Ontolog Forum
OOR Panel Discussion Session - Fri 19-Feb-2010
Title: Coordinating our Open Ontology Repository Software Development
Session Chair: MikeDean (Raytheon BBN)
Panelists:
- JimChatigny (Raytheon BBN)
- MichaelGruninger (University of Toronto)
- KenBaclawski (Northeastern University)
- NatashaNoy (NCBO / Stanford University)
Archives
- Agenda
- Our panel's prepared slides can be accessed by clicking on each of the title links below:
- Slides: . [ 0-Chair ] . [ 1-Chatigny ] . [ 2-Gruninger ] . [ 3-Baclawski ]
- [ Audio Recording of the session ] (mp3)
- [ Transcript of the online chat session ] during the panel discussion
- Resources
Conference Call Details
- Date: Friday, 19-February-2010
- Start Time: 8:00am PST / 11:00am EST / 5:00pm CET / 4:00pm GMT / 16:00 UTC
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Attendees
- Attended:
- Matthew Hettinger
- Peter P. Yim
- Misha Dorf
- Jim Chatigny
- Jack Park
- David Eddy
- Michelle Raymond
- Doug Foxvog
- AlexGarcia
- Line Pouchard
- Bart Gajderowicz
- Jim Disbrow
- Michael Grüninger
- Terry Longstreth
- Natasha Noy
- Jim Rhyne
- Paul Alexander
- Ali Hashemi
- Ravi Sharma
- Lin Zhang (Forest)
- Mike Dean
- Pavithra Kenjige
- Jeff Abbott
- Pat Cassidy
- Frank Olken
- Dan Cerys
- Ken Baclawski
- Leo Obrst
- Expecting:
-
- ... if you are coming to the session, please add your name above (please include your affiliation, if you aren't already a member of the community); or e-mail <peter.yim@cim3.com> so that we can reserve enough resources to support everyone's participation. ...
- Regrets:
- Comments:
- Ed Dodds This process will serve as a case study on open innovation best practices in coordinating "big databases in the sky" solutions which are becoming increasingly relevant (given the availability and affordability of cloud computing) in the nonprofit sector, as well as global businesses, state and federal government services--so NO PRESSURE ;-)
Agenda
1. Introduction (MikeDean) - [ slides ]
- recent installations
2. Recent OOR development
- Federation (JimChatigny) - [ slides ]
- Common Logic (MichaelGruninger) - [ slides ]
- Gatekeeping and Provenance (KenBaclawski) - [ slides ]
3. Upcoming BioPortal plans (NatashaNoy, et al)
4. Software management (discussion)
- OOR branch
- feeding back changes
- BioPortal and OOR change requests
- commit rights?
- Wiki access?
- Other ...
5. Q & A and Open discussion (All) -- please refer to process above
6. Conclusion / Follow-up (MikeDean)
Proceedings
Please refer to the archives above
Transcript of the online chat during the session
see raw transcript here.
(for better clarity, the version below is a re-organized and lightly edited chat-transcript.)
Participants are welcome to make light edits to their own contributions as they see fit.
Peter P. Yim: .
Welcome to the OOR Panel Discussion Session - Fri 19-Feb-2010
Title: Coordinating our Open Ontology Repository Software Development
Session Chair: Mike Dean (Raytheon BBN)
Panelists:
- Jim Chatigny (Raytheon BBN)
- Michael Grüninger (University of Toronto)
- Ken Baclawski (Northeastern University)
- Natasha Noy (NCBO / Stanford University)
Please refer to details on the session page
at: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2010_02_19
.
anonymous1 morphed into Misha Dorf
anonymous1 morphed into Jim Disbrow
Peter P. Yim: another plea (while we are waiting) ... please hep with our Ontology Summit 2010 Surveys -
see: http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2010_Survey
Peter P. Yim: take a look at the solicitation too, at:
http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2010_Survey_Solicit
anonymous morphed into Paul Alexander
anonymous1 morphed into Line Pouchard
anonymous morphed into Jack Park
Line Pouchard: we're not funded yet, but am working on http://dataone.org
Jim Disbrow: @Line: consider joining us - go to http://ET.gov, on the left is a "Search" button,
click it and the next screen will show a list of ET.gov components - one of which is
"Energy-Water Nexus vis-a-vis the Climate"; click on the referenced XML file and it will lead you
into what the project is doing
anonymous morphed into Bart Gajderowicz
anonymous1 morphed into Doug Foxvog
anonymous2 morphed into Lin Zhang (Forest)
David Eddy: I see you here Jim Disbrow
Ravi Sharma: Hi Jim
Jim Disbrow: hi Ravi, David
Doug Foxvog: Could anonymous3 click "settings" and put in their name?
anonymous morphed into Matt Hettinger
David Eddy: SCM (software conf mgmt) is EXTREMELY important around repository... a fatal missing
component over past 40 years
Lin Zhang (Forest): To Session Chair: I'm Lin Zhang (Forest) from China. And I'm on.
Peter P. Yim: @JimChatigny - I noticed on your slide 4, you were federating from the OOR-sandbox at
<oor-01f.cim3.net> ... please note that the OOR-sandbox is now at http://oor-01.cim3.net
(the <oor-01f> name was for testing only ... for everyone's information)
Ravi Sharma: @MikeDean and Jim Chatigny: Is there an architecture diagram to look at that shows
pattern or Ontology Beans, etc? or did I miss it?
Paul Alexander: You can view a complete description of NCBO REST services (which at this point match
OOR) here: http://www.bioontology.org/wiki/index.php/NCBO_REST_services
Peter P. Yim: @Ravi - guess you are aware of this:
http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2010_02_19#nid2955 ... maybe Jim could
work with Todd and consider adding to it
Ravi Sharma: Peter: great link and lot of architecture information in UML that Todd Schneider
developed that I had missed so far. Thanks
anonymous2 morphed into Frank Olken
Terry Longstreth: Have you trained anyone to administer the system in your absence?
Jim Rhyne: Is there an introduction and rationale for this particular OOR architecture? Not obvious
to me why Spring would be a good basis.
Paul Alexander: @JimRhyne: Misha may be able to speak to the decision to use Spring. It's in OOR
because it is used in NCBO BioPortal (which OOR is an instance of right now)
Jim Rhyne: @MishaDorf - can you post a link to information on NCBO BioPortal architecture and
implementation?
Peter P. Yim: @JimRhyne - see resources listed under:
http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2010_02_19#nid2950
Paul Alexander: Here's a BioPortal/OOR architecture overview:
http://www.bioontology.org/wiki/index.php/NCBO-OOR_Architecture
Jim Rhyne: @PaulAlexander - exactly what I was looking for, thanks.
anonymous morphed into Dan Cerys
Natasha Noy: @JimChatigny Is there a link where we can try the federated server?
Natasha Noy: Also @JimChatigny: I think I missed this: do you download only metadata, or the
ontologies themselves as well?
Natasha Noy: And Q3 @JimChatigny: Is there a way to limit what to federate from a particular
repository (e.g., only OWL ontologies)?
Ravi Sharma: @JimChatigny: Are you restricted to RDF? especially due to REST requiring a resource?
Ravi Sharma: @MichaelGruninger: What about intermodule integration? Does CL fully prescribe a unique
way of putting them together?
Ravi Sharma: @MichaelGruninger and Ali Hashemi: Hope you are aware of current progress being made by
Mike Linehan and others in our efforts at OMG on SBVR Data-Time?
Ravi Sharma: @MichaelGruninger and Ali Hashemi: These have time and duration vocabularies that would
be helpful in developing ontologies of temporal aspects?
Lin Zhang (Forest): @MichaelGruninger: Did the current use case include the natural language
translation of ontologies? If yes, maybe we can use the term "converter" rather than
translator for the syntax conversion. What do you think of this? Thanks.
Pat Cassidy: @MikeGruninger: Do you think that JohnSowa's idea of using OpenCyc as the base for
relating multiple ontologies could be implemented in COLORE? Any ideas on what such
an exercise would need in terms of work.resources?
Michael Grüninger: @PatCassidy: We have found that we do not need to use any ontology as an a priori
base for relating multiple ontologies. Once the axioms of the ontologies have
been explicitly stated, their relationships are much easier to identify. The problem is that nobody
bothers to specify their axioms when discussing the relationships between
ontologies. One motivation for COLORE was to get people to actually submit axioms.
Pat Cassidy: @MikeGruninger: Yes, but axioms can only be related to each other if the namespaces are
identical, or if some translation is provided. The issue I am concerned with in
relating ontologies is to specify the bridging axioms that convert the assertions in one domain
ontology into the equivalent assertion in the other ontologies. So if the 25,000 -
60,000 OpenCYc hierarchy is loaded and axioms are added, how do you imagine this will interact with
the other modules in COLORE?
Doug Foxvog: @MikeGruninger: without a base for relating ontologies, axioms expressed in one ontology
could not be interpreted in another. Relationships between them could not be
determined without mappings expressed.
Ali Hashemi: @DougFoxvog - can you elaborate what you mean by "base" ?
Doug Foxvog: I used MikeGruninger's term..
Michael Grüninger: @DougFoxvog: If one ontology is interpretable by another, we don't need a "base
ontology" to show this. You simply specify a mapping from the lexicon of one to the lexicon of
the other and then show that theorems are preserved.
Doug Foxvog: there should be some way to specify a mapping betweens terms. A star mapping is much
simpler than creating an N-N mapping; but the center
Michael Grüninger: BTW, the term "base ontology" is PatCassidy's and John Sowa's.
Doug Foxvog: of the radial star might be more than one ontology
Ali Hashemi: @DougFoxvog - one need not create N-N mappings. If you map A to B and perhaps
map B to C, then you have an implicit mapping, from A to C through B. The star structure emerges.
David Eddy: I'd be interesting in talking with anyone who's interested in examining the lessons
learned from 40 years of repository efforts... 95% of which have gone to the bit
bucket in the sky. WHY did they fail & what can we avoid repeating?
Peter P. Yim: @KenBaclawski- (slide#6) what is KEEPER? is it s software tool? if so, is it an opensource
software?
Ken Baclawski: @Peter: KEEPER was the name of the project in my course. It is a web service
(supporting WSDL, SOAP and REST) and will be open source.
Jim Rhyne: @PeterYim phone battery died, back on now.
Peter P. Yim: @JimRhyne - glad you're back
Ravi Sharma: @KenBaclawski: I believe you are simply executing the OOR gatekeeping function without
touching the content or relationships or internal structure of ontology, ie. using BPEL for that purpose?
Terry Longstreth: @KenBaclawski - you mention 11179. Are you familiar with XMDR? Has it provided
anything useful?
Ken Baclawski: @Terry: Yes, we did look at XMDR and we hope to use some of it in KEEPER.
Lin Zhang (Forest): @TerryLongstreth: XMDR is a good resource. In some way, OOR is like XMDR.
Peter P. Yim: we actually have XMDR folks on the OOR team (notably Bruce Bargmeyer ... although he has
been less active lately)
Ken Baclawski: @Peter: I have been in contact with the XMDR people, but not much has occurred in this
direction.
Lin Zhang (Forest): @MichaelGruninger: Do the current use cases include the natural language
translation of ontolgies? Thanks.
Ali Hashemi: @Lin, as far as I know, the current use cases do not include NL translation of
ontologies.
Lin Zhang (Forest): Years ago, I tranlated some wiki pages into Chinese and post there.
Lin Zhang (Forest): @AliHashemi: Thanks. But the feature is desirabe.
Ken Baclawski: @Ali, the use cases are still being developed. If you are interested in this, please
come to the Use Cases meeting.
Lin Zhang (Forest): I uploaded some ontologies with Chinese concept names onto the BioPortal, but it
couldn't display the Chinese character correctly.
Paul Alexander: @LinZhang: We recently discovered a bug that was preventing these characters from
displaying properly. BioPortal now displays them properly, but the OOR Sandbox may be running code
from prior to the bug fix.
Lin Zhang (Forest): @PaulAlexander: Oh, that's great! I'll check that later after the t-con. Thanks.
Lin Zhang (Forest): Amino Acid with Simplified Chinese annotations
(View for Amino Acid) Version 1.3:
http://bioportal.bioontology.org/visualize/41006?view=true
Lin Zhang (Forest): @PaulAlexander: Thanks. It works.
Amino Acid with Simplified Chinese annotations (View for Amino Acid) Version 1.3:
http://bioportal.bioontology.org/visualize/41006?view=true
Biomedical Resource Ontology with Simplified Chinese annotations:
http://bioportal.bioontology.org/ontologies/40656#views
Ali Hashemi: @DougFoxvog, slide 4 in MichaelGruninger's presentation provides a high level view of
some way to specify a mapping between terms
Doug Foxvog: The star model is what John F. Sowa was suggesting for the FO (Foundation Ontology). That
was also one of original ideas behind Cyc. A center of the star might have
multiple inter-related ontologies (SUMO, Cyc, etc.). Sowa is considering an FO w/ multiple modules
(for different topics).
Ali Hashemi: @DougFoxvog, the problem with top-down star models are exactly that, they are top down.
Another approach is to have them emerge from the mappings that exist between
theories. For example, mathematical concepts (i.e. geometries, orderings) provide the backbone for
many many ontologies. They serve in many was a central star. Of course, one
doesn't know unless axioms are inputted, and mappings are generated.
Doug Foxvog: On slide 4, pi specifies a mapping function from T0 to T1. This does not explain whether
Pi0-1 is calculated via a star, N-N, chain of mappings, or any other specific mapping.
Pat Cassidy: @AliHashemi: If you map all of A to all of B, there are likely to still be terms in one
that are not in the other and vice versa, so there will be terms not mapped.
Then if you map C to B, some of the terms in A (that have not been mapped to B because they don't
exist in B) will not be mapped from B to C for the same reason. The transitivity
will only be complete by this mechanism if all ontologies have the same set of terms. One can use
this case-by-case mechanism, but if you keep a "foundation" ontology that contains
all of the terms that have been mapped in common between any two ontologies, then the foundation
ontology will be able to serve as a reliable and complete intermediate for
translation among all of the ontologies in the repository. That is the principle I have suggested
for the FO; it is not disjoint from your approach, it just *adds* an FO to serve
as the most complete inventory of terms needed for translation.
Michael Grüninger: @DougFoxvog: The definition of interpretation (on my slide 4) does not assume any
algorithm for generating the mapping. Ali's thesis and the current paper discuss
ways of generating new mappings from the relationships between ontologies that are specified in the
repository.
Ali Hashemi: @PatCassidy, a partial mapping will be a partial mapping, regardless of whether it is
into a foundation ontology or not. You can create a new module which enables a full
mapping (i.e. extend the FO), but then we are moving away from an FO. Note you could also do this
for A to B in the above example. ... The goal you have outlined is laudable, I've
already voiced some concerns. You are right however that attempting to identify ontological
primitives is complementary to much work being done and could help in the generation of mappings.
Bart Gajderowicz: @Pat, @Ali: Pat as you mentioned getting every single term in A to match every term
in B is very unlikely, simply because A and B were created separately. Could
Ontology Granulation assist in this, where it identifies key low-level terms (properties) which may
be sufficient to *differentiate* higher level terms (concepts). Then these
partial mappings will have been chosen based on *best* terms from the limited number of available
terms. *best* terms may introduce a level of stability in the partial mappings.
Ali Hashemi: Bart, that might be a useful approach in identifying what Pat calls primitives. I would
note that before one can identify primitives, one needs to _at least_ specify
mappings between some of the dominant upper ontologies, and i would suggest, mathematical theories.
Pat Cassidy: @BartGajderowicz: The Foundation Ontology as I envision it would be an ontology that is
mapped (by complete translations) to every other ontology in the repository. So
if terms in different ontologies have some conceptual overlap, but are not identical, the part that
overlaps will be identifiable via the FO. This FO could be created by performing
the kind of mappings that Ali suggests, but also performing a mapping to the FO. When there are
terms needed that are not in the FO, they can be added. But the additions to the FO
are kept to a minimum by only adding the most basic terms (primitives) that are required to
logically specify the terms in all of the mapped ontologies. This mechanism would
guarantee an automatic translation of assertions in any ontology into assertions in any other mapped
ontology.
Doug Foxvog: @MichaelGruninger: Re your page 10, without a base for relating ontologies, axioms
expressed in one ontology could not be interpreted in another. Relationships between
them could not be determined without mappings expressed. For computers, a ROT-13 of the names of one
ontology would make no difference.
Doug Foxvog: OOPS. Ignore my last comment. I meant:
Doug Foxvog: @MichaelGruninger: Re your page 10, By having ontology terms for modules as instances,
common logic could be used to express simple relationships among ontologies. The
issue would be whether Common Logic can associate such terms with the modules themselves.
Doug Foxvog: @PatCassidy, do you envision a functional description of terms in the FO for mapping to
more specific terms. E.g.,
(NthInSeriesFn (AnatomicalPartTypeFn (LeftFn Hand-AnatomicalPart) FingerSeries) 3)
for a SNOMED term for the third finger of the left hand?
Pat Cassidy: @DougFoxvog: The FO only needs to have the basic elements that can be combined by FOL to
produce the terms in the domain ontologies. So Nth in series might be a
primitive, but applied to the hand it could be a domain-specific combination.
David Eddy: can someone point to a ontology glossary... I have no idea what a "theory" or "axiom" is
please?
Lin Zhang (Forest): @PeterYim and Mike Dean: I'll be out about 20 min later because my skype card is
running out.
Paul Alexander: Is anyone familiar with/using Git SCM? It could work very well for this type of
distributed development.
Paul Alexander: Or Mercurial or some other distributed SCM system
Ravi Sharma: @KenBaclawski: My Question is for you from above relating to ISO 11179 that defines
metadata Registry and data element definitions hence the question, does OOR
automatically assume that things and relationships are "data Elements"? Also BPEL Q from Above
repeated here for you.I believe you are simply executing the OOR gatekeeping function
without touching the content or relationships or internal structure of ontology, ie. using BPEL for
that purpose?
Ken Baclawski: @RaviSharma: ISO 11179 can specify content and relationships. However, the granularity
of administered item for OOR remains to be determined. This is related to
modularity. The administered items are the units being managed with a BPEL process.
Line Pouchard: @KenBaclawski: Is your NIH project planning to develop a new "environement" ontology?
Do you have a list of existing ones?
Ken Baclawski: @LinePouchard: We will be using existing ontologies when possible. Send me email.
Line Pouchard: Ken, Peter and all: I have to go. Ken: I will be in touch by email. Thank you.
Peter P. Yim: on code repository - Mike Dean, on consultation with Natasha Noy and everyone at this call:
decision reached (confirmed between the OOR-team and NCBO-team) - OOR will be
using the repository at semwebcentral for the OOR-branch (of the BioPortal extensions)
located at: http://oor.projects.semwebcentral.org/
- ref: http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository#nid1JSY
Jim Rhyne: Unfortunately have to leave the call.
Doug Foxvog: Signing off at 6:30 p.m. (UTC), i need to head home from work.
Peter P. Yim: thanks for joining us Doug
Ravi Sharma: Thanks Mike Peter and Speakers.
Ali Hashemi: Thanks all. Bye
Paul Alexander: Thanks everyone, please let me know if you have questions as you move the OOR
codebase to the new SVN repository.
Peter P. Yim: - session ended 2010.02.19 - 10:31am PST -
-- end of chat session --
- due to time limitation, agenda items we were not able to cover will be deferred to the regular team meetings and/or the next two community panel discussion sessions
- Further Question & Remarks - please post them to the [ oor-forum ] listserv
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- if you are not yet subscribed, see: http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository#nid17YX
Audio Recording of this Session
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- Conference Date and Time: 19-Feb-2010 8:32am~10:31am PST
- Duration of Recording: 1 Hour 53 Minutes
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- Take a look, also, at the rich body of knowledge that this community has built together, over the years, by going through the archives of noteworthy past Ontolog & OOR events. (References on how to subscribe to our podcast can also be found there.)
Resources
- OpenOntologyRepository - homepage for the OOR initiative - http://OpenOntologyRepository.org
- OOR-sandbox - http://oor-01.cim3.net/
- NCBO BioPortal project sites
- NCBO-OOR development documentation - http://www.bioontology.org/wiki/index.php/NCBO-OOR_Development
- Code repository: http://oor.projects.semwebcentral.org/ (see also: ref.)
- UML-EA diagrams on the BioPortal (v1016 of Jul-2009) system (prepared by ToddSchneider)
- from the more recent Ontolog-OOR panel sessions:
- ConferenceCall_2009_07_16
- ConferenceCall_2009_07_30
- ConferenceCall_2009_08_06
- ConferenceCall_2009_10_15
- archives of past OOR-team meetings
- Key Content Pages for the OOR Initiative
- Join the OOR team by emailing the OOR co-conveners: Mike Dean <mdean@bbn.com>, Leo Obrst <lobrst@mitre.org> and Peter P. Yim <peter.yim@cim3.com>
- subscribe to our mailing lists by referring to details here.
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