Latest revision as of 15:10, 14 December 2022

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

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

@@ Line 1: / Line 1: @@
 [[File:OOR-Logo.png]]
-= [[OpenOntologyRepository]] ([[OOR]]) Initiative - Approach  =
+= [[OpenOntologyRepository]] ([[OOR]]) Initiative - Architecture  =
-This page is for documentation related to the [[OOR]] initiative's approach, and the process being used.
+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 [[OntologySummit2008|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: [[ToddSchneider|Todd Schneider]] &amp; [[MichaelGruninger|Michael Gr&uuml;ninger]] - Panelists: [[ToddSchneider|Todd Schneider]], [[MikeDean|Mike Dean]], Natasha Noy, [[ImmanuelNormann|Immanuel Normann]], [[User:KennethBaclawski|Ken Baclawski]], [[MichaelGruninger|Michael Gr&uuml;ninger]] - OOR/ConferenceCall_2010_09_17 &nbsp;&nbsp;
+* 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 &nbsp;&nbsp;
+* 2010_11_19 - Friday: OOR Panel Discussion - "(Post-BioPortal fork) OOR Architecture and API - Take-II" - Co-chairs: [[User:KennethBaclawski|Ken Baclawski]] &amp; [[MichaelGruninger|Michael Gr&uuml;ninger]] - Panelists: KenBaclawski+ToddSchneider, AldoGangemi+AlessandroAdamou, JouniTuominen+KimViljanen, [[EricChan|Eric Chan]] - OOR/ConferenceCall_2010_11_19 &nbsp;&nbsp;
+* [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_02_04#nid2MIV 2011.02.04 discussion]
+* 2011_03_04 - Friday: OOR "Architecture &amp; API Specification Development Workshop-I" - Co-chairs: [[User:KennethBaclawski|Ken Baclawski]] &amp; [[ToddSchneider|Todd Schneider]] - OOR/ConferenceCall_2011_03_04 &nbsp;&nbsp;
+* 2011_03_11 - Friday: OOR - "Architecture &amp; API Specification Development Workshop-II" - Co-chairs: [[User:KennethBaclawski|Ken Baclawski]] &amp; [[ToddSchneider|Todd Schneider]] - OOR/ConferenceCall_2011_03_11 &nbsp;&nbsp;
 == Proposed for Adoption  ==
-... ''(enter adopted items here)''
+From the 11 March 2001 Meeting -
+'''<nowiki>searchOntologyMetadata</nowiki>'''
+March 2011 - I'd like to suggest a small change to the (first)
+proposed method of the OOR specification.
+Instead of <nowiki>'searchOntologyMetadata'</nowiki> 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.
+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 [[OpenOntologyRepository_Architecture|above]]
+== Ideas, Candidates, Proposals and References  ==
-== Ideas & Candidates  ==
+* /Candidate02 - proposed by [[MikeDean|Mike Dean]]
-... ''(enter ideas and candidates here)''
+* [[OpenOntologyRepository_Architecture/From_BioPortal]] (NatashaNoy) - [[BioPortal]] architecture (by [[NCBO]])
-* Candidate01 - proposed by: LeoObrst/2008.01.21
+* /Candidate03 (KenBaclawski & ToddSchneider) - OOR Software Architecture (Draft)
-** '''A 4-phased approach''' - ref. http://ontolog.cim3.net/forum/oor-forum/2008-01/msg00016.html
-*
+* /From_COLORE (MichaelGruninger)
-** '''Phase 1:''' Storage, Access, Business Processes, and Tools for Ontologies.
-::In the first phase three major aspects are addressed.
+* [[OpenOntologyRepository_Architecture/From_HeTS]] (TillMossakowski & JohnBateman)
-::The '''first''' aspect emphasizes storing, searching, and locating ontologies. The architecture consists of 1) an index that contains metadata about an ontology or an RDF store, 2) the ontology and RDF stores, 3) user services to support storing, searching, and locating ontologies.
+* /From_ONKI (JouniTuominen & KimViljanen)
-::The '''second''' aspect addresses business processes. Policies will be developed to guide the naming, management and partitioning of ontologies and the collection of simple metrics to help understand how the Repository is used. Ontology development will focus on the representation of simple taxonomies, on so-called facet ontologies (i.e., simple property hierarchies; typically facets define terminological dimensions as in thesauri), or more, depending on their needs. Important subject areas during this phase include general reference information, such as Country Codes and similar categories. Core metadata requirements for ontologies will be refined during this period. Translation services will be defined or provided for simple cases, e.g., OWL to HTML.
+* /From_ICOM (EricChan)
-::A '''very important''' business process function is the notification of ontology changes to ontology clients (either humans or automated services). During Phase 1, various mechanisms, such as the use of RSS feeds, should be investigated, as well as the appropriate vocabulary needed to communicate these changes.
+* /From_STLab (AlessandroAdamou & AldoGangemi)
-::The '''third''' area addresses downloadable tools appropriate to use in the development and maintenance of ontologies and related functions. An example is an ontology editor: some editors, like Protégé, are relatively mature, are open source, and are generally available.
+* [[OpenOntologyRepository_Architecture/Beyond_NeOn]] (MathieuDaquin)
-::Initially, the architecture itself should in principle support a de-centralized storage of ontologies and data stores. To facilitate searching and to reduce response time for search and discovery, the ontology metadata index itself can be centralized. Research during this period will focus on ontology editing tools, ontology mapping tools, the linking of ontologies to RDF "instance" stores of facts, ontology modularity and composability, representation of numerics, and the scalability of Semantic Web technology.
+* /Candidate01 - Java interfaces and shell classes - proposed by FarrukhNajmi/2008.01.28
+** ... [[FarrukhNajmi|Farrukh Najmi]] has subsequently decided to leave the OOR team as he needs to pursue his repository ideas for commercial purposes
-:: Achievement of Phase 1 goals themselves will be a significant achievement. The Repository could, for example, precisely define the concepts that are usually associated with a subject authority, such as geographic region codes, various subject matter codes and categories, and taxonomies used by search engines to identify broader and narrower terms.
+----
-*
+== OOR Architecture preliminary alignment call - Tue 17-Feb-2009  ==
-** '''Phase 2:''' Better Access, Search, Validation, Importing, and Mapping of Ontologies
-::Phase 2 emphasizes providing a broader array of machine services for access and use of repository contents. These will include validation and searching of ontology contents with path-type queries and conceptual queries. Ontologies will be developed to describe or even generate database schema and interfaces traditionally defined only by the use of a hardcopy Interface Control Document. Ontology domains will expand to include service and rule-based descriptions. The facet ontologies developed during Phase 1 will be used to define and describe integrating, conceptual ontologies in various domains. Search technology will use ontologies to search over RDF data stores.
+Date / Time:  Tue 2009.02.17 - 10:00am PST / 1:00pm EST
-::During Phase 2, special attention will be paid to issues including ontology importing, composition, and mapping. Downloads of additional semantic tools will be provided in Phase 2. These tools will be tested for interoperability with Repository services and other tools. An example is an OWL editor, which should produce OWL code that a validator can recognize as valid OWL.
+Attended: BenjaminDai, [[MikeDean|Mike Dean]], [[MichaelGruninger|Michael Gr&uuml;ninger]], [[User:KennethBaclawski|Ken Baclawski]], [[ToddSchneider|Todd Schneider]], [[PeterYim|Peter P. Yim]]
-*
+'''Discussion notes:'''
-** '''Phase 3:''' Distributed Query Support and Automated Inference
-::Phase 3 marks a shift in the use of the Repository. In Phase 3, the use of the Repository to support inferencing and intelligent distributed query automatically will be expanded. Web crawling, indexing, and ontology-aided classification/categorization will be more prominent. The use of Repository ontologies to access and search "back-end" databases will be implemented. Mechanisms will be added to automatically notify human and machine subscribers of changes in the repository contents. Security features will be added to support restrictions by community of interest. Translation services for OWL to other target languages, e.g. UML, will be expanded. It is expected that a class of ontologies will be identified as approved or certified during this phase.
+* 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
-** '''Phase 4:''' Expanded Community Support
+** 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
-::Phase 4 is an expansion of the capabilities developed in previous Phases to support large-scale RDF and OWL stores and federated search across community resources. The ontology repository will more actively support the needs of community information interoperability and large-scale information exchange mechanisms as identified by the community.
+* 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)
-* Candidate02 - proposed by: FarrukhNajmi/2008.01.23
+* Going foward with the OOR development
-** ref. http://ontolog.cim3.net/forum/oor-forum/2008-01/msg00019.html
+** 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)
-** '''A 3-step approach:'''
-::1. A set of tangible deliverables are established
+* 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
-::2. Participants volunteer for one or more deliverables and offer effort / cost estimates for the required R&D
+* Mike: suggest doing sessions of "code walkthrough" for developers who will be joining the team
-::3. Sponsor organizations are identified that wish to make use of the deliverables. They step up to fund the cost of R&D, thus incenting the participants to produce the deliverables
+- call adjourned: 10:55am PST
-*
+- Notes by [[PeterYim|Peter P. Yim]] - for those who were at the meeting, please review and edit the notes as you see fit.   =ppy
-** also: (ref. http://ontolog.cim3.net/forum/oor-forum/2008-01/msg00020.html)
-:: Perhaps it would be good in future meetings to give the meetings a more R&D flavor rather than an academic flavor. This would mean '''focusing more on Deliverables, ACTION ITEMS, Participants, Roles, Sponsors, dependencies, status, issues''' etc.
+----
 [[Category:OOR]]

OpenOntologyRepository Approach and OpenOntologyRepository Architecture: Difference between pages

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