ConferenceCall 2010 09 16

= Joint OOR-Ontolog-NCBO-CC-IAOA-OASIS "OpenOntologyRepository_IPR Policy and Issues" Panel Discussion (session-2) - Thu 16-Sep-2010 =


 * Topic: "OOR-IPR session 2: what are the IPR issues relating to open ontology repositories (and ontologies in general)?"


 * Chair: Professor MarkMusen (NCBO; Stanford) - [ slides ]


 * Panelists:
 * Mr. CameronRoss (Kojeware; OOR) - "Ecosystems, Ontology Repositories, and IPR" - [ slides ]
 * Professor AlanRector (University of Manchester) - Remarks: "The GALEN and SNOMED IPR experience" - [ abstract ]
 * Dr. JohnSowa (Vivomind Intelligence; SIO) - Remarks: "Issues with Patents" - [ slides ]
 * Mr. BrucePerens (original author of the "Open Source Definition") - Commentary
 * Mr. JohnWilbanks (VP of Science, Creative Commons) - Commentary
 * Mr. PeterYim (Co-convener, Ontolog & OOR; Secretary, IAOA) - "Questions to ALL: what are our issues now?" - [ slides ]


 * Archive:
 * Agenda & Proceedings
 * Abstracts
 * Prepared presentation material can be accessed by clicking on each of the title links below:
 * [ 0-Chair ] . [ 1-Ross ] . [ 2-Rector ] . [ 3-Sowa ] . [ 4-Yim ]
 * Audio recording of the session ( 1:43:15 ; mp3 ; 11.8 MB )
 * Transcript of the online chat session during the panel discussion
 * Other Resources

Conference Call Details:

 * Date: Thursday, 16-September-2010
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Attendees:

 * Attended (or registered to attend):
 * MarkMusen
 * CameronRoss
 * JohnSowa
 * AlanRector
 * JohnWilbanks
 * BrucePerens
 * PeterYim
 * JackPark
 * YuriyMilov
 * JerrySmith
 * PavithraKenjige
 * Xavier Lopez (Oracle)
 * Matt Liebenson (Creative Commons)
 * RaviSharma
 * TerryLongstreth
 * KenBaclawski
 * AliHashemi
 * PatCassidy
 * YuriyMilov
 * FrankOlken
 * ... if you are coming to the session, please add your name above (plus your affiliation, if you aren't already a member of the community) above; or e-mail  so that we can reserve enough resources to support everyone's participation. ...
 * ... if you are coming to the session, please add your name above (plus your affiliation, if you aren't already a member of the community) above; or e-mail  so that we can reserve enough resources to support everyone's participation. ...


 * Regrets:
 * JamieClark (traveling)
 * FrankChum
 * MikeDean

Resources

 * OpenOntologyRepository - Homepage for the OOR initiative
 * This OpenOntologyRepository_IPR mini-series
 * A recent presentation on OOR - OOR Presentation at SemTech2010
 * The OOR-sandbox v2.5 (powered by the NCBO BioPortal Core v2.5) instance, now online at: http://oor-01.cim3.net ref.
 * OOR Project site and code repository at SemWebCentral - http://oor.semwebcentral.org
 * OntologySummit2008_Communique
 * our last regular OOR-team meeting - OOR/ConferenceCall_2010_08_20
 * [ oor-forum ] message archive - http://ontolog.cim3.net/forum/oor-forum/
 * (if you are not yet subscribed) you may subscribe yourself to the [ oor-forum ] listserv, by sending a blank email to  from your subscribing email address, and then follow the instructions you receive back from the mailing list system.
 * check out our other mailing lists and join us

Agenda & Proceedings:
Panel Discussion Session: "OOR-IPR session 2: what are the IPR issues relating to open ontology repositories (and ontologies in general)?"


 * Session Format & Agenda: this is a virtual session conducted over an augmented conference call:
 * 1. Opening - chair ... [ slides ]
 * 2. Panelists Briefings - CameronRoss, AlanRector, JohnSowa ... (15 min. each)
 * 3. Reactions from our session-1 IPR experts - BrucePerens, JohnWilbanks ... (5 min. each)
 * 4. Q & A and open discussion - All (30 min.) ... please refer to [ process above]
 * 4.1 within this segment, we will try to capture ontology-repository-related IPR issues that have been bothering our participants as well (please come prepared with your input!) - moderated by PeterYim
 * 5. Conclusion / Follow-up - co-chairs

Abstracts:

 * Session Topic: "OOR-IPR session 2: what are the IPR issues relating to open ontology repositories (and ontologies in general)?"


 * This "OOR-IPR mini-series" will, hopefully, start a dialog among the global ontology community, to specifically address IPR issues relating to the "open ontology repository (OOR)" initiative. The discussion will, invariably, touch upon IPR issues pertaining to ontology in general as well.


 * This mini-series is jointly organized by the OOR initiative, the Ontolog-community, NCBO (US National Center for Biomedical Ontology), CC (Creative Commons), IAOA (the International Association for Ontology and its Applications) and OASIS (Organization for the Advancement of Structured Information Standards).


 * Given the complexity of the issues involved, one can look as this mini-series to merely be the beginning of a quest, by the collaborating parties and their communities, to fully understand the issues, and to get themselves into a position to address them.


 * In this 2nd session, we will try to find out what, really, are the IPR issues relating to open ontology repositories in particular, and to ontologies, or even the science and technology of Ontology, in general. We will attempt to enumerate the pertinent issues and try to mitigate or address them one-by-one, if we can.


 * Please refer also to the background and thoughts collected during the process of organizing this mini-series, at: OpenOntologyRepository_IPR


 * Check out the full proceedings of the Launch Session of this OOR-IPR mini-series - ConferenceCall_2010_09_09

Panel Members Briefings:

 * Title: "Ecosystems, Ontology Repositories, and IPR" - [ slides ]
 * by CameronRoss
 * Abstract: ... This presentation will summarize some of the objectives, assumptions and issues that motivate this series of sessions on IPR. A brief explanation of how the OOR fits in to a larger ecosystem for semantic applications will also be presented, along with a recommendation to give IP provenance due consideration within the OOR initiative.


 * Title: "The GALEN and SNOMED IPR experience"
 * by AlanRector
 * Abstract: ... We have two experiences to share:


 * i) GALEN, which was a large collaborative development in the 1990s. In that development, all attempts to determine shares of intellectual property proved both expensive and futile.  It was eventually made open source as the only practical solution.
 * ii) The continuing saga with SNOMED, which is currently "half open" and supported by different governments joining the parent organisation. However the lack of a completely open license continues to be a major issue and cost of dealing with SNOMED.  For example, the WHO and the SNOMED organisation have taken at least two years and untold legal and executive time to reach an agreement.
 * IP is intimately related to funding models.
 * Both GALEN and SNOMED's experience point to the difficulty of achieving a revenue stream for ontologies meant to enable interoperability without strong legal backing, at least in health care. The only organisations that do so as far as I know are those that are backed by some form of mandate - CPT for clinical procedures in the US, ICD-CM in the US (to a lesser degree), ( I don't know how MEDDRA is funded - the reporting standard for adverse drug reactions).
 * Closed IP does not work well, but alternatives are difficult to point to.


 * Title: "Issues with Patents" - [ slides ]
 * by JohnSowa
 * Abstract: ... with the two slides - one for a questionable patent which was issued, and another for a continuation that adds more claims, John will discuss how patents may, in fact, defeat its intended purpose of fostering creativity.
 * JohnSowa: let us collect pertinent prior art to the two problematic patent/patent applications as a group effort ... please post to:
 * PriorArt_Patent_7493253
 * PriorArt_PatentApplication_20090259459
 * also, PriorArt_PatentApplication_20090055437 (added after the session, with reference to JohnSowa's  ontolog-forum post dated 1-Sep-2010.)
 * on BrucePerens recommendation, anything one year prior to the application date should be relevant

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.

-- begin of chat session --

PeterYim:.

Welcome to the Joint OOR-Ontolog-NCBO-CC-IAOA-OASIS "OpenOntologyRepository_IPR Policy and Issues" Panel Discussion (session-2) - Thu 16-Sep-2010


 * Topic: "OOR-IPR session 2: what are the IPR issues relating to open ontology repositories (and ontologies in general)?"


 * Chair: Professor MarkMusen (NCBO; Stanford)

o Mr. CameronRoss (Kojeware; OOR) - "Ecosystems, Ontology Repositories, and IPR" o Professor AlanRector (University of Manchester) - Remarks: "The GALEN and SNOMED IPR experience" o Dr. JohnSowa (Vivomind Intelligence; SIO) - Remarks: "Issues with Patents" o Mr. BrucePerens (original author of the "Open Source Definition") - Commentary o Mr. JohnWilbanks (VP of Science, Creative Commons) - Commentary o Mr. PeterYim (Co-convener, Ontolog & OOR; Secretary, IAOA) - "Questions to ALL: what are our issues now?"
 * Panelists:   (2HFZ)

see details on session page at: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2010_09_16

.

anonymous morphed into TerryLongstreth

JohnWilbanks: PeterYim, I am on the line but muted

JohnWilbanks: in a noisy environment

PeterYim: Hi John

anonymous morphed into AlanRector

AliHashemi: Hello all!

YuriyMilov: Hi All

JohnWilbanks: PeterYim, can you speak up or increase your mic volume?

RaviSharma: @Cameron: why should OOR Support proprietary extensions? as mentioned in your slide.

CameronRoss: @RaviSharma - Proprietary extension allow commercial entities to utilize the OOR.

BrucePerens: BrucePerens is on the line.

PeterYim: great ... Hi Bruce

RaviSharma: @Cameron: i view the OOR as a container, kindly compare the keystone unix Kernel with technologies involved in creating and supporting OOR lifecycle, I also envisage OOR lifecycle to have ecosystem like evolution where some technologies and ontologies will not be able to survive?

CameronRoss: @RaviSharma - OOR being a compilation of the OOR content, the software used to implement the OOR and the federation of specific OOR instances. The tools for creating and supporting the OOR life-cycle help to define the content... the keystone would result from the uses of this content. Imagine that the OOR grows in terms of content and we have all kinds of applications that build on top of it (define applications in a very general sense here). Now, take away the OOR... ouch!

RaviSharma: @Cameron: excellent ELP

AlanRector: One moment please - moving the microphone nearer I got cut off

AliHashemi: Are there slides online?

PeterYim: @Ali - no slides for Alan's remarks

JohnWilbanks: this point is essential - the need to clarify and edit ontologies, not just refer to them

JohnWilbanks: here's an old example from 2007 - http://neurocommons.org/page/2007_prototype_queries#Creating_class_level_relations_for_easier_queryi ng_of_the_GO.

JohnWilbanks: or here: http://neurocommons.org/page/Bundles/obo/all

JohnWilbanks: "The part_of relation in all OBO ontologies (and elsewhere in the RDF distribution) is normalized to http://purl.org/obo/owl/OBO_REL#part_of before being included in the Neurocommons RDF distribution."

CameronRoss: @Alan - Contributions to Eclipse are also "viral" in the sense that you must contribute to the project under the Eclipse Public License. The primary difference, I believe, is that the EPL is open whereas the contribution to SNOMED is not.

FrankOlken: Hi

BrucePerens: I would like to speak about challenging the patent.

RaviSharma: @Dr. John Sowa - for obvious reasons given by you - Can such a patent be made to be rescinded or there is too much process involved?

RaviSharma: @Bruce and John: can we request patent office to open their process in this particular case to determine if SMEs who understand Text Processing, Ontology, concepts were consulted or can now be inducted to review?

JohnWilbanks: +1 for public patent foundation

FrankOlken: Public Patent Foundation web site: http://www.pubpat.org/

PeterYim: @Bruce - would you please type out the name and contact for Dan R so we can be sure we got his name right, please

JohnWilbanks: http://www.pubpat.org/

BrucePerens: Daniel Ravisher at pubpat.org

FrankOlken: PUBPAT Board of Directors - Daniel B. Ravicher, President and Executive Director

JohnWilbanks: email is dan at pubpat dot org

JohnSowa: I suggest that Peter starts a wiki page (each) to collect prior art that is pertinent to the two example problematic patent/patent-application

PeterYim: will do ... thank you for the suggestion, John

PeterYim: @JohnSowa and All - I have initialized the wiki pages (to collect prior art for your two artifacts) ... see under: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2010_09_16#nid2HIH

RaviSharma: @All- can we also sign a petition from community for patent office.

RaviSharma: @ALL- I would like to know opinion in this group whether Ontology as a concept should not be communicated by us to be non-patentable as it is based on reasoning - (foundation of free thinking and use of intellect), common knowledge from centuries, and connectedness to knowledge some prior and some current that is inherently difficult to parse and separate.

JohnWilbanks: http://www.patent-commons.org/

RaviSharma: @JohnWilbanks - on the referred site above there is no entry for other-patents search for Ontology?

CameronRoss: So I guess ignorance is bliss!

CameronRoss: @JohnWilbanks - Could you elaborate a bit on ontology interoperability v.s. openness?

CameronRoss: @JohnWilbanks - Got it. Thanks.

RaviSharma: IS the question valid - whether ontologies are patentable?

CameronRoss: @BrucePerens - What are your thoughts on the EPL 1.0?

CameronRoss: EPL = Eclipse Public Lincese

JohnWilbanks: there is also the issue of US *public funding* for vast amounts of ontology work...

BrucePerens: Freedom of thinking went out with the recent court decision in Vernor v. Autodesk. The publisher can now license the WAY you use the information, as Sun has tried to do for a decade with the Java reference books.

JohnWilbanks:

CameronRoss: not funded = not sustainable

PeterYim: refer to PeterYim's slides #5 to #12 on "Questions to All participants"

PeterYim: '''#6: Are you planning to contribute to the OOR effort; if yes, what would your contribution(s) be?'''

JohnWilbanks: CC is on board

JohnWilbanks: we can bring our own research to the table

AliHashemi: 1) Yes (mainly COLORE). 2) Software/services(?)[requires other resources to be better developed] - more so things that work with ontologies than ontologies themselves

CameronRoss: Maybe, contributing mostly code and infrastructure, but the degree of my contribution will be dictated by the level of commitment of others and also on the licensing model(s) that is eventually adopted.

PeterYim: '''#7: If you are contributing code, what would be your (top 2 or 3) open license preferences?'''

BrucePerens: Bruce says GPL, BSD, LGPL together provide all the common sorts of Open Source license and are compatible with each other.

RaviSharma: @All - since there is no kernel agreed for ontologies or for OOR, unix parallels may not be directly applicable?

CameronRoss: License preferences: in order of preferences for OOR code: #1: EPL, #2: BSD, #3 some other gifting license. Not acceptable from my perspective would be GPL.

RaviSharma: general open license

PeterYim: @Ravi - not sure what license you are referring to in the above statement.

PeterYim: '''#8: If you are contributing content, what would be your (top 2 or 3) open license preferences?'''

CameronRoss: Content license preference at this point would be CC-by 3.0, but this isn't all that clear to me at this point.

BrucePerens: BSD, or just declare it to be in the public domain if you don't care about attribution.

Pat Cassidy1: For ontology content, I suggest that the freest possible license be used; if not public domain, then a gift license with at most an attribution requirement. If control of the name of an ontology is desirable, I would suggest that the name be trademarked.

PeterYim: #9; If you are planning to run an ontology repository ... Will you federate with the open instance of the OOR? ... What kind of software license do you plan to adopt? ... What kind of content license do you plan to adopt?

CameronRoss: Yes! Absolutely! As long as the OOR interfaces were reasonable to interface with. Current plan is to use EPL 1.0 for software and CC-by 3.0.

PeterYim: '''#10: Should we, as a community, take a position on Software patents? if so, what position should we take?'''

RaviSharma: consensus communique

BrucePerens: Unfortunately software patenting is potentially a show-stopper for Open Source, so you need to do something about it. The W3C process is probably good.

PeterYim: '''#11: Should we, as a community, take a position on Ontology patents? if so, what position should we take?'''

RaviSharma: Peter your Q lists what i wanted to communicate anyway. Thanks.

RaviSharma: Can we attempt a communique style brief as consensus of community in the next 2-3 wks?

RaviSharma: Ontologies should not be patentable, but some effort attribution ought to be allowed.

CameronRoss: I don't think that ontologies should be patentable, but I see the whole patent situation to be entirely misguided.

CameronRoss: I guess we should take a position, but I wouldn't dedicate a lot of resources to it... its seems like a black hole... I think that our resources would be better spent just doing real work.

PeterYim: '''#12: Any suggestion on how we can get open efforts funded ... ?'''

BrucePerens: Write grants?

AliHashemi: Re funding: case studies demonstrating real $ savings for companies?

AliHashemi: i.e. form a committee or a group via ontolog to demonstrate a business case for open efforts in ontologies?

AliHashemi: (dunno if this is pie in the sky...)

AliHashemi: case can/should also be made to government organizations. Electronic health records, etc... The case just needs to be documented and made.

BrucePerens: Someone's going to have to tilt at this windmill some day.

RaviSharma: Peter: Will some of the answers in chat find their way on the active pages?

PeterYim: @Ravi - the chat transcript will be captured onto the session page shortly (as usual)

RaviSharma: Thanks.

BrucePerens: Bye.

CameronRoss: Thanks everyone.

PeterYim: thanks

PeterYim: -- session ended 12:27pm PDT --

-- end of chat session --


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 * Conference Date and Time:	16-Sep-2010 10:39am ~ 12:27pm PDT
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