Difference between revisions of "Resource Index"
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| − | ''Indexing biomedical resources with ontology concepts | + | ''Indexing biomedical resources with ontology concepts '' |
=== Presentation & Demonstration === | === Presentation & Demonstration === | ||
| Line 5: | Line 5: | ||
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 | + | 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 | + | 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: | + | [[Image:NCBO_Resource_Index_workflow.png|thumb|NCBO Resource Index workflow]] |
| − | [[Image:OBR_index_creation_resources.png|thumb|NCBO | + | [[Image:OBR_index_creation_resources.png|thumb|NCBO Resource Index creation]] |
| − | Please try the [ | + | Please try the [http://bioportal.bioontology.org/resources NCBO Resource Index] in BioPortal. |
=== Contacts === | === Contacts === | ||
| Line 19: | Line 19: | ||
*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 | + | === Documentation === |
* [[Resource Index REST Web Service User Guide]] | * [[Resource Index REST Web Service User Guide]] | ||
| Line 25: | Line 25: | ||
* [http://rest.bioontology.org/resource_index/resources/list/ Currently available resource list.] | * [http://rest.bioontology.org/resource_index/resources/list/ Currently available resource list.] | ||
| − | * | + | * Add your own resource by developing a [http://stanford.edu/~whetzel/downloads/RATDevelopment.pdf Resource Access Tool] |
| − | * | + | * 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]] |
| − | * | + | * [[Processing_OBR_Resources]] - Notes on resources being processed - Developers only. |
| + | |||
| + | * [[Populating_OBS_database]] - Notes on the population of the NCBO Resource Index DB used in the annotation workflow - Developers only. | ||
| + | |||
| + | * [https://bmir-gforge.stanford.edu/gf/project/obs/ Corresponding Gforge project] - 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. [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] | ||
| − | |||
| − | |||
=== Versions (prototypes & releases) === | === Versions (prototypes & releases) === | ||
| Line 49: | Line 53: | ||
=== Collaboration & Acknowledgment === | === Collaboration & Acknowledgment === | ||
| − | * The annotation workflow used to create the NCBO | + | * 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 | + | * 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 18:16, 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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Please try the NCBO Resource Index in BioPortal.
Contacts
- For questions or feature requests, contact Support
Documentation
- Add your own resource by developing a Resource Access Tool
- Resource index design and underlying data model (see the bottom image on the right) Error creating thumbnail: /srv/www/vhosts/www.bioontology.org/app/mediawiki-1.35.9/includes/shell/limit.sh: line 61: ulimit: cpu time: cannot modify limit: Permission denied /srv/www/vhosts/www.bioontology.org/app/mediawiki-1.35.9/includes/shell/limit.sh: line 84: ulimit: virtual memory: cannot modify limit: Permission denied /srv/www/vhosts/www.bioontology.org/app/mediawiki-1.35.9/includes/shell/limit.sh: line 90: ulimit: file size: cannot modify limit: Permission denied /bin/bash: /usr/bin/convert: No such file or directory Error code: 127
- Processing_OBR_Resources - Notes on resources being processed - Developers only.
- Populating_OBS_database - Notes on the population of the NCBO Resource Index DB used in the annotation workflow - Developers only.
- Corresponding Gforge project - 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)
- 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, 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 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 Resource Index client in BioPortal (http://bioportal.bioontology.org/all_resources) is designed & developed by NCBO members from University of Victoria