ZOOMA

ZOOMA is an application for discovering optimal ontology mappings, designed to automatically map text values to ontology terms.

Background

Firstly, to coin a couple of phrases:

• "Text values" are things that a user, or maybe a curator has entered
  • This isn't necessarily (but probably is) some sort of controlled term
• "Ontology Terms" are things which come (only) from an ontology
  • If you can't find it, it's not an ontology term!
• A "mapping" is an assertion that some text value somehow relates to some ontology term(s).

ZOOMA is an application developed at the EBI, and originally grew out of the need to offer queries against EFO (EFO) for data in the (Atlas).

On the simplest level, this requires taking user submitted text values, and matching them against "ontology terms" (actually, OWL classes) recorded in EFO. On a more complex level, we actually need to do lots more - such as reusing mappings that have already been asserted in the database, exploring which mapping is best when multiple mappings occur, recording contextual information (such as species) in order to derive better mappings, improving EFO by suggesting new terms, and so on.

To this end, we developed ZOOMA - an application designed to automate most of this process, and requiring minimal manual intervention for the commonly observed values.

ZOOMA performs text to ontology term mappings by operating over "repositories of mappings". Normally, this means Bioportal, OLS or an ontology you have supplied: terms are matched to these resources based on vendor-specific search algorithms (or, reasoning and text matching over supplied ontologies). However, it is also possible to interface ZOOMA with databases - as we do at the EBI - to allow mappings to be reused whenever they're encountered again.

There is further information about ZOOMA available in these slides.

Getting started

ZOOMA will be available to download here. Please check back soon.