Poster presentation from Biocuration 2012.

1. Using the NCBO Annotator to Develop an Ontology-Based Index of Biomedical Resources
Trish Whetzel, Paea LePendu, Clement Jonquet, Adrian Coulet, Natalya F. Noy, Mark A. Musen, Nigam H. Shah
Stanford University, Stanford, CA
Acknowledgements
The National Center for Biomedical Ontology is one of the National Centers for Biomedical
Computing supported by the NHGRI, the NHLBI, and the NIH Common Fund under grant U54-
HG004028.
Contact
Ontological Discovery Environment
For more information on the NCBO, visit http://www.bioontology.org or email support@bioontology.org
Abstract
Biomedical researchers generate an enormous amount of data covering a variety of domains from genomic information and
pathways to drug descriptions, clinical trials, and diseases. The data is published on the Web, however using idiosyncratic
schemas and access mechanisms making it difficult to search and analyze the data. While the biomedical community agrees
that terminologies and ontologies are essential for data integration and translational discoveries to occur, semantic annotation of
biomedical resources is still minimal and is often restricted to a few ontologies. The NCBO Resource Index addresses these
problems by providing a unified ontology-based index of and access to multiple heterogeneous biomedical resources.
To create the Resource Index, textual metadata from selected data elements in publicly available biomedical resources is
processed using a resource-specific access tool to create semantic annotations. We use ontologies from BioPortal as a source
of terms, their synonyms, and relations between terms. The ontology-based index is generated using the NCBO Annotator to
tag the metadata and both direct and expanded annotations are created using available ontology knowledge, e.g. term
mappings and ontology hierarchy. Currently, our dictionary contains 5,670,771 terms from 294 ontologies and has been used to
index 3,920,921 indexed data elements from 23 resources.
The ontology-based index is accessible from the BioPortal Web site and directly via the Resource Index Web services. The
web interface provides a search box that displays auto-complete suggestions for the search terms and source ontology for
these terms. For each resulting resource record, the details of the annotation are highlighted in the original text and additional
terms used to tag the resource record are displayed. The Resource Index Web services support access by specifying either the
ontology term or the resource record. For example, given the term “melanoma” return all records across one or more resources
annotated with this term or given a resource record identifier, return all annotations. In addition, search by union and intersection
is also supported. Therefore, heterogeneous, independently developed resources can be searched from a universal ontology-based
index.
Resource Index
Annotator Workflow
Applications using the Annotator
The NCBO Annotator uses ontologies from BioPortal, which includes content from the OBO Foundry, UMLS, and other user
submitted ontologies, as the source of terms to generate a dictionary containing the preferred name and synonyms from these
ontologies. The dictionary is then used with the concept recognizer Mgrep to identify these entities in text submitted to the
Annotator Web service creating direct annotations. The annotations can also be expanded to include terms based on the
ontology hierarchy and term mappings.
GeneWiki
Annotator
http://en.wikipedia.org/wiki/Portal:Gene_Wiki
Statistical Tracking of Ontological
Phrases
http://www.mooneygroup.org/content/webtools
http://ontologicaldiscovery.org
SciVerse Hub - ODiSSea
http://www.hub.sciverse.com/action/home
The Resource Index is an ontology-based index of publicly available biomedical data generated using the Annotator. Data
can be searched from BioPortal or using the Resource Index Web services. Searching the ontology-based index returns
results that otherwise would not be found. Contact us to suggest a resource.
http://bioportal.bioontology.org/resources