, MGRAST, etc -- across GSC-associated projects
…On Wed, Jun 26, 2019 at 11:57 AM Chris Mungall ***@***.***> wrote:
@lschriml <https://github.com/lschriml> any update on details on
whether/how GAZ is used in BioSample (EBI or NCBI)
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Lynn M. Schriml, Ph.D.
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University of Maryland School of Medicine
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Working with @turbomam @wdduncan we now have a normalized tidied version of the INSDC sample database, so we can do some analysis of usage of GAZ with mixs:geo_loc_name 77159 distinct geo_loc_name values GAZ IDs have been used 8 times in total in the whole database: the vast majority of usages are simple strings, so it's not clear GAZ is not being meaningfully used or adds value beyond other gazetteers Top uses: |
Anyone using GAZ, please add comments to this ticket!
Also include whether you use the obo or owl file, if you download or use an API, etc. Note any specific things you would like to see at a general level (or link to a ticket)
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