Changes between Version 8 and Version 9 of OpenBioSemantics

Show
Ignore:
Timestamp:
2008/02/12 13:56:26 (11 years ago)
Author:
r.bruskiewich
Comment:

--

Legend:

Unmodified
Added
Removed
Modified
  • OpenBioSemantics

    v8 v9  
    11= Overview = 
    22 
    3 Most of the discussions at this hackathon deal with technology issues relating to interoperability. A few of the discussions are discuss OpenBio* "platform specific implementations" - language APIs (BioRuby, BioJava, BioPerl, etc.), web service protocols (BioMoby ''et. al.'') and database implementations (i.e. BioSQL).  A general issue relating to harmonization of community semantics or, at least, establishing a community process for semantics management, is recognized. This OpenSpace discussion is targeting this issue for further progress. 
     3Most of the discussions at this hackathon deal with technology issues relating to interoperability. A few of the discussions are discuss [http://www.open-bio.org/wiki/Main_Page OpenBio*] "platform specific implementations" - language APIs (!BioRuby, !BioJava, !BioPerl, etc.), web service protocols (!BioMoby ''et. al.'') and database implementations (i.e. !BioSQL).  A general issue relating to harmonization of community semantics or, at least, establishing a community process for semantics management, is recognized. This !OpenSpace discussion is targeting this issue for further progress. 
    44 
    55The broader scope of this discussion is titled '''OpenBioSemantics''' rather than simply '''Ontology'''. 
     
    1515Cathedral versus the Bazaar: the global community of bioinformatics are struggling with the issue of semantics, and various formalisms are currently being used to capture such semantics, i.e. 
    1616 
    17  * '''Formal Code Implementations:''' expressed as a body of computer code (e.g. [http://www.open-bio.org/wiki/Main_Page OpenBio*] initiatives) 
     17 * '''Formal Code Implementations:''' implied semantics expressed as an API and body of computer code (e.g. [http://www.open-bio.org/wiki/Main_Page OpenBio*] initiatives) 
    1818 * '''Data Formats:''' expressed as standard, human readable semi-structured text (e.g. sequence formats: FASTA, Genbank, EMBL) 
    1919 * '''Object models:''' expressed in Unified Modeling Language (UML) (e.g. [http://fuge.sourceforge.net/ Functional Genomics Experiment model] and [http://pantheon.generationcp.org/demeter Generation Challenge Programme domain model]) 
    2020 * '''Ontology initiatives:''' 
    21    * '''OBO format driven:''' e.g. Gene Ontology (GO), Sequence Ontology (SO), etc. 
    22    * '''OWL format initiatives:''' OBI 
    23  * '''XML Schema driven languages:''' EMBRACE WS-I, !BioCase, Tapir, etc. 
     21   * '''OBO format driven:''' e.g. [http://www.geneontology.org Gene Ontology (GO)], [http://www.sequenceontology.org/ Sequence Ontology (SO)], etc. 
     22   * '''OWL format initiatives:''' [http://obi.sourceforge.net/ Ontology for Biomedical Investigations] 
     23 * '''XML Schema driven languages:''' [http://www.embracegrid.info/page.php?page=home EMBRACE WS-I], [http://www.tdwg.org TDWG ABCD schema in !BioCase+Tapir], etc. 
    2424 * '''Common Database Schemata and Queries:''' BioSQL, [http://www.gmod.org Generic Model Organism (GMOD) Chado], [http://www.icis.cgiar.org International Crop Information System], etc. 
     25 * '''Web Service Protocol Data Types:''' e.g. [http://biomoby.org BioMoby data type object hierarchy] 
    2526 
    26 At this meeting, a general desire is being expressed to achieve some level of interoperability, at least, between OpenBio* initiatives generally, and more specifically, between OpenBio* and web services protocols like BioMoby and EMBRACE. 
     27At this meeting, a general desire is being expressed to achieve some level of interoperability, at least, between [http://www.open-bio.org/wiki/Main_Page OpenBio*] initiatives generally, and more specifically, between [http://www.open-bio.org/wiki/Main_Page OpenBio*] and web services protocols like [http://biomoby.org BioMoby] and [http://www.embracegrid.info/page.php?page=home EMBRACE]. 
    2728 
    2829An addition targeted need is simply to harmonize specific ontology pertinent to key interoperability technology. A specific example of such a need (from M. Wilkinson) is the harmonization of [http://www.biomoby.org BioMoby] and [http://www.mygrid.ac.uk myGrid] service ontology.