Changes between Version 31 and Version 32 of OpenBioSemantics

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Timestamp:
2008/02/15 11:56:26 (10 years ago)
Author:
r.bruskiewich
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  • OpenBioSemantics

    v31 v32  
     1= Semantics and Ontology for OpenBio* and Web Services = 
     2 
    13Back to [ListOfTopics Hackathon List of Topics] 
    24 
    3 = Overview = 
     5== Overview == 
    46 
    57Most 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. 
     
    2022 * ''please add your name if you were there! I apologize if I missed recording you....'' 
    2123 
    22 = Quick Links to Workshop Outputs = 
     24== Quick Links to Workshop Outputs == 
    2325 
    24 == !OpenBio* Domain Models for Comparison == 
     26=== !OpenBio* Domain Models for Comparison === 
    2527  
    2628 * [BioJavaDomainModel (Simplified) Model of BioJava semantics] (new: constructed at workshop) 
     
    2830 * [http://code.open-bio.org/svnweb/index.cgi/biosql/checkout/biosql-schema/trunk/doc/biosql-ERD.pdf (Simplified) Model of BioSQL semantics] (not a new piece of work - just identified for inclusion in this page, from the BioSQL team) 
    2931 
    30 == Other Ontology Work == 
     32=== Other Ontology Work === 
    3133 
    3234 * [http://www.mygrid.org.uk/mygrid-moby-service/ joint myGrid-Moby service ontology] 
    3335 
    34 = Proceedings = 
     36== Proceedings == 
    3537 
    36 = Summary of Day 1 Discussions (11th Feb. Afternoon !AcademyHills) =  
     38== Summary of Day 1 Discussions (11th Feb. Afternoon !AcademyHills) ==  
    3739 
    38 == Observations: Framing the Problem == 
     40=== Observations: Framing the Problem === 
    3941 
    4042Cathedral 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. 
     
    5658It is generally agreed that semantics is a hard community problem ("herding the cats") but can be made tractable by "divide and conquer" (witness the relative success of GO and other similar ontology development communities).  Efforts should and generally are, driven by a specific set of practical tasks in the community, on an "as needed" basis. The expectation to create a consensual "mother-of-all-biological-data-models" is most likely unrealistic, but can some agreement on the general principles, process and tools of semantic collaboration be achieved? 
    5759 
    58 == Preliminary Questions == 
     60=== Preliminary Questions === 
    5961 
    6062 1. Can a formal community strategy (akin to that in successful ontology consortia) for the specification and evolution of open bio semantics be specified and endorsed? 
     
    6466   * Can the task be partitioned down to size to make it tractable, yet large enough to be useful (achieve "buy-in")? Can guidelines for modular (community specific) code/data type modules be stipulated? e.g. glycoinformatics 
    6567   
    66 = Summary of Day 2 (12th Feb. AIST/CBRC) =  
     68== Summary of Day 2 (12th Feb. AIST/CBRC) ==  
    6769 
    6870 * Group facilitator caught up with capturing day 1 proceedings (above) from poster notes. 
     
    7072 * Moving forward this idea that a shared domain model might facilitate interoperability in !OpenBio* projects and web services, Richard Holland and Richard Bruskiewich spent part of the afternoon of day 2 drawing [BioJavaDomainModel UML diagrams reflecting the BioJava object data types], and started tracking down (over email) a !BioPerl UML model that is rumoured to be available. 
    7173 
    72 = Summary of Day 3 =  
     74== Summary of Day 3 ==  
    7375 
    7476 * No specific ontology team discussions convened but theme specific discussions underway (e.g. with Glycoinformatics team). 
    7577 
    76 = Summary of Day 4 =  
     78== Summary of Day 4 ==  
    7779 
    7880 * GCP domain model and !BioMoby data types: 
     
    8284 * Harmonization of !BioMoby and myGrid service ontology underway by myGrid community (with the collusion of Mark W.). See [http://www.mygrid.org.uk/mygrid-moby-service/ joint myGrid-Moby service ontology]. 
    8385  
    84 = Summary of Day 5 =  
     86== Summary of Day 5 ==  
    8587 
    8688 * Link to !BioPerl model