Literature DB >> 19964601

Composite annotations: requirements for mapping multiscale data and models to biomedical ontologies.

Daniel L Cook1, Jose L V Mejino, Maxwell L Neal, John H Gennari.   

Abstract

Current methods for annotating biomedical data resources rely on simple mappings between data elements and the contents of a variety of biomedical ontologies and controlled vocabularies. Here we point out that such simple mappings are inadequate for large-scale multiscale, multidomain integrative "virtual human" projects. For such integrative challenges, we describe a "composite annotation" schema that is simple yet sufficiently extensible for mapping the biomedical content of a variety of data sources and biosimulation models to available biomedical ontologies.

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Year:  2009        PMID: 19964601      PMCID: PMC2797541          DOI: 10.1109/IEMBS.2009.5333830

Source DB:  PubMed          Journal:  Conf Proc IEEE Eng Med Biol Soc        ISSN: 1557-170X


  8 in total

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Journal:  Nat Rev Mol Cell Biol       Date:  2003-03       Impact factor: 94.444

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Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

3.  Integration of multi-scale biosimulation models via light-weight semantics.

Authors:  John H Gennari; Maxwell L Neal; Brian E Carlson; Daniel L Cook
Journal:  Pac Symp Biocomput       Date:  2008

4.  Advances in semantic representation for multiscale biosimulation: a case study in merging models.

Authors:  Maxwell Lewis Neal; John H Gennari; Theo Arts; Daniel L Cook
Journal:  Pac Symp Biocomput       Date:  2009

5.  Bridging biological ontologies and biosimulation: the ontology of physics for biology.

Authors:  Daniel L Cook; Jose L V Mejino; Maxwell L Neal; John H Gennari
Journal:  AMIA Annu Symp Proc       Date:  2008-11-06

6.  Relations in biomedical ontologies.

Authors:  Barry Smith; Werner Ceusters; Bert Klagges; Jacob Köhler; Anand Kumar; Jane Lomax; Chris Mungall; Fabian Neuhaus; Alan L Rector; Cornelius Rosse
Journal:  Genome Biol       Date:  2005-04-28       Impact factor: 13.583

7.  An ontology for cell types.

Authors:  Jonathan Bard; Seung Y Rhee; Michael Ashburner
Journal:  Genome Biol       Date:  2005-01-14       Impact factor: 13.583

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Journal:  Nucleic Acids Res       Date:  2007-10-11       Impact factor: 16.971

  8 in total
  5 in total

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2.  Multiscale modeling and data integration in the virtual physiological rat project.

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3.  The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions.

Authors:  Bernard de Bono; Robert Hoehndorf; Sarala Wimalaratne; George Gkoutos; Pierre Grenon
Journal:  BMC Res Notes       Date:  2011-08-30

4.  Physical properties of biological entities: an introduction to the ontology of physics for biology.

Authors:  Daniel L Cook; Fred L Bookstein; John H Gennari
Journal:  PLoS One       Date:  2011-12-27       Impact factor: 3.240

5.  Ontology of physics for biology: representing physical dependencies as a basis for biological processes.

Authors:  Daniel L Cook; Maxwell L Neal; Fred L Bookstein; John H Gennari
Journal:  J Biomed Semantics       Date:  2013-12-02
  5 in total

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