Difference between revisions of "NCBO Annotator community"

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== Annotator GoogleGroup ==
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For discussions on use cases and experiences with the NCBO Annotator, e.g. parameters, ontologies, semantic expansion, see the [http://groups.google.com/group/annotator-discuss Annotator Users GoogleGroup] and join in discussions with fellow users (group started March 2010).
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== Mouse Genome Informatics (MGI), The Jackson Laboratory ==
 
== Mouse Genome Informatics (MGI), The Jackson Laboratory ==
  
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=== Use case ===
 
=== Use case ===
  
Researchers at the [http://www.jax.org 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.
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Researchers at the [http://www.jax.org 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.
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=== Latest news ===
 
  
 
=== Ontologies used ===
 
=== Ontologies used ===
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Researchers at the [http://www.compbio.iupui.edu/mooney/ Mooney Lab] are evaluating the utility of embedding the service in their research management system called [http://laboratree.org Laboratree]; so that any textual annotation created in Laboratree would also have corresponding ontology concept annotations.
 
Researchers at the [http://www.compbio.iupui.edu/mooney/ Mooney Lab] are evaluating the utility of embedding the service in their research management system called [http://laboratree.org Laboratree]; so that any textual annotation created in Laboratree would also have corresponding ontology concept annotations.
 
=== Latest news ===
 
  
  
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=== Use case ===
 
=== Use case ===
  
Researchers at the [http://compbio.uchsc.edu/Hunter_lab/CCP_website/index.html Center for Computational Pharmacology] are testing the OBA in their UIMA plafform.
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Researchers at the [http://compbio.uchsc.edu/Hunter_lab/CCP_website/index.html Center for Computational Pharmacology] are testing the Annotator in their UIMA platform.
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=== Latest news ===
 
  
 
=== Ontologies used ===
 
=== Ontologies used ===
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This reasearch was initiated in the context of the NCBO DBP: [http://bioontology.org/dbp_hiv.html Analyzing Evidence in HIV Clinical Trials].
 
This reasearch was initiated in the context of the NCBO DBP: [http://bioontology.org/dbp_hiv.html 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 ===
 
=== Ontologies used ===
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This research was initiated in the context of the NCBO RO1: [[Ontology Development Information Extraction (ODIE)]].  
 
This research was initiated in the context of the NCBO RO1: [[Ontology Development Information Extraction (ODIE)]].  
  
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=== Use case ===
 
=== Use case ===
  
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=== Use case ===
 
=== Use case ===
  
=== Latest news ===
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=== Ontologies used ===
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Developers at [http://collabrx.com 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.
 
Developers at [http://collabrx.com 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.
  
=== Latest news ===
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* SNOMEDCT
 
* SNOMEDCT
 
* NCBI Taxonomy
 
* NCBI Taxonomy
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== The Ontological Discovery Environmeny (ODE), The Jackson Laboratory ==
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Contacts: [[mailto:Elissa.Chesler@jax.org Elissa Chesler]]
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=== Use case ===
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The [[http://ontologicaldiscovery.org/ 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.
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=== Ontologies used ===
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* Mouse adult gross anatomy (MA)
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* Mammalian phenotype (MP)
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* Gene Ontology (GO)
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* Medical Subject Headings (MeSH)

Latest revision as of 16:54, 18 August 2010

Contents

[edit] 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).

[edit] Mouse Genome Informatics (MGI), The Jackson Laboratory

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

[edit] 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.


[edit] 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)

[edit] Center for Computational Biology and Bioinformatics, Indiana University

Contacts: Sean Mooney and Peter H. Baenziger

[edit] 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.


[edit] Ontologies used

  • SNOMEDCT
  • MeSH
  • NCI

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

Contacts: Larry Hunter and Bill Baumgartner

[edit] Use case

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


[edit] 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)

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

Contacts: Ida Sim and Michael Bobak

[edit] 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.


[edit] Ontologies used

  • Human disease
  • Infectious disease
  • GALEN
  • UMLS

[edit] Department of Biomedical Informatics (DBMI), University of Pittsburgh

Contacts: Rebecca Crowley and Kevin Mitchell

[edit] 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).


[edit] Ontologies used

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

Contacts: Simon Twigger and Joey Geiger

[edit] Use case

[edit] Ontologies used

[edit] Radiological Sciences Lab (RSL), Stanford University

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

[edit] Use case

[edit] Ontologies used

  • NPO
  • GO
  • ChEBI

[edit] CollabRx

Contacts: Jeff Shrager and Mike Travers

[edit] 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.


[edit] Ontologies used

[edit] Butte Lab, Center for Biomedical Informatics Research, Stanford University

Contacts: Atul Butte and Shai Shen-Orr

[edit] Use case

[edit] Ontologies used

  • SNOMEDCT
  • NCBI Taxonomy


[edit] The Ontological Discovery Environmeny (ODE), The Jackson Laboratory

Contacts: [Elissa Chesler]

[edit] 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.


[edit] Ontologies used

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