oor_chat-transcript_20100219b.txt Please change your name from 'anonymous' using the Settings button anonymous morphed into PeterYim PeterYim: . Welcome to the 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) 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 MishaDorf anonymous1 morphed into JimDisbrow PeterYim: another plea (while we are waiting) ... please hep with our OntologySummit2010 Surveys - see: http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2010_Survey PeterYim: take a look at the solicitation too, at: http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2010_Survey_Solicit anonymous morphed into PaulAlexander anonymous1 morphed into LinePouchard LinePouchard: http://dataone.org anonymous morphed into JackPark DavidEddy: 3rd time's the charm! PaulAlexander1 morphed into PaulAlexander JimDisbrow: 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 BartGajderowicz anonymous1 morphed into doug foxvog anonymous2 morphed into Lin Zhang (Forest) DavidEddy1: I see you here JimD RaviSharma: Hi Jim RaviSharma: JimD JimDisbrow: hi Ravi, David doug foxvog: Could anonymous3 click "settings" and put in their name? anonymous morphed into Matt Hettinger DavidEddy1: 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. PeterYim: @JimChatigny - I noticed on your slide 4, you were federating from the OOR-sandbox at ... please note that the OOR-sandbox is now at http://oor-01.cim3.net (the name was for testing only ... for everyone's information) RaviSharma: Mike and Jim: Is there an architecture diagram to look at that shows pattern or Ontology Beans, etc? or did I miss it? anonymous2 morphed into FrankOlken TerryLongstreth: Have you tarined anyon to administer the sysgtem in your absence? PaulAlexander: 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 PeterYim: @Ravi - guess you are aware of this: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2010_02_19#nid2955 ... guess Jim could work with Todd and consider adding to it JimRhyne: Is there an introduction and rationale for this particular OOR architecture? Not obvious to me why Spring would be a good basis. anonymous morphed into DanCerys 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)? PaulAlexander: @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) RaviSharma: Mike: What about intermodule integration? Does CL fully prescribe a unique way of putting them together? RaviSharma: Mike and Ali: Hope you are aware of current progress being made by Mike Linehan and others in our efforts at OMG on SBVR Data-Time? RaviSharma: Mike & Ali: These have time and duration vocabularies that would be helpful in developing ontologies of temporal aspects? Lin Zhang (Forest): @Michael: Did the current use case include the nature language translation of ontolgies? If yes, maybe we can use the term "converter" rather than "translator" for the sytax conversion. What do you think of this? Thanks. Pat Cassidy: MikeG: Do you think that John Sowa'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? DavidEddy1: 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? MichaelGruninger: @Pat Cassidy: 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. PeterYim: @KenBaclawski- (slide#6) what is KEEPER? is it s software tool? if so, is it an opensource software? JimRhyne: @PeterYim phone battery died, back on now. RaviSharma: MikeG: 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? TerryLongstreth: @Ken - you mention 11179. Are you familiar with XMDR? Has it provided anything useful? PeterYim: @JimRhyne - glad you're back JimRhyne: @MishaDorf - can you post a link to information on NCBO BioPortal architecture and implementation? PeterYim: @JimRhyne - see below: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2010_02_19#nid2950 KenBaclawski: @Terry: Yes, we did look at XMDR and we hope to use some of it in KEEPER. PaulAlexander: Here's a BioPortal/OOR architecture overview: http://www.bioontology.org/wiki/index.php/NCBO-OOR_Architecture Lin Zhang (Forest): @TerryLongstreth: XMDR is a good resource. In some way, OOR is like XMDR. Pat Cassidy: @MIkeG: 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? KenBaclawski: @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. PeterYim: we actually have XMDR folks on the OOR team (notably BruceBargmeyer ... although he has been less active lately) Lin Zhang (Forest): @MichaelG: Do the current use cases include the nature language translation of ontolgies? Thanks. doug foxvog: @MikeG: 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: @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. Ali Hashemi: @Doug - can you elaborate what you mean by "base" ? KenBaclawski: @Peter: I have been in contact with the XMDR people, but not much has occurred in this direction. Lin Zhang (Forest): @Ali Hashemi: Thanks. But the feature is desirabe. doug foxvog: I used Mike G's term.. MichaelGruninger: @Doug: 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 MichaelGruninger: BTW, the term "base ontology" is Pat Cassidy's and John Sowa's. doug foxvog: of the radial star might be more than one ontology KenBaclawski: @Ali, the use cases are still being developed. If you are interested in this, please come to the Use Cases meeting. Ali Hashemi: @Doug - 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. Lin Zhang (Forest): I uploaded some ontologies with Chinese concept names onto the BioPortal, but it couldn't display the Chinese character correctly. PaulAlexander: @Lin: 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. Ali Hashemi: @Doug, slide 4 in Michael G's presentation provides a high level view of "some way to specify a mapping between terms" Lin Zhang (Forest): @Peter and MikeDean: I'll be out about 20 min later because my skype card is running out. doug foxvog: The star model is what John Sowa was suggesting for the FO. 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). JimRhyne: @PaulAlexander - exactly what I was looking for, thanks. Lin Zhang (Forest): @PaulAlexander: Oh, that's great! I'll check that later after the t-con. Thanks. PaulAlexander: Is anyone familiar with/using Git SCM? It could work very well for this type of distributed development. Ali Hashemi: @Doug, 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. PaulAlexander: Or Mercurial or some other distributed SCM system RaviSharma: Ken: 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? Lin Zhang (Forest): Amino Acid with Simplified Chinese annotations (View for Amino Acid) Version 1.3:http://bioportal.bioontology.org/visualize/41006?view=true 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. DavidEddy1: can someone point to a ontology glossary... I have no idea what a "theory" or "axiom" is please? LinePouchard: @Ken: Is your NIH project planning to develop a new "environement" ontology? Do you have a list of existing ones? Pat Cassidy: Ali: 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. PeterYim: on code repository - MikeDean: decision (confirmed between the OOR-team and NCBO-team) - OOR will be using the repository at semwebcentral for the OOR-branch (of the BioPortal extensions) MichaelGruninger: @doug: 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. 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: Pat, 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. KenBaclawski: @LinePouchard: We will be using existing ontologies when possible. Send me email. LinePouchard: Ken, Peter and all: I have to go. Ken: I will be in touch by email. Thank you. BartGajderowicz: @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. RaviSharma: Jim: Are you restricted to RDF? especailly due to REST requiring a resource? KenBaclawski: @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. JimRhyne: Unfortunately have to leave the call. 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. doug foxvog: @MikeG: 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. Pat Cassidy: @Bart: 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: OOPS. Ignore my last comment. I meant: doug foxvog: @MikeG: 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. RaviSharma: Peter: great link and lot of architecture information in UML that TRodd developed that i had missed so far. Thanks RaviSharma: I meant Todd Schneider doug foxvog: Pat, 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? doug foxvog: Signing off at 6:30 p.m. (UTC), i need to head home from work. RaviSharma: Thanks Mike Peter and Speakers. PeterYim: thanks for joining us Doug Ali Hashemi: Thanks all. By Ali Hashemi: e Pat Cassidy: @Doug: 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 primivie, but applied to the hand it could be a domain-specific comnbination. PaulAlexander: Thanks everyone, please let me know if you have questions as you move the OOR codebase to the new SVN repository. PeterYim: - session ended 2010.02.19 - 10:31am PST - PeterYim: I'll leave this chat room on for another few minutes if anyone wants that (if so, please speak up) PeterYim: no ... that this is going offline (or, at least, I won't capture further IM's into today's proceedings) PeterYim: - chat session ended -