NCBO Annotator community

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Annotator GoogleGroup

For discussions on use cases and experiences with the NCBO Annotator, e.g. parameters, ontologies, semantic expansion, see the Annotator Users GoogleGroup and join in discussions with fellow users (group started March 2010).

Mouse Genome Informatics (MGI), The Jackson Laboratory

Contacts: [Judith A. Blake] and [Karen Dowell]

Use case

Researchers at the Jackson Lab are evaluating the utility of the Annotator Web service in triaging articles for curation based on the ontology terms recognized in their title and abstract.


Ontologies used

  • Mouse gross anatomy and development (EMAP)
  • Mouse adult gross anatomy (MA)
  • Mouse pathology (MPATH)
  • Mammalian phenotype (MP)
  • Human disease (DOID)
  • Human developmental anatomy – Timed version (EHDA)
  • Human developmental anatomy – Abstract version (EHDAA)
  • Biological process
  • Cellular component
  • Molecular function
  • Mouse/Human Gene dictionary (JAXMGD)

Center for Computational Biology and Bioinformatics, Indiana University

Contacts: Sean Mooney and Peter H. Baenziger

Use case

Researchers at the Mooney Lab are evaluating the utility of embedding the service in their research management system called Laboratree; so that any textual annotation created in Laboratree would also have corresponding ontology concept annotations.


Ontologies used

  • SNOMEDCT
  • MeSH
  • NCI

Center for Computational Pharmacology (CCP), University of Colorado, Denver

Contacts: Larry Hunter and Bill Baumgartner

Use case

Researchers at the Center for Computational Pharmacology are testing the Annotator in their UIMA platform.


Ontologies used

  • GO (BP, MF, CC)
  • BRENDA tissue / enzyme source (BTO)
  • Cell Type (CL)
  • Chemical entities of biological interest (ChEBI)
  • Evidence codes (ECO)
  • FMA
  • Mammalian phenotype (MP)
  • OBO relationship types (OBO_REL)
  • Protein Ontology (PRO)
  • Protein-protein Interaction (MI)
  • Sequence Ontology (SO)

Center for Computational Pharmacology, University of California, San Francisco (UCSF)

Contacts: Ida Sim and Michael Bobak

Use case

Researchers working on Trialbank create annotations for HIV/AIDS clinical trials in order to provide a Web application for visualizing, and comparing the trials. They are evaluating the use of OBA to process the ‘health condition’, ‘intervention’ and ‘outcomes’ fields for trial records from [clinicaltrials.gov].

This reasearch was initiated in the context of the NCBO DBP: Analyzing Evidence in HIV Clinical Trials.


Ontologies used

  • Human disease
  • Infectious disease
  • GALEN
  • UMLS

Department of Biomedical Informatics (DBMI), University of Pittsburgh

Contacts: Rebecca Crowley and Kevin Mitchell

Use case

Researcher of Pr. Crowley's group are testing the OBA in the context of developing ODIE, a toolkit for using ontologies to extract information from free-text clinical documents and using free-text clinical documents to enrich existing ontologies.

This research was initiated in the context of the NCBO RO1: Ontology Development Information Extraction (ODIE).


Ontologies used

Human and Molecular Genetics Center (HMGC), Medical College of Wisconsin

Contacts: Simon Twigger and Joey Geiger

Use case

Ontologies used

Radiological Sciences Lab (RSL), Stanford University

Contacts: David Paik and Nathan Baker and Srikanth Adiga and Madhurima Bhattacharjee

Use case

Ontologies used

  • NPO
  • GO
  • ChEBI

CollabRx

Contacts: Jeff Shrager and Mike Travers

Use case

Developers at Collabrx are embedding the service in their Rex platform for processing user generated content; and will evaluate the suitability of using medical dictionaries for processing such content.


Ontologies used

Butte Lab, Center for Biomedical Informatics Research, Stanford University

Contacts: Atul Butte and Shai Shen-Orr

Use case

Ontologies used

  • SNOMEDCT
  • NCBI Taxonomy


The Ontological Discovery Environmeny (ODE), The Jackson Laboratory

Contacts: [Elissa Chesler]

Use case

The [Ontological Discovery Environment] uses the Annotator Web service to automatically annotate user uploaded Gene Sets. By automating this step, our users can quickly get up and running without tedious manual selection. The ontology terms enable diverse data integration for ODE's built-in analysis tools and facilitate data discovery through comprehensive search indexing.


Ontologies used

  • Mouse adult gross anatomy (MA)
  • Mammalian phenotype (MP)
  • Gene Ontology (GO)
  • Medical Subject Headings (MeSH)
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