Annotator Web service

To automatically process a piece of data text to annotate it with relevant ontology concepts and return the annotations

Presentation & Demonstration

The range of publicly available biomedical data is enormous and is expanding fast. This expansion means that researchers now face a hurdle to extracting the data they need from the large numbers of data that are available. Biomedical researchers have turned to ontologies and terminologies to structure and annotate their data with ontology concepts for better search and retrieval. However, this annotation process cannot be easily automated and often requires expert curators. Plus, there is a lack of easy-to-use systems that facilitate the use of ontologies for annotation. The NCBO Annotator (or Open Biomedical Annotator (OBA)) is an ontology-based Web service that annotates public datasets with biomedical ontology concepts based on their textual metadata. The biomedical community can use the annotator service to tag thier data automatically with ontology concepts. These concepts come from the Unified Medical Language System (UMLS) Metathesaurus and the National Center for Biomedical Ontology (NCBO) BioPortal ontologies. Such annotations facilitate translational discoveries by integrating annotated data.

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OBA web service workflow

Please try the [NCBO Annotator service in BioPortal http://bioportal.bioontology.org/annotate].

Contacts

• Community & usage: [Trish Whetzel]
• Design, utility & applications: [Nigam Shah] and [Clement Jonquet]
• Technical support: [Cherie Youn]

Documentation & References

• Annotator REST Web Service User Guide Annotator User Guide

• Annotator REST Web Service client examples [Annotator_Client_Examples | Annotator Client Examples]]

• Annotator Design and underlying Data model: Documentation here... to be move to the wiki soon.

• Please refer to:
  • Clement Jonquet, Nigam H. Shah, Mark A. Musen, The Open Biomedical Annotator, AMIA Summit on Translational Bioinformatics, p. 56-60, March 2009, San Francisco, CA, USA. conference's web site pdf - 201Kb

Versions (prototypes & releases)

• April 2009 - First production release in BioPortal 2.1

• March 2009 - Prototype user interface has been deployed on the BioPortal staging server.

• October 2008 - The prototype (v1.1) has bee released for testing and evaluation. The prototype is still available but please don't use it anymore: [1]

• May 2008 - First prototype (v1.0) - Has been removed from servers.

Community

After 8 months of existence OBA counts already 8 academic groups (Univ. of California, San Francisco, Univ. of Indiana, Jackson Lab) that use and experiment the service in specific scenarios. Internally, we have used the annotation workflow to index biomedical data resources with ontology concepts (cf. Resources index Web services).

Learn more about NCBO Annotator users & use cases: NCBO Annotator community

Collaboration & Acknowledgment

• The OBA service uses Mgrep in the concept recognition step. We acknowledge the assistance of Manhong Dai and Fan Meng from the National Center for Integrative Biomedical Informatics (NCIBI).

• The user interface for the annotator client in BioPortal (http://bioportal.bioontology.org/annotate) is designed & developped by NCBO members from University of Victoria