template meta builder (entry of select lists for lazy people)

[turbomam]

There is a geo_loc_name section in the CanCOGeN template. I assume somebody entered the content below mostly by hand?

I would be interested in a tool that could populate the following into the template just by specifying the parent term GAZ:00002561 'Province (Canada)'. Then the user could add, delete or modify any of that.

Or instead of a tool, it could just be some documentation/hints... see further down

Ontology ID	Meaning (LinkML)	parent class	label
ID		SC %
GAZ_00002566		geo_loc_name (state/province/territory)	Alberta
GAZ_00002562		geo_loc_name (state/province/territory)	British Columbia
GAZ_00002571		geo_loc_name (state/province/territory)	Manitoba
GAZ_00002570		geo_loc_name (state/province/territory)	New Brunswick
GAZ_00002567		geo_loc_name (state/province/territory)	Newfoundland and Labrador
GAZ_00002575		geo_loc_name (state/province/territory)	Northwest Territories
GAZ_00002565		geo_loc_name (state/province/territory)	Nova Scotia
GAZ:00002574		geo_loc_name (state/province/territory)	Nunavut
GAZ_00002563		geo_loc_name (state/province/territory)	Ontario
GAZ_00002572		geo_loc_name (state/province/territory)	Prince Edward Island
GAZ_00002569		geo_loc_name (state/province/territory)	Quebec
GAZ_00002564		geo_loc_name (state/province/territory)	Saskatchewan
GAZ_00002576		geo_loc_name (state/province/territory)	Yukon

Sample documentation

"Run the following query at" http://sparql.hegroup.org/sparql/

PREFIX  GAZ:  <http://purl.obolibrary.org/obo/GAZ_>
PREFIX  rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX  oio:  <http://www.geneontology.org/formats/oboInOwl#>

SELECT  (str(?i) AS ?Ontology_ID) ("" AS ?Meaning_LinkML) 
("geo_loc_name (state/province/territory)" AS ?parent_class) (str(?l) AS ?label)
WHERE
  { GRAPH <http://purl.obolibrary.org/obo/merged/GAZ>
      { ?s  rdfs:subClassOf  GAZ:00002561 ;
            rdfs:label       ?l ;
            oio:id           ?i
      }
  }

[turbomam]

@cmungall is suggesting that I do as much of the template building by parsing the LinkML model of the various MIxS yaml files at https://github.com/GenomicsStandardsConsortium/mixs-source

[turbomam]

So GAZ content isn't important to us and SPARQL against OntoBee isn't a solution we would probably use.

This issue is just a worked example on "how would you do automated template generation?"

[ddooley]

As a first step a LinkML version of DataHarmonizer would at least allow select field sources to identify the ontology vocabulary branch(es) to fetch terms from - but there would likely need to be features for placing constraints around that, like fetch terms to a certain depth. A past project offered a dynamic lookup service so that the project config files didn't need to have the whole vocabulary loaded. But this becomes a bit of a load when validation is required on such fields.

[ddooley]

P.s. our previous GAZ and DO dynamic lookup system went straight to OLS API. You can see it in action in example form https://genepio.org/geem/form.html#GENEPIO:0001777 - any of the "lookup choice" fields will provide a popup if you provide an initial choice to start from. (Its a prototype we would redo the code for btw). If OntoBee isn't a solution would OLS be for dynamic lookup?

[turbomam]

Thanks @ddooley

I think I was too eager to create an issue here. I'm well on my way to creating templates by parsing LinkML files. I think that should be self sufficient and not require any external lookups. I'll share my code soon.

direct answer to your question: yes, I use OLS a lot and using it for this poorly worded issue would make sense, if external lookups were required.

[turbomam]

Here's my work in progress for creating a DataHarmonizer template from a LinkML schema

I've shared the converted website as a github page

None of this is guaranteed to stay in the same location or to be up 100% of the time