NCBO Biomedical Resources Index - Revision history

Jonquet: Redirecting to Resource Index

2009-09-14T18:01:58Z

Redirecting to Resource Index

Jonquet: Replacing page with 'Page moved to Resource_Index'

2009-09-12T00:57:09Z

Replacing page with 'Page moved to Resource_Index'

Jonquet: /* Documentation & References */

2009-09-09T18:03:47Z

Documentation & References

Jonquet: /* Documentation & References */

2009-09-09T18:03:37Z

Documentation & References

Whetzel at 22:32, 22 August 2009

2009-08-22T22:32:50Z

Jonquet: /* Presentation & Demonstration */

2009-07-23T00:29:08Z

Presentation & Demonstration

Jonquet: /* Presentation & Demonstration */

2009-07-23T00:28:50Z

Presentation & Demonstration

Jonquet: /* Versions (prototypes & releases) */

2009-07-17T22:25:45Z

Versions (prototypes & releases)

Jonquet: /* Documentation & References */

2009-05-15T17:04:10Z

Documentation & References

Jonquet: /* Documentation & References */

2009-05-13T00:24:14Z

Documentation & References

← Older revision		Revision as of 18:01, 14 September 2009
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−	~~Page moved to~~ [[Resource_Index]]	+	#REDIRECT [[Resource_Index]]

← Older revision		Revision as of 00:57, 12 September 2009
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−	~~''Indexing biomedical resources with ontology concepts thanks~~ to ~~semantic annotations ''~~	+	Page moved to [[Resource_Index]]
−
−	~~=== 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.
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−	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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−	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.
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−	~~[[Image:NCBO_BRI_workflow.png\|thumb\|NCBO Biomedical Resources Index workflow]]~~
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−	~~[[Image:OBR_index_creation_resources.png\|thumb\|NCBO Biomedical Resources Index creation]]~~
−
−	~~Please try the [NCBO Biomedical Resource Index in BioPortal http://bioportal.bioontology.org/all_resources].~~
−
−	~~=== Contacts ===~~
−
−	*For questions or feature requests, contact [mailto:support@bioontology.org?subject=NCBO%20Resources%20Index%20support Support]
−
−	~~=== Documentation & References ===~~
−
−	* [[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 and updated 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] [~~http://www.stanford.edu/~jonquet/Publications/Documents/Article-DILS08_Jonquet_Musen_Shah_published.pdf 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]~~
−
−	* [[Processing_OBR_Resources]] - Notes on resources being processed - Developers only.
−
−	* [[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) ===~~
−
−	* February 2009 - New prototype release (v1.2). API: http://obs.bioontology.org/obr/OBR_v1.2_rest.html
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−	* March 2008 - First prototype (v1 and v1.1) API: http://ncbolabs-dev2.stanford.edu:8080/Ontrez_v1_API/ - not maintained anymore, please do not use.
−
−	* December 2008 - API specification for the new prototype (v1.2) - not maintained anymore, please do not use.
−
−	~~=== 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 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]

@@ Line 35: / Line 35: @@
 * [[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.
+* [https://bmir-gforge.stanford.edu/gf/project/obs/ Corresponding Gforge project] - Developers only.
 === Versions (prototypes & releases) ===

← Older revision		Revision as of 18:03, 9 September 2009
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	* [[Populating_OBS_database]] - Notes on the population of the OBS DB used in the annotation workflow - Developers only.		* [[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) ===

@@ Line 17: / Line 17: @@
 === Contacts ===
-* Community & usage: [[mailto:whetzel@stanford.edu Trish Whetzel]]
+*For questions or feature requests, contact [mailto:support@bioontology.org?subject=NCBO%20Resources%20Index%20support Support]
 === Documentation & References ===

@@ Line 11: / Line 11: @@
 [[Image:NCBO_BRI_workflow.png|thumb|NCBO Biomedical Resources Index workflow]]
-[[Image:OBR_index_creation_resources.pngthumb|NCBO Biomedical Resources Index creation]]
+[[Image:OBR_index_creation_resources.png|thumb|NCBO Biomedical Resources Index creation]]
 Please try the [NCBO Biomedical Resource Index in BioPortal http://bioportal.bioontology.org/all_resources].

← Older revision		Revision as of 00:28, 23 July 2009
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	[[Image:NCBO_BRI_workflow.png\|thumb\|NCBO Biomedical Resources Index workflow]]		[[Image:NCBO_BRI_workflow.png\|thumb\|NCBO Biomedical Resources Index workflow]]
		+
		+	[[Image:OBR_index_creation_resources.pngthumb\|NCBO Biomedical Resources Index creation]]

	Please try the [NCBO Biomedical Resource Index in BioPortal http://bioportal.bioontology.org/all_resources].		Please try the [NCBO Biomedical Resource Index in BioPortal http://bioportal.bioontology.org/all_resources].

@@ Line 39: / Line 39: @@
 * February 2009 - New prototype release (v1.2). API: http://obs.bioontology.org/obr/OBR_v1.2_rest.html
-* March 2008 - First prototype (v1 and v1.1) API: http://ncbolabs-dev2.stanford.edu:8080/Ontrez_v1_API/ - not maintained anymore.
+* March 2008 - First prototype (v1 and v1.1) API: http://ncbolabs-dev2.stanford.edu:8080/Ontrez_v1_API/ - not maintained anymore, please do not use.
-* December 2008 - API specification for the new prototype (v1.2) - not maintained anymore.
+* December 2008 - API specification for the new prototype (v1.2) - not maintained anymore, please do not use.
 === Collaboration & Acknowledgment ===

← Older revision		Revision as of 17:04, 15 May 2009
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	* [[Processing_OBR_Resources]] - Notes on resources being processed - Developers only.		* [[Processing_OBR_Resources]] - Notes on resources being processed - Developers only.
		+
		+	* [[Populating_OBS_database]] - Notes on the population of the OBS DB used in the annotation workflow - Developers only.

	=== Versions (prototypes & releases) ===		=== Versions (prototypes & releases) ===

@@ Line 20: / Line 20: @@
 === Documentation & References ===
 * [[Resource Index REST Web Service User Guide]]
@@ Line 32: / Line 30: @@
 ** 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) ===