Difference between revisions of "Annotator Web service"

From NCBO Wiki
Jump to: navigation, search
(Annotator XSD)
Line 28: Line 28:
=== Annotator XSD ===
=== Annotator XSD ===
* ''Coming soon''
=== Prototype releases ===
=== Prototype releases ===

Revision as of 08:30, 1 May 2011

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 continues to rapidly expand. 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 (formerly referred to as the 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 their 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.

Error creating thumbnail: /srv/www/vhosts/ncbo.bioontology.org/app/mediawiki-1.30.2/includes/shell/limit.sh: line 61: ulimit: cpu time: cannot modify limit: Permission denied /srv/www/vhosts/ncbo.bioontology.org/app/mediawiki-1.30.2/includes/shell/limit.sh: line 84: ulimit: virtual memory: cannot modify limit: Permission denied /srv/www/vhosts/ncbo.bioontology.org/app/mediawiki-1.30.2/includes/shell/limit.sh: line 90: ulimit: file size: cannot modify limit: Permission denied /bin/bash: /usr/bin/convert: No such file or directory Error code: 127
NCBO Annotator Web service workflow

Please try the NCBO Annotator service in BioPortal.


  • For questions or feature requests, contact Support


  • Annotator GoogleGroup for discussions on use cases and experiences, e.g. parameters, ontologies, semantic expansion, with the Annotator.

How to Cite

  • Jonquet C, Shah NH, Musen MA. The open biomedical annotator. Summit on Translat Bioinforma. 2009 Mar 1;2009:56-60. PubMed PMID: 21347171; PubMed Central PMCID: PMC3041576.

Client Examples

Annotator XSD

  • Coming soon

Prototype releases

  • November 2009 - Second prototype including Mmtx: [1]
  • 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: [2]
  • May 2008 - First prototype (v1.0) - Has been removed from servers.


After eight months of existence the NCBO Annotator counts already eight academic groups including UCSF, University of Indiana and the Jackson Laboratory 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. Resource_Index).

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

Press Releases


  • Integrating text mining into the MGI biocuration workflow. Dowell KG, McAndrews-Hill MS, Hill DP, Drabkin HJ, Blake JA. Database (Oxford). 2009;2009:bap019. Epub 2009 Nov 21. PMID: 20157492 [PubMed] Free article
  • Using the NCBO Web Services for Concept Recognition and Ontology Annotation of Expression Datasets Simon Twigger, Joey Geiger, Jennifer Smith. SWAT4LS-2009.

Collaboration & Acknowledgment