OpenOntologyRepository Architecture

OpenOntologyRepository (OOR) Initiative - Architecture

This page is for documentation related to the architecture of the "open ontology repository" we are planning to implement through the OOR initiative.

Adopted

... (enter adopted items here)

Key Discussions

• Summarizing from the Ontology Summit 2008 discourse
  • see: http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2008_Communique#nid1GWK
• 2010_09_17 - Friday: OOR Panel Discussion - "Getting OOR Development Going - Take-IV" Workshop - Co-chairs: Todd Schneider & Michael Grüninger - Panelists: Todd Schneider, Mike Dean, Natasha Noy, Immanuel Normann, Ken Baclawski, Michael Grüninger - OOR/ConferenceCall_2010_09_17   
• 2010_10_15 - Friday: OOR Project Team Member Conference Call - discussion on the (post-BioPortal fork) OOR Architecture and API - OOR/ConferenceCall_2010_10_15   
• 2010_11_19 - Friday: OOR Panel Discussion - "(Post-BioPortal fork) OOR Architecture and API - Take-II" - Co-chairs: Ken Baclawski & Michael Grüninger - Panelists: KenBaclawski+ToddSchneider, AldoGangemi+AlessandroAdamou, JouniTuominen+KimViljanen, Eric Chan - OOR/ConferenceCall_2010_11_19   
• 2011.02.04 discussion
• 2011_03_04 - Friday: OOR "Architecture & API Specification Development Workshop-I" - Co-chairs: Ken Baclawski & Todd Schneider - OOR/ConferenceCall_2011_03_04   
• 2011_03_11 - Friday: OOR - "Architecture & API Specification Development Workshop-II" - Co-chairs: Ken Baclawski & Todd Schneider - OOR/ConferenceCall_2011_03_11   

Proposed for Adoption

From the 11 March 2001 Meeting -

searchOntologyMetadata

11 March 2011 - I'd like to suggest a small change to the (first) proposed method of the OOR specification.

Instead of 'searchOntologyMetadata' I suggest 'findOntologies'. Of course, as agreed, to execute or actualize this method the system would need to search the metadata. But the intent, from a user's perspective, is to find the ontology/ontologies that meet their criteria (the arguments of the method): the what.

Searching is a 'how' - there can many ways to find what is being looked for.

Finding is a 'what' - The end goal or intent of taking the action.

And yes, I'm also appealing to the semantic differences between these two words. From WordNet 2.0,

Search - the activity of looking thoroughly in order to find something

Find - discover or determine the existence

Again from a users perspective, and the one I think best used to understand the intent of any system, they want to find something. Searching is just one way to accomplish this.

13 March 2011 - I like to suggest a revision to my revision, just 'find()'. The argument would define what is to be found.

Getting Organized

• Organizing Plan - see: /GettingOrganized
• and ... Key Discussion above

Ideas, Candidates, Proposals and References

• /Candidate02 - proposed by Mike Dean

• OpenOntologyRepository_Architecture/From_BioPortal (NatashaNoy) - BioPortal architecture (by NCBO)

• /Candidate03 (KenBaclawski & ToddSchneider) - OOR Software Architecture (Draft)

• /From_COLORE (MichaelGruninger)

• OpenOntologyRepository_Architecture/From_HeTS (TillMossakowski & JohnBateman)

• /From_ONKI (JouniTuominen & KimViljanen)

• /From_ICOM (EricChan)

• /From_STLab (AlessandroAdamou & AldoGangemi)

• OpenOntologyRepository_Architecture/Beyond_NeOn (MathieuDaquin)

• /Candidate01 - Java interfaces and shell classes - proposed by FarrukhNajmi/2008.01.28
  • ... Farrukh Najmi has subsequently decided to leave the OOR team as he needs to pursue his repository ideas for commercial purposes

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OOR Architecture preliminary alignment call - Tue 17-Feb-2009

Date / Time: Tue 2009.02.17 - 10:00am PST / 1:00pm EST

Attended: BenjaminDai, Mike Dean, Michael Grüninger, Ken Baclawski, Todd Schneider, Peter P. Yim

Discussion notes:

• trying to get ready for a software architecture that the oor-dev (OOR development) community can contribute into

• first "sandbox" instance, based on the NCBO-BioPortal technology, being built out
  • first "sandbox" virtual machine just became ready (from CIM3)
  • Benjamin & team is trying to get the instance ready by the Feb-19 session
    • Benjamin will have some initial content
    • Mike will be happy to add some seed content too
      • Benjamin ask if Mike could sent those to him (for now)
      • Benjamin will also let Mike know when the sandbox is ready for user upload

• For the Feb-19 session
  • Mike: suggest the NCBO folks provide a list of features working on now, and near-term on BioPortal
  • Ken: asking for an OOR architecture
  • Todd: asked Mark for the BioPortal architecture
    • Benjamin has been working on this - see:
      • http://www.bioontology.org/wiki/index.php/NCBO-OOR_Development
      • Benjamin solicits feedback on how this developer documentation can be improved to better help the expanding development community. This wiki page focuses on both developer architects and developers with familiarity with aspect-oriented programming.
      • http://www.bioontology.org/wiki/index.php/NCBO_Developer_Communications
      • Benjamin shares this documentation to potentially re-use developer collaboration strategies currently used by the NCBO. Of course, OOR developers will have their own OOR tools (e.g., the OOR dev mailing list).
    • Todd will help to get a set of UML diagrams made for the architecture (maybe not before Feb-19, though)

• Going foward with the OOR development
  • Benjamin & Mike: a fork? or a subversion branch which will eventually merging back to BioPortal?
  • on the BioPortal gforge repository or on the oor-SemWebCentral gforge repository?
  • ALL: decision to, at least for the time being, OOR will take a subversion branch and work off the BioPortal gforge repository
    • we'll aim at eventually merging the code back to BioPortal
    • Mike: the oor-SemWebCentral gforge repository will still be available if anyone (say, for a sub-project) needs it
    • we'll defer to Benjamin & Mike to develop some simply controls as to who can commit, who has access, etc.

• Benjamin: BioPortal development is in two major projects - Core (REST services) and Presentation (ruby on rails)

• Todd requested that Benjamin makes a comparison between what BioPortal has to offer against the OpenOntologyRepository_Requirement. This will occur after the Feb-19th session

• Mike: suggest doing sessions of "code walkthrough" for developers who will be joining the team

- call adjourned: 10:55am PST

- Notes by Peter P. Yim - for those who were at the meeting, please review and edit the notes as you see fit. =ppy

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