Synthetic Biology:Semantic web ontology/Examples: Difference between revisions

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**The SPECIALIST lexicon has been developed to provide the lexical information needed for the SPECIALIST Natural Language Processing System (NLP). It is intended to be a general English lexicon that includes many biomedical terms.
**The SPECIALIST lexicon has been developed to provide the lexical information needed for the SPECIALIST Natural Language Processing System (NLP). It is intended to be a general English lexicon that includes many biomedical terms.
**MetamorphoSys is the UMLS installation wizard and customization tool included in each UMLS release.
**MetamorphoSys is the UMLS installation wizard and customization tool included in each UMLS release.
*[http://www.snomed.org/ SNOMED Clinical Terms® (SNOMED CT®)] is the universal health care terminology that makes health care knowledge usable and accessible wherever and whenever it is needed (included in UMLS since 2003).  [http://www.connectingforhealth.nhs.uk/technical/standards/snomed/browser/ SNOMED browser].
*[http://lin.ncgr.org/ The Legume Information Network (LIN)] This is a prototype to demonstrate the power of semantic-MOBY framework to integrate disparate data sources into a virtual legume information network.
*[http://lin.ncgr.org/ The Legume Information Network (LIN)] This is a prototype to demonstrate the power of semantic-MOBY framework to integrate disparate data sources into a virtual legume information network.
*[http://pkb.stanford.edu/ Pathway Knowledge Base] @ Stanford - integrated human, ecoli and yeast pathway data in BioPAX format from Kegg, BioCyc and Reactome.  The underlying data is stored in an RDF triple store and all queries are made directly on the BioPAX model. This has some drawbacks in terms of performance but has allowed us to preserve the semantics specified in the BioPAX model.
*[http://pkb.stanford.edu/ Pathway Knowledge Base] @ Stanford - integrated human, ecoli and yeast pathway data in BioPAX format from Kegg, BioCyc and Reactome.  The underlying data is stored in an RDF triple store and all queries are made directly on the BioPAX model. This has some drawbacks in terms of performance but has allowed us to preserve the semantics specified in the BioPAX model.

Revision as of 16:04, 11 May 2006

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Ontology - essentially, a formal description of objects and their interrelationships Described using RDF Schema and/or OWL.

Life Sciences

Diagram of synthetic biology ontology v0.01 (developed using existing terminology described on the Registry website):

Upper ontologies

Other

Metadata applications

  • Swoogle Search and metadata for semantic web
  • Google Base
  • Biozon - a unified biological resource on DNA sequences, proteins, complexes and cellular pathways. The information in Biozon is logically represented as a graph in which nodes represent some unit of data, and edges indicate a relationship between two nodes.
  • Unified Medical Language System (UMLS) project develops and distributes multi-purpose, electronic "Knowledge Sources" and associated lexical programs for system developers. Researchers will find the UMLS products useful in investigating knowledge representation and retrieval questions.
    • Metathesaurus is a very large, multi-purpose, and multi-lingual vocabulary database that contains information about biomedical and health related concepts, their various names, and the relationships among them
    • Semantic Network provides a consistent categorization of all concepts represented in the UMLS Metathesaurus and to provide a set of useful relationships between these concepts.
    • The SPECIALIST lexicon has been developed to provide the lexical information needed for the SPECIALIST Natural Language Processing System (NLP). It is intended to be a general English lexicon that includes many biomedical terms.
    • MetamorphoSys is the UMLS installation wizard and customization tool included in each UMLS release.
  • SNOMED Clinical Terms® (SNOMED CT®) is the universal health care terminology that makes health care knowledge usable and accessible wherever and whenever it is needed (included in UMLS since 2003). SNOMED browser.
  • The Legume Information Network (LIN) This is a prototype to demonstrate the power of semantic-MOBY framework to integrate disparate data sources into a virtual legume information network.
  • Pathway Knowledge Base @ Stanford - integrated human, ecoli and yeast pathway data in BioPAX format from Kegg, BioCyc and Reactome. The underlying data is stored in an RDF triple store and all queries are made directly on the BioPAX model. This has some drawbacks in terms of performance but has allowed us to preserve the semantics specified in the BioPAX model.
  • Bibster - A Semantics-Based Bibliographic Peer-to-Peer System
  • Ontoware - Semantic Web related software projects

Datasets

  • Open Directory RDF dump The Open Directory Project is the largest, most comprehensive human-edited directory of the Web. It is constructed and maintained by a vast, global community of volunteer editors.
  • Wikipedia³ is a conversion of the English Wikipedia into RDF.
  • ConceptNet is a semantic network, a freely available commonsense knowledgebase and natural-language-processing toolkit
  • WordNet is a semantic lexicon for the English language

Resources

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