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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

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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  • Please note that this session will be recorded, and the entire proceedings including the audio archives are expected to be made available as open content to our community membership and the public at-large under our prevailing open IPR policy.

Attendees

  • 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
  • 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:

  • 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

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  • Conference Date and Time: 19-Feb-2010 8:32am~10:31am PST
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