Changes between Version 8 and Version 9 of OpenBioSemantics

Timestamp:

2008/02/12 13:56:26 (16 years ago)

Author:

r.bruskiewich

Comment:

--

OpenBioSemantics

@@ -1 +1 @@
 = Overview =
 
-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.
+Most 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.
 
 The broader scope of this discussion is titled '''OpenBioSemantics''' rather than simply '''Ontology'''.
@@ -15 +15 @@
 Cathedral 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.
 
- * '''Formal Code Implementations:''' expressed as a body of computer code (e.g. [http://www.open-bio.org/wiki/Main_Page OpenBio*] initiatives)
+ * '''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)
  * '''Data Formats:''' expressed as standard, human readable semi-structured text (e.g. sequence formats: FASTA, Genbank, EMBL)
  * '''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])
  * '''Ontology initiatives:'''
-   * '''OBO format driven:''' e.g. Gene Ontology (GO), Sequence Ontology (SO), etc.
-   * '''OWL format initiatives:''' OBI
- * '''XML Schema driven languages:''' EMBRACE WS-I, !BioCase, Tapir, etc.
+   * '''OBO format driven:''' e.g. [http://www.geneontology.org Gene Ontology (GO)], [http://www.sequenceontology.org/ Sequence Ontology (SO)], etc.
+   * '''OWL format initiatives:''' [http://obi.sourceforge.net/ Ontology for Biomedical Investigations]
+ * '''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.
  * '''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.
+ * '''Web Service Protocol Data Types:''' e.g. [http://biomoby.org BioMoby data type object hierarchy]
 
-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.
+At 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].
 
 An 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.