obo_wikidata_mapping

STATUS: ROUGH DRAFT

A repo discussion and specification of mappings to wikidata from ontologies in OWL that follow the OBO 1.4 standard for annotation properties and the OBO Foundry standard ID specification.

Motiviations:

1. Linkouts from wikipedia to resources displaying annotations to ontology terms.

• Why? Added value for WP: Provides links from, for example, biological processes on WP to lists of genes involved. Added value for ontology resources: Traffic.
• How? Wikidata is used to populate info boxes on Wikipedia. Loading ontologies into Wikidata - with mapping of terms to Wikidata entries corresponding to Wikipedia pages, provides a potential route for linkouts from Wikipedia info boxes.

2. Wikidata has broader ambitions as a curated respository of linked-data. It is in the interests of those developing ontologies to be part of this, especially if the work required is minimal.

Mapping issues:

1. How to map from wiki-(data/pedia) items to onotology terms:

• Likely solution: A mix of harvesting curated mappings from xrefs and lexical mapping.

1. ID mapping from the OBO Foundry URI standard.
2. Mapping annotation properties to wikidata properties/built-ins

• Note that there are character limits on the wd side.

1. What resources should be linked out to?

• There are limits on this set by WD, and any linkouts would need community approval.

Please see notes.md for general notes on mapping written during SWAT4LS2015 hackathon.

Some starting points for mapping:

1. Direct parsing of OWL files. Draft mapping in yaml in obo_wikidata_mapping.yml
2. From OLS API - draft mapping table: OLS_mapping.tsv. Table based on 'retrieve a term' query.

The OLS API is appealing for a number of reasons:

• One central location for all the latest versions of OBO ontologies
• It is much easier to query and to work with results than tools working directly with rdf or owl.
• It hides some complexity:
  • provides a graphy representation for both classification and key relation types (part_of, develops_from)
  • xref on term (provisional mapping WD:'see also') vs xref on definition (new wikidata property) - (pending addition to EBISPOT/OLS#2)