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Document the contents of the NMDC AWS GraphDB #638

Open turbomam opened 3 months ago

turbomam commented 3 months ago

Load https://w3id.org/linkml/meta.owl into https://w3id.org/linkml/meta

Takes ~ 5 seconds

ontologies loaded query

PREFIX owl: <http://www.w3.org/2002/07/owl#>
select distinct * where {
    {
        graph ?g {
            ?s a owl:Ontology
        }
    }
}
turbomam commented 3 months ago

Load https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/project/owl/nmdc.owl.ttl into https://w3id.org/nmdc/nmdc

Takes ~ 5 seconds

Confirm with "ontologies loaded" query

turbomam commented 3 months ago

load https://raw.githubusercontent.com/microbiomedata/nmdc-ontology/main/nmdco.owl into http://purl.obolibrary.org/obo/nmdco.owl

Takes ~ 10 seconds

Confirm with "ontologies loaded" query

This isn't actually an OBO Foundry ontology. Maybe it's URIs should be refactored.

turbomam commented 3 months ago

load local/mongo_as_nmdc_database_cuire_repaired_stamped.ttl -> https://api.microbiomedata.org

local/mongo_as_nmdc_database_cuire_repaired_stamped.ttl can be created with make make-rdf

Blank node dateCreated query

select * where {
    graph ?g {
        [ <https://schema.org/dateCreated> ?dateCreated ;
          <http://www.w3.org/2000/01/rdf-schema#comment> ?comment ]  
    }
}
turbomam commented 3 months ago

load local/nmdc_materialized.ttl into https://w3id.org/nmdc/nmdc_relation_graph

create with make local/nmdc_materialized.ttl

Not detected by either the "ontologies loaded" query or the "blank node dateCreated" query

select distinct ?g
where {
      graph ?g {
          ?s ?p ?o .
      }
}
turbomam commented 3 months ago

Followup actions:

turbomam commented 3 months ago

TODO: