Using uberon for text mining

Synonyms in uberon

Authors and contributors:

• Chris Mungall (author)

Date: 2012

Document Type: ontology_usage_article

Abstract

This article describes how to use uberon synonymy metadata for text mining

Synonym scopes

Uberon uses the standard 4 OBO synonym scopes:

• EXACT
• BROAD
• NARROW
• RELATED

The standard obo2owl mapping is used here consult the (obo spec)[http://oboformat.org] for details; currently the following annotation properties are used:

• hasExactSynonym
• hasBroadSynonym
• hasNarrowSynonym
• hasRelatedSynonym

Label uniqueness

The uberon build pipeline ensures that no two classes share the same string as either a label or exact synonym. This helps detect common categories of errors.

Languages

Languages are indicated by a lang tag, e.g. '@fr'. Note that this is not yet currently translated in the owl correctly.

The exception is latin, for which a LATIN synonym type is used

Synonym types

The ontology contains a growing list of synonym types or tags, which may be useful for text mining. See the ontology for a full list.

• ABBREVIATION - Acronym or abbreviation
• LATIN - Typically the TA preferred term
• DUBIOUS - the synonym may be contested or midleading
• DEPRECATED - a historic synonym that may be used in older texts but discouraged in modern usage
• SENSU - a term typically used within a certain taxonomic scope
• ...

Synonym provenance

We aim to eventually have provenance for all synonyms. Currently most of these are xrefs to species anatomy ontologies, but in future more will be PMIDs etc.

In some cases an NCBITaxon ID is used as synonym provenance. This indicates when a term is preferred or used within a particular taxonomic context.

Relational adjectives

We include a has_relational_adjective annotation property to indicate what the adjectival form of the noun that describes the structure is. For example, 'hippocampal' for Ammon's horn.

OBO Foundry Unique Label

In the Uberon bridging axiom ontologies the 'OBO Foundry unique label' property is used to provide a label that is intended to be unique across the whole OBO Foundry. The unique labels are generated automatically be suffixing the ontology-provided label with a qualifying term.

For example, the FMA class for 'heart' has the OBO Foundry unique label 'heart (canonical adult human)' to disambiguate it from 'heart (adult mouse)' in MA or the embryonic heart as represented in EHDAA2.