Task

Task Objectives

Map ontologies from the Open Biomedical Ontologies repository (OBO) and Medical Subject Headings (MeSH) to DBpedia
Publish mappings and add them to the HCLS KB
Demo

Rationale

Scope

Participants

Matthias Samwald, DERI Galway and Konrad Lorenz Institute for Evolution and Cognition Research
Holger Stenzhorn, DERI Galway

Deliverables

'DBpedia - OBO mapping based on cross references to Wikipedia contained in the OBO ontologies'

A PHP script that creates the mapping by accessing the DERI Health Care and Life Science Knowledge Base.
Mapping file generated by this script: http://samwald.info/res/dbpedia_obo_mapping_based_on_xrefs.ttl
Note that due to the nature of the cross-references, this mapping is rather loose.

'DBpedia - MeSH mapping based on cross references in DBpedia'

A PHP script that creates the mapping.
Mapping file generated by this script: http://samwald.info/res/dbpedia_mesh_mapping.ttl

All mappings are also loaded into the DERI Health Care and Life Science Knowledge Base.

Related resources

Notes

Converting existing Wikipedia mappings

SPARQL Query for Neurocommons KB that retrieves explicit Wikipedia references:

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

SELECT DISTINCT ?entity ?wikipedia_uri 
WHERE {
?entity obo:hasDefinition ?definition_bnode .
?definition_bnode obo:hasDbXref ?dbxref_bnode .
?dbxref_bnode obo:hasURI ?wikipedia_uri .
FILTER regex(str(?wikipedia_uri), "en.wikipedia.org/wiki/", "i")
}

SPARQL Query for recent version of OBI that retrieves explicit Wikipedia references (based on suggestion by Melanie Courtot:

PREFIX owl:<http://www.w3.org/2002/07/owl#>
PREFIX obi:<http://purl.obofoundry.org/obo/>
PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>

SELECT DISTINCT ?entity ?wikipedia_uri
WHERE {
?entity obi:IAO_0000119 ?wikipedia_uri.
FILTER regex(str(?wikipedia_uri), "en.wikipedia.org/wiki/", "i")
}

SPARQL Query to get entities (e.g., from disease ontology) via UMLS IDs, using C0014544 as an example UMLS ID:

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

SELECT DISTINCT ?entity 
WHERE {
?entity obo:hasDbXref ?dbxref_bnode .
?dbxref_bnode rdfs:label ?xref_label .
FILTER regex(?xref_label, "C0014544", "i")
}

Generating Mapping from DBpedia to MeSH

To be executed on http://dbpedia.org/sparql . The results of the queries below require further processing to generate RDF mappings

SELECT * WHERE {?dbpedia_uri <http://dbpedia.org/property/meshname> ?mesh_name . } 

SELECT * WHERE {?dbpedia_uri <http://dbpedia.org/ontology/meshid> ?mesh_id . }

SELECT * WHERE {?dbpedia_uri <http://dbpedia.org/ontology/meshnumber> ?mesh_number . }

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