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hubmapconsortium / ontology-api

The HuBMAP Ontology Service
MIT License
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Ontology: Test Ontology Neo4j on DEV built using CSVs built using Alan's script #147

Closed ChuckKollar closed 1 year ago

ChuckKollar commented 2 years ago

It would be nice if this testing created the beginnings of some scripts that could run after every build verifying expected relationships that should be in the database.

AlanSimmons commented 2 years ago

TESTS:

  1. match p=()-[r {SAB:'X'}]-() Return p limit 10

where X is in (PATO UBERON CL DOID CCFASCTB OBI EDAM HSAPDV SBO MI CHEBI MP ORDO PR UNIPROTKB BAO SWO CHMO HUBMAP)

  1. match p=()-[:X]-() return p limit 10 where X in (has_representation, contains, implements, has_interface, assay_type, has_preparation_method, has_form, has_analyte)
AlanSimmons commented 2 years ago

John generated a set of UMLS CSV files to this path.

AlanSimmons commented 2 years ago

Script for converting HuBMAP specific ontology is here.

AlanSimmons commented 2 years ago

Version of an ontology input spreadsheet for HuBMAP is here.

AlanSimmons commented 2 years ago

ontologies.json file updated to direct generation of HuBMAP-specific OWLNETS files. PR at https://github.com/hubmapconsortium/ontology-api/pull/149