Principled design of the modern Web architecture
ACM Transactions on Internet Technology (TOIT)
Towards the development of a conceptual distance metric for the UMLS
Journal of Biomedical Informatics
A review of ontology based query expansion
Information Processing and Management: an International Journal
Using annotations from controlled vocabularies to find meaningful associations
DILS'07 Proceedings of the 4th international conference on Data integration in the life sciences
Collecting Community-Based Mappings in an Ontology Repository
ISWC '08 Proceedings of the 7th International Conference on The Semantic Web
Biomedical publication knowledge acquisition, processing and dissemination with CORAAL
OTM'10 Proceedings of the 2010 international conference on On the move to meaningful internet systems: Part II
Resource discovery considering semantic properties in data grid environments
Globe'11 Proceedings of the 4th international conference on Data management in grid and peer-to-peer systems
Web Semantics: Science, Services and Agents on the World Wide Web
ReVeaLD: A user-driven domain-specific interactive search platform for biomedical research
Journal of Biomedical Informatics
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We present a system for ontology based annotation and indexing of biomedical data; the key functionality of this system is to provide a service that enables users to locate biomedical data resources related to particular ontology concepts. The system's indexing workflow processes the text metadata of diverse resource elements such as gene expression data sets, descriptions of radiology images, clinical-trial reports, and PubMed article abstracts to annotate and index them with concepts from appropriate ontologies. The system enables researchers to search biomedical data sources using ontology concepts. What distinguishes this work from other biomedical search tools is:(i) the use of ontology semantics to expand the initial set of annotations automatically generated by a concept recognition tool; (ii) the unique ability to use almost all publicly available biomedical ontologies in the indexing workflow; (iii) the ability to provide the user with integrated results from different biomedical resource in one place. We discuss the system architecture as well as our experiences during its prototype implementation (http://www.bioontology.org/tools.html).