NCBO Annotator community

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 OBA 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 OBA in their UIAA plafform.

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].

Latest news

Requirement: recent interaction with Michael has confirmed they would need annotations in OWL in order to open them into an application like Protege and query them.

Requirement: semantic distance service(s) provided (i) within the annotation workflow and (ii) independently within NCBO ontology services.

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 reasearch was initiated in the context of the NCBO RO1: [Ontology Development Information Extraction (ODIE)].

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

Contacts: [Simon Twigger] and [Joey Geiger]

Radiological Sciences Lab (RSL), Stanford University

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

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.

Butte Lab, Center for Biomedical Informatics Research, Stanford University

Contacts: [Atul Butte] and [Shai Shen-Orr]

Ontologies used

• SNOMEDCT
• NCBI Taxonomy