Help will be provided for this task : Ontology-Based Annotator Web Service

Semantic annotation is part of the vision for the semantic web. Ontologies are required for this task, and although they are in common use, there is a lack of annotation tools for users that are convenient, simple to use and easily integrated into their processes. This paper presents an ontology-based annotator web service methodology that can annotate a piece of text with ontology concepts and return annotations in OWL. Currently, the annotation workflow is based on syntactic concept recognition (using concept names and synonyms) and on a set of semantic expansion algorithms that leverage the semantics in ontologies (e.g., is_a relations). The paper also describes an implementation of this service for life sciences and biomedicine. Our biomedical annotator service uses one of the largest available set of publicly available terminologies and ontologies. We used it to create an index of open biomedical resources. Both the deployed web service and a user interface can be accessed at (http://www.bioontology.org/tools.html).

[1]  Dina Demner-Fushman,et al.  Application of Information Technology: Essie: A Concept-based Search Engine for Structured Biomedical Text , 2007, J. Am. Medical Informatics Assoc..

[2]  Alan R. Aronson,et al.  Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program , 2001, AMIA.

[3]  James J. Cimino,et al.  Towards the development of a conceptual distance metric for the UMLS , 2004, J. Biomed. Informatics.

[4]  Catherine Faron-Zucker,et al.  Searching the semantic Web: approximate query processing based on ontologies , 2006, IEEE Intelligent Systems.

[5]  Yuval Shahar,et al.  Application of Information Technology: A Comparative Evaluation of Full-text, Concept-based, and Context-sensitive Search , 2007, J. Am. Medical Informatics Assoc..

[6]  Jos de Bruijn,et al.  Web Service Modeling Ontology , 2005, Appl. Ontology.

[7]  Aysu Betin Can,et al.  MedicoPort: A medical search engine for all , 2007, Comput. Methods Programs Biomed..

[8]  Rose Dieng,et al.  An Ontology-based Approach to Support Text Mining and Information Retrieval in the Biological Domain , 2007, J. Univers. Comput. Sci..

[9]  Hyoil Han,et al.  CONANN: An Online Biomedical Concept Annotator , 2007, DILS.

[10]  Hans-Peter Kriegel,et al.  Extraction of semantic biomedical relations from text using conditional random fields , 2008, BMC Bioinformatics.

[11]  Louiqa Raschid,et al.  Using Annotations from Controlled Vocabularies to Find Meaningful Associations , 2007, DILS.

[12]  Deborah L. McGuinness,et al.  Bringing Semantics to Web Services: The OWL-S Approach , 2004, SWSWPC.

[13]  Mark A. Musen,et al.  A System for Ontology-Based Annotation of Biomedical Data , 2008, DILS.

[14]  Steffen Staab,et al.  Annotation for the semantic web , 2003 .

[15]  Craig A. Morioka,et al.  IndexFinder: A Method of Extracting Key Concepts from Clinical Texts for Indexing , 2003, AMIA.

[16]  Steffen Staab,et al.  Leveraging Metadata Creation for the Semantic Web with CREAM , 2003, KI.

[17]  A. T. Schreiber,et al.  Semantic Annotation of Image Collections , 2003 .

[18]  Mark A. Musen,et al.  Comparing Concept Recognizers for Ontology-Based Indexing : MGREP vs . MetaMap , 2008 .

[19]  Munindar P. Singh,et al.  Service-Oriented Computing: Semantics, Processes, Agents , 2010 .

[20]  Mark A. Musen,et al.  Comparison of Ontology-based Semantic-Similarity Measures , 2008, AMIA.

[21]  Anand Kumar,et al.  Text mining and ontologies in biomedicine: Making sense of raw text , 2005, Briefings Bioinform..

[22]  Siegfried Handschuh,et al.  Semantic annotation for knowledge management: Requirements and a survey of the state of the art , 2006, J. Web Semant..

[23]  Daniel L. Rubin,et al.  Ontology-based Annotation and Query of Tissue Microarray Data , 2006, AMIA.

[24]  Enrico Motta,et al.  Approaches to Semantic Web Services: an Overview and Comparisons , 2004, ESWS.

[25]  Maged N Kamel Boulos,et al.  A first look at HealthCyberMap medical semantic subject search engine. , 2004, Technology and health care : official journal of the European Society for Engineering and Medicine.

[26]  R A Greenes,et al.  SAPHIRE--an information retrieval system featuring concept matching, automatic indexing, probabilistic retrieval, and hierarchical relationships. , 1990, Computers and biomedical research, an international journal.

[27]  Christopher G Chute,et al.  National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledge. , 2006, Omics : a journal of integrative biology.

[28]  Heiner Stuckenschmidt,et al.  Ontology-Based Integration of Information - A Survey of Existing Approaches , 2001, OIS@IJCAI.

[29]  Eric Prud'hommeaux,et al.  Annotea: an open RDF infrastructure for shared Web annotations , 2002, Comput. Networks.

[30]  Enrico Motta,et al.  Configuring Online Problem-Solving Resources with the Internet Reasoning Service , 2002, Intelligent Information Processing.

[31]  Jun'ichi Tsujii,et al.  Corpus annotation for mining biomedical events from literature , 2008, BMC Bioinformatics.

[32]  Vasant Honavar,et al.  A Tool for Collaborative Construction of Large Biological Ontologies , 2006, 17th International Workshop on Database and Expert Systems Applications (DEXA'06).

[33]  Olivier Bodenreider,et al.  Bio-ontologies: current trends and future directions , 2006, Briefings Bioinform..

[34]  Nigam H. Shah,et al.  The Stanford Tissue Microarray Database , 2007, Nucleic Acids Res..

[35]  M. Ashburner,et al.  The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration , 2007, Nature Biotechnology.

[36]  Benjamin N. Grosof,et al.  Supporting Rule System Interoperability on the Semantic Web with SWRL , 2005, SEMWEB.