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 direclty 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.
Please try the NCBO Resource Index in BioPortal.
- For questions or feature requests, contact Support
- Resource index design and underlying data model (see the bottom image on the right) Error creating thumbnail: /srv/www/vhosts/ncbo.bioontology.org/app/mediawiki-1.30.2/includes/shell/limit.sh: line 61: ulimit: cpu time: cannot modify limit: Permission denied /srv/www/vhosts/ncbo.bioontology.org/app/mediawiki-1.30.2/includes/shell/limit.sh: line 84: ulimit: virtual memory: cannot modify limit: Permission denied /srv/www/vhosts/ncbo.bioontology.org/app/mediawiki-1.30.2/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.
- 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 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).