https://www.bioontology.org//mediawiki/api.php?action=feedcontributions&user=Jjay&feedformat=atomNCBO Wiki - User contributions [en]2024-03-29T12:57:26ZUser contributionsMediaWiki 1.35.9https://www.bioontology.org//mediawiki/index.php?title=NCBO_Annotator_community&diff=10114NCBO Annotator community2010-08-18T23:54:46Z<p>Jjay: Adding our site to the wiki</p>
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<div>== Annotator GoogleGroup ==<br />
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). <br />
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== Mouse Genome Informatics (MGI), The Jackson Laboratory ==<br />
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Contacts: [[mailto:judith.blake@jax.org Judith A. Blake]] and [[mailto:kgd@informatics.jax.org Karen Dowell]]<br />
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=== Use case ===<br />
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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.<br />
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=== Ontologies used ===<br />
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* Mouse gross anatomy and development (EMAP)<br />
* Mouse adult gross anatomy (MA)<br />
* Mouse pathology (MPATH)<br />
* Mammalian phenotype (MP)<br />
* Human disease (DOID)<br />
* Human developmental anatomy – Timed version (EHDA)<br />
* Human developmental anatomy – Abstract version (EHDAA)<br />
* Biological process<br />
* Cellular component<br />
* Molecular function<br />
* Mouse/Human Gene dictionary (JAXMGD)<br />
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== Center for Computational Biology and Bioinformatics, Indiana University ==<br />
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Contacts: [mailto:sdmooney@iupui.edu Sean Mooney] and [mailto:peter@compbio.iupui.edu Peter H. Baenziger]<br />
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=== Use case ===<br />
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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.<br />
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=== Ontologies used ===<br />
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* SNOMEDCT<br />
* MeSH<br />
* NCI<br />
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== Center for Computational Pharmacology (CCP), University of Colorado, Denver ==<br />
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Contacts: [mailto:Larry.Hunter@uchsc.edu Larry Hunter] and [mailto:William.Baumgartner@ucdenver.edu Bill Baumgartner]<br />
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=== Use case ===<br />
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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.<br />
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=== Ontologies used ===<br />
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* GO (BP, MF, CC)<br />
* BRENDA tissue / enzyme source (BTO)<br />
* Cell Type (CL)<br />
* Chemical entities of biological interest (ChEBI)<br />
* Evidence codes (ECO)<br />
* FMA<br />
* Mammalian phenotype (MP)<br />
* OBO relationship types (OBO_REL)<br />
* Protein Ontology (PRO)<br />
* Protein-protein Interaction (MI)<br />
* Sequence Ontology (SO)<br />
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== Center for Computational Pharmacology, University of California, San Francisco (UCSF) ==<br />
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Contacts: [mailto:ida.sim@ucsf.edu Ida Sim] and [mailto:michael.bobak@ucsf.edu Michael Bobak]<br />
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=== Use case ===<br />
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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]].<br />
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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].<br />
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=== Ontologies used ===<br />
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* Human disease<br />
* Infectious disease<br />
* GALEN<br />
* UMLS<br />
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== Department of Biomedical Informatics (DBMI), University of Pittsburgh ==<br />
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Contacts: [mailto:CrowleyRS@upmc.edu Rebecca Crowley] and [mailto:mitchellkj@upmc.edu Kevin Mitchell]<br />
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=== Use case ===<br />
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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.<br />
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This research was initiated in the context of the NCBO RO1: [[Ontology Development Information Extraction (ODIE)]]. <br />
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=== Ontologies used ===<br />
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== Human and Molecular Genetics Center (HMGC), Medical College of Wisconsin ==<br />
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Contacts: [mailto:simont@hmgc.mcw.edu Simon Twigger] and [mailto:jfgeiger@mcw.edu Joey Geiger]<br />
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=== Use case ===<br />
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=== Ontologies used ===<br />
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== Radiological Sciences Lab (RSL), Stanford University ==<br />
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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]<br />
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=== Use case ===<br />
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=== Ontologies used ===<br />
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* NPO<br />
* GO<br />
* ChEBI<br />
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== CollabRx ==<br />
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Contacts: [mailto:jshrager@stanford.edu Jeff Shrager] and [mailto:mt@alum.mit.edu Mike Travers]<br />
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=== Use case ===<br />
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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.<br />
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=== Ontologies used ===<br />
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== Butte Lab, Center for Biomedical Informatics Research, Stanford University ==<br />
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Contacts: [mailto:abutte@stanford.edu Atul Butte] and [mailto:shenorr@stanford.edu Shai Shen-Orr]<br />
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=== Use case ===<br />
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=== Ontologies used ===<br />
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* SNOMEDCT<br />
* NCBI Taxonomy<br />
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== The Ontological Discovery Environmeny (ODE), The Jackson Laboratory ==<br />
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Contacts: [[mailto:Elissa.Chesler@jax.org Elissa Chesler]]<br />
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=== Use case ===<br />
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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.<br />
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=== Ontologies used ===<br />
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* Mouse adult gross anatomy (MA)<br />
* Mammalian phenotype (MP)<br />
* Gene Ontology (GO)<br />
* Medical Subject Headings (MeSH)</div>Jjay