Difference between revisions of "Resource Index"

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''Indexing biomedical resources with ontology concepts thanks to semantic annotations ''
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''Indexing biomedical resources with ontology concepts ''
  
 
=== Presentation & Demonstration ===
 
=== Presentation & Demonstration ===
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The range of publicly available biomedical data is enormous and is expanding fast. This expansion means that researchers now face a hurdle to extracting the data they need from the large numbers of data that are available. Biomedical researchers have turned to ontologies and terminologies to structure and annotate their data with ontology concepts for better search and retrieval.  
 
The range of publicly available biomedical data is enormous and is expanding fast. This expansion means that researchers now face a hurdle to extracting the data they need from the large numbers of data that are available. Biomedical researchers have turned to ontologies and terminologies to structure and annotate their data with ontology concepts for better search and retrieval.  
  
Using the annotation workflow of the [[Annotator_Web_service]] NCBO has built an biomedical resources index in which biomedical data is indexed by ontology concepts. The index allows a user to search for biomedical data based on ontology concepts. The NCBO Resource Index is directly queriable in the [[http://bioportal.bioontology.org BioPortal]] ontology repository: when a user browses a given concept, he has access (link) to the list of resource elements that have been annotated with this concept. A user can also search for resources direclty using the 'All resources' tab.
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Using the annotation workflow of the [[Annotator_Web_service|Annotator Web Service]] NCBO has built an biomedical resources index in which biomedical data is indexed by ontology concepts. The index allows a user to search for biomedical data based on ontology concepts. The NCBO Resource Index is directly queriable in the [http://bioportal.bioontology.org BioPortal] ontology repository: when a user browses a given concept, he has access (link) to the list of resource elements that have been annotated with this concept. A user can also search for resources directly using the 'All resources' tab.
  
In the OBR index, we have processed the textual metadata of elements from several biomedical resources such as: [http://www.ebi.ac.uk/arrayexpress/ ArrayExpress], [http://clinicaltrials.gov/ Clinical Trials.gov], [http://goldminer.arrs.org GoldMiner], [http://www.ncbi.nlm.nih.gov/geo/ Gene Expression Omnibus (GEO)] and others. The annotations in the index keeps track of the structures of elements that have been annotated i.e., from which part of the element (e.g., title, description) an annotation has been produced. This information is used to score annotations.  
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In the NCBO Resource Index, we have processed the textual metadata of elements from several biomedical resources such as: [http://www.ebi.ac.uk/arrayexpress/ ArrayExpress], [http://clinicaltrials.gov/ Clinical Trials.gov], [http://goldminer.arrs.org GoldMiner], [http://www.ncbi.nlm.nih.gov/geo/ Gene Expression Omnibus (GEO)] and others. The annotations in the index keeps track of the structures of elements that have been annotated i.e., from which part of the element (e.g., title, description) an annotation has been produced. This information is used to score annotations.  
  
[[Image:NCBO_BRI_workflow.png|thumb|NCBO Biomedical Resources Index workflow]]
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[[Image:NCBO_Resource_Index_workflow.png|thumb|NCBO Resource Index workflow]]
  
[[Image:OBR_index_creation_resources.png|thumb|NCBO Biomedical Resources Index creation]]
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[[Image:OBR_index_creation_resources.png|thumb|NCBO Resource Index creation]]
  
Please try the [NCBO Biomedical Resource Index in BioPortal http://bioportal.bioontology.org/all_resources].
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Please try the [http://bioportal.bioontology.org/resources NCBO Resource Index] in BioPortal.
  
 
=== Contacts ===
 
=== Contacts ===
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*For questions or feature requests, contact [mailto:support@bioontology.org?subject=NCBO%20Resources%20Index%20support Support]  
 
*For questions or feature requests, contact [mailto:support@bioontology.org?subject=NCBO%20Resources%20Index%20support Support]  
  
=== Documentation & References ===
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=== Documentation ===
  
 
* [[Resource Index REST Web Service User Guide]]
 
* [[Resource Index REST Web Service User Guide]]
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* [http://rest.bioontology.org/resource_index/resources/list/ Currently available resource list.]
 
* [http://rest.bioontology.org/resource_index/resources/list/ Currently available resource list.]
  
* Resource index design and underlying data model: [[Image:OBR_result_model.png|thumb| NCBO Biomedical Resources Index data model]]
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* Add your own resource by developing a [http://stanford.edu/~whetzel/downloads/RATDevelopment.pdf Resource Access Tool]  
  
* Please refer to:  
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* Resource index design and underlying data model (see the bottom image on the right) [[Image:OBR_result_model.png|thumb| NCBO Resource Index data model]]
  
** Clement Jonquet, Mark A. Musen and Nigam H. Shah, '''A System for Ontology-Based Annotation of Biomedical Data''', ''In A. Bairoch, S. Cohen-Boulakia and C. Froidevaux (eds): International Workshop on Data Integration in The Life Sciences 2008, DILS'08,''  Vol. 5109, Lecture Notes in BioInformatics, p.144-152, Springer-Verlag, June 2008, Evry, France. [http://dils2008.lri.fr/ conference's web site] [http://www.stanford.edu/~jonquet/Publications/Documents/Article-DILS08_Jonquet_Musen_Shah_published.pdf pdf - 431Kb]
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* [[Processing_OBR_Resources]] - Notes on resources being processed - Developers only.
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* [[Populating_OBS_database]] - Notes on the population of the NCBO Resource Index DB used in the annotation workflow - Developers only.
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* [https://bmir-gforge.stanford.edu/gf/project/obs/ Corresponding Gforge project] - Developers only.
  
** Nigam H. Shah, Clement Jonquet, Annie P. Chiang, Atul J. Butte, Rong Chen, Mark A. Musen, '''Ontology-driven Indexing of Public Datasets for Translational Bioinformatics''', ''BMC Bioinformatics'', Vol. 10, February 2009. [http://www.biomedcentral.com/bmcbioinformatics/ journal's web site]  [http://www.stanford.edu/~jonquet/Publications/Documents/Article-BMCBioInformatics08-Shah-Jonquet-Ontolgy-based_Indexing.pdf pdf - 651 Kb]
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=== References ===
  
* [[Processing_OBR_Resources]] - Notes on resources being processed - Developers only.
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* Clement Jonquet, Mark A. Musen and Nigam H. Shah, '''A System for Ontology-Based Annotation of Biomedical Data''', ''In A. Bairoch, S. Cohen-Boulakia and C. Froidevaux (eds): International Workshop on Data Integration in The Life Sciences 2008, DILS'08,''  Vol. 5109, Lecture Notes in BioInformatics, p.144-152, Springer-Verlag, June 2008, Evry, France. [http://dils2008.lri.fr/ conference's web site] [http://www.stanford.edu/~jonquet/Publications/Documents/Article-DILS08_Jonquet_Musen_Shah_published.pdf pdf - 431Kb]
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*  Nigam H. Shah, Clement Jonquet, Annie P. Chiang, Atul J. Butte, Rong Chen, Mark A. Musen, '''Ontology-driven Indexing of Public Datasets for Translational Bioinformatics''', ''BMC Bioinformatics'', Vol. 10, February 2009. [http://www.biomedcentral.com/bmcbioinformatics/ journal's web site] [http://www.stanford.edu/~jonquet/Publications/Documents/Article-BMCBioInformatics08-Shah-Jonquet-Ontolgy-based_Indexing.pdf pdf - 651 Kb]
  
* [[Populating_OBS_database]] - Notes on the population of the OBS DB used in the annotation workflow - Developers only.
 
  
* [https://bmir-gforge.stanford.edu/gf/project/obs/ Corresponding Gforge project] - Developers only.
 
  
 
=== Versions (prototypes & releases) ===
 
=== Versions (prototypes & releases) ===
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=== Collaboration & Acknowledgment ===
 
=== Collaboration & Acknowledgment ===
  
* The annotation workflow used to create the NCBO Biomedical Resource Index uses Mgrep in the concept recognition step. We acknowledge the assistance of Manhong Dai and Fan Meng from the [http://portal.ncibi.org/gateway/ National Center for Integrative Biomedical Informatics] (NCIBI).
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* The annotation workflow used to create the NCBO Resource Index uses Mgrep in the concept recognition step. We acknowledge the assistance of Manhong Dai and Fan Meng from the [http://portal.ncibi.org/gateway/ National Center for Integrative Biomedical Informatics] (NCIBI).
  
* The user interface for the NCBO Biomedical Resource Index client in BioPortal (http://bioportal.bioontology.org/all_resources) is designed & developped by NCBO members from [http://www.thechiselgroup.org/ University of Victoria]
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* The user interface for the NCBO Resource Index client in BioPortal (http://bioportal.bioontology.org/all_resources) is designed & developed by NCBO members from [http://www.thechiselgroup.org/ University of Victoria]

Latest revision as of 19:16, 8 April 2013

Indexing biomedical resources with ontology concepts

Presentation & Demonstration

The range of publicly available biomedical data is enormous and is expanding fast. This expansion means that researchers now face a hurdle to extracting the data they need from the large numbers of data that are available. Biomedical researchers have turned to ontologies and terminologies to structure and annotate their data with ontology concepts for better search and retrieval.

Using the annotation workflow of the Annotator Web Service NCBO has built an biomedical resources index in which biomedical data is indexed by ontology concepts. The index allows a user to search for biomedical data based on ontology concepts. The NCBO Resource Index is directly queriable in the BioPortal ontology repository: when a user browses a given concept, he has access (link) to the list of resource elements that have been annotated with this concept. A user can also search for resources directly using the 'All resources' tab.

In the NCBO Resource Index, we have processed the textual metadata of elements from several biomedical resources such as: ArrayExpress, Clinical Trials.gov, GoldMiner, Gene Expression Omnibus (GEO) and others. The annotations in the index keeps track of the structures of elements that have been annotated i.e., from which part of the element (e.g., title, description) an annotation has been produced. This information is used to score annotations.

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NCBO Resource Index workflow
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NCBO Resource Index creation

Please try the NCBO Resource Index in BioPortal.

Contacts

  • For questions or feature requests, contact Support

Documentation

  • Resource index design and underlying data model (see the bottom image on the right)
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    NCBO Resource Index data model
  • Populating_OBS_database - Notes on the population of the NCBO Resource Index DB used in the annotation workflow - Developers only.

References

  • Clement Jonquet, Mark A. Musen and Nigam H. Shah, A System for Ontology-Based Annotation of Biomedical Data, In A. Bairoch, S. Cohen-Boulakia and C. Froidevaux (eds): International Workshop on Data Integration in The Life Sciences 2008, DILS'08, Vol. 5109, Lecture Notes in BioInformatics, p.144-152, Springer-Verlag, June 2008, Evry, France. conference's web site pdf - 431Kb
  • Nigam H. Shah, Clement Jonquet, Annie P. Chiang, Atul J. Butte, Rong Chen, Mark A. Musen, Ontology-driven Indexing of Public Datasets for Translational Bioinformatics, BMC Bioinformatics, Vol. 10, February 2009. journal's web site pdf - 651 Kb


Versions (prototypes & releases)

  • December 2008 - API specification for the new prototype (v1.2) - not maintained anymore, please do not use.

Collaboration & Acknowledgment