Difference between revisions of "NCBO Biomedical Resources Index"

Revision as of 16:12, 12 May 2009

Indexing biomedical resources with ontology concepts thanks to semantic annotations

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 direclty using the 'All resources' tab.

In the OBR index, we have processed the textual metadata of elements from five biomedical resources: [www.ebi.ac.uk/arrayexpress/ Array Express], Clinical Trials.gov, GoldMiner, [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:|thumb|NCBO Biomedical Resources Index workflow]]

Please try the [NCBO Annotator service in BioPortal http://bioportal.bioontology.org/annotate].

Contacts

Community & usage: [Trish Whetzel]
Design, utility & applications: [Nigam Shah] and [Clement Jonquet]
Technical support: [Clement Jonquet]

Documentation & References

Processing_OBR_Resources - Notes on resources being processed

Resource Index REST Web Service User Guide

Resource index design and underlying data model: Documentation here... to be move to the wiki soon.

Please refer to:

- 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)

February 2009 - New prototype release (v1.2).

March 2008 - First prototype (v1 and v1.1) API: http://ncbolabs-dev2.stanford.edu:8080/Ontrez_v1_API/ - not maintained anymore.

December 2008 - API specification for the new prototype (v1.2) - not maintained anymore.

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 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 University of Victoria

@@ Line 1: / Line 1: @@
-To come.
+''Indexing biomedical resources with ontology concepts thanks to semantic annotations ''
-Refers now to http://obs.bioontology.org
+=== 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 [[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.
+In the OBR index, we have processed the textual metadata of elements from five biomedical resources: [www.ebi.ac.uk/arrayexpress/ Array Express], [http://clinicaltrials.gov/ Clinical Trials.gov], [http://goldminer.arrs.org GoldMiner], [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:|thumb|NCBO Biomedical Resources Index workflow]]
+Please try the [NCBO Annotator service in BioPortal http://bioportal.bioontology.org/annotate].
+=== Contacts ===
+* Community & usage: [[mailto:whetzel@stanford.edu Trish Whetzel]]
+* Design, utility & applications: [[mailto:nigam@stanford.edu Nigam Shah]] and [[mailto:jonquet@stanford.edu Clement Jonquet]]
+* Technical support: [[mailto:jonquet@stanford.edu Clement Jonquet]]
+=== Documentation & References ===
+* [[Processing_OBR_Resources]] - Notes on resources being processed
+* [[Resource Index REST Web Service User Guide]]
+* Resource index design and underlying data model: [http://obs.bioontology.org/docs/obr/OBR_1.2_documentation.htm Documentation here]... to be move to the wiki soon.
+* Please refer to:
+** 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] [
+ 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. [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]
+=== Versions (prototypes & releases) ===
+* February 2009 - New prototype release (v1.2).
+* March 2008 - First prototype (v1 and v1.1) API: http://ncbolabs-dev2.stanford.edu:8080/Ontrez_v1_API/ - not maintained anymore.
+* December 2008 - API specification for the new prototype (v1.2) - not maintained anymore.
+=== 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).
+* 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]