Difference between revisions of "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 [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 Annotator Web service in triaging articles for curation based on the ontology terms recognized in their title and abstract. | |
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=== Ontologies used === | === Ontologies used === | ||
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* Mouse/Human Gene dictionary (JAXMGD) | * Mouse/Human Gene dictionary (JAXMGD) | ||
| − | == Center for Computational Biology and Bioinformatics | + | == Center for Computational Biology and Bioinformatics, Indiana University == |
| − | Contacts: | + | Contacts: [mailto:sdmooney@iupui.edu Sean Mooney] and [mailto:peter@compbio.iupui.edu Peter H. Baenziger] |
=== Use case === | === Use case === | ||
| − | + | 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. | |
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=== Ontologies used === | === Ontologies used === | ||
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* NCI | * NCI | ||
| − | == Center for Computational Pharmacology ( | + | == Center for Computational Pharmacology (CCP), University of Colorado, Denver == |
| − | Contacts: | + | Contacts: [mailto:Larry.Hunter@uchsc.edu Larry Hunter] and [mailto:William.Baumgartner@ucdenver.edu Bill Baumgartner] |
=== Use case === | === Use case === | ||
| − | + | 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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=== Ontologies used === | === Ontologies used === | ||
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* Sequence Ontology (SO) | * Sequence Ontology (SO) | ||
| − | == Center for Computational Pharmacology (UCSF) == | + | == Center for Computational Pharmacology, University of California, San Francisco (UCSF) == |
| − | Contacts: | + | Contacts: [mailto:ida.sim@ucsf.edu Ida Sim] and [mailto:michael.bobak@ucsf.edu Michael Bobak] |
=== Use case === | === Use case === | ||
| − | + | Researchers working on [http://rctbank.ucsf.edu/ 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 [[http://clinicaltrials.gov/ clinicaltrials.gov]]. | |
| + | |||
| + | This reasearch was initiated in the context of the NCBO DBP: [http://bioontology.org/dbp_hiv.html Analyzing Evidence in HIV Clinical Trials]. | ||
| + | |||
| + | |||
=== Ontologies used === | === Ontologies used === | ||
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== Department of Biomedical Informatics (DBMI), University of Pittsburgh == | == Department of Biomedical Informatics (DBMI), University of Pittsburgh == | ||
| − | Contacts: | + | Contacts: [mailto:CrowleyRS@upmc.edu Rebecca Crowley] and [mailto:mitchellkj@upmc.edu Kevin Mitchell] |
=== Use case === | === 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 === | === Ontologies used === | ||
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== Human and Molecular Genetics Center (HMGC), Medical College of Wisconsin == | == Human and Molecular Genetics Center (HMGC), Medical College of Wisconsin == | ||
| − | Contacts: | + | Contacts: [mailto:simont@hmgc.mcw.edu Simon Twigger] and [mailto:jfgeiger@mcw.edu Joey Geiger] |
=== Use case === | === Use case === | ||
| − | + | ||
=== Ontologies used === | === Ontologies used === | ||
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== Radiological Sciences Lab (RSL), Stanford University == | == Radiological Sciences Lab (RSL), Stanford University == | ||
| − | Contacts: | + | Contacts: [mailto:david.paik@stanford.edu David Paik] and [mailto:baker@biochem.wustl.edu Nathan Baker] and [mailto:srikanth_adiga@persistent.co.in Srikanth Adiga] and [mailto:madhurima_bhattacharjee@persistent.co.in Madhurima Bhattacharjee] |
=== Use case === | === Use case === | ||
| − | + | ||
=== Ontologies used === | === Ontologies used === | ||
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== CollabRx == | == CollabRx == | ||
| − | Contacts: | + | Contacts: [mailto:jshrager@stanford.edu Jeff Shrager] and [mailto:mt@alum.mit.edu Mike Travers] |
| + | |||
| + | === Use case === | ||
| + | |||
| + | 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. | ||
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| + | |||
| + | |||
| + | === Ontologies used === | ||
| + | |||
| + | == Butte Lab, Center for Biomedical Informatics Research, Stanford University == | ||
| + | |||
| + | Contacts: [mailto:abutte@stanford.edu Atul Butte] and [mailto:shenorr@stanford.edu Shai Shen-Orr] | ||
| + | |||
| + | === Use case === | ||
| + | |||
| + | |||
| + | |||
| + | === Ontologies used === | ||
| + | |||
| + | * SNOMEDCT | ||
| + | * NCBI Taxonomy | ||
| + | |||
| + | |||
| + | == The Ontological Discovery Environmeny (ODE), The Jackson Laboratory == | ||
| + | |||
| + | Contacts: [[mailto:Elissa.Chesler@jax.org Elissa Chesler]] | ||
=== Use case === | === Use case === | ||
| − | + | 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. | |
| + | |||
| + | |||
=== Ontologies used === | === Ontologies used === | ||
| + | |||
| + | * Mouse adult gross anatomy (MA) | ||
| + | * Mammalian phenotype (MP) | ||
| + | * Gene Ontology (GO) | ||
| + | * Medical Subject Headings (MeSH) | ||
Latest revision as of 15:54, 18 August 2010
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)