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= [[OpenOntologyRepository]]: Metadata Workshop-IV - Tue 2011_10_18 =
= [[OpenOntologyRepository]]: OOR Team Conference Call - Tue 2011_11_01 =


Topic: '''OOR Metadata Workshop-IV'''  
This is a regular OOR Team meeting. ... ''please refer to proceedings from the last team meeting at [[OOR/ConferenceCall_2011_10_04]]''  


Session Chair: '''MichaelGruninger'''  
'''* * * Please pay special attention to the time of this event, as the US is still on Daylight Saving Time (summer time), while Europe is back to Standard Time (winter time) * * *'''  


== [http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-metadata-workshop/ Archives]  ==
'''* * * Please also note that we are calling into a new conference bridge starting from this session, note the new dial-in information! * * *'''  
 
* Please refer to the proceedings of:
** ''(This session)'' '''OOR Metadata Workshop-IV''' [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_10_18#nid2XX1 below]
** '''OOR Metadata Workshop-III''' at [[OOR/ConferenceCall_2011_05_27]]
** '''OOR Metadata Workshop-II''' at [[OOR/ConferenceCall_2011_05_13]]
** '''OOR Metadata Workshop-I''' at [[OOR/ConferenceCall_2011_03_18]]
* '''[http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-metadata-workshop/oor-metadata-04_20111018b.mp3 Audio recording of this session]''' [ 1:17:07 ; mp3 ; 8.83 MB ]
* '''[http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_10_18#nid2Y3B chat-transcript from this session]'''  


=== [[MeetingsCalls|Conference Call]] Details  ===
=== [[MeetingsCalls|Conference Call]] Details  ===


* Date: '''Tuesday, 18-Oct-2011'''  
* Date: '''Tuesday, 1-Nov-2011'''  
* Start Time: 8:30am PDT / 11:30am EDT / 5:30pm CEST / 4:30pm BST / 15:30 UTC  
* Start Time: 8:30am PDT / 11:30am EDT / 4:30pm CET / 15:30 UTC  
** ref: [http://www.timeanddate.com/worldclock/fixedtime.html?month=10&day=18&year=2011&hour=8&min=30&sec=0&p1=224 World Clock]  
** ref: [http://www.timeanddate.com/worldclock/fixedtime.html?month=11&day=1&year=2011&hour=8&min=30&sec=0&p1=224 World Clock]  
* Expected Call Duration: 1.0~1.5 hours  
* Expected Call Duration: 1.0~1.5 hours  
* Dial-in Number:
** from a '''US telephone (US): +1-218-844-8060''' (domestic long distance cost will apply)
** When calling in from a phone, use '''Conference ID: "4389979#"'''
** '''from Europe, call:'''
*** Austria 0820-4000-1577
*** Belgium 070-35-9992
*** France 0826-100-280
*** Germany 01805-00-7642
*** Ireland 0818-270-037
*** Italy 848-390-179
*** Spain 0902-886-056
*** Switzerland 0848-560-327
*** UK 0844-581-9148
** callers '''from other countries''' please dial into either one of the US or European numbers


* '''In-session chat'''-room url: http://webconf.soaphub.org/conf/room/oor_20111018
* Dial-in:
** '''Phone (US): +1 (206) 402-0100''' (long distance cost will apply)
** '''Skype: joinconference'''
** when prompted enter '''PIN: 141184#'''


* '''Shared-screen support''' (VNC session), if applicable, will be started 5 minutes before the call at: http://vnc2.cim3.net:5800/  
* '''In-session chat'''-room url: http://webconf.soaphub.org/conf/room/oor_20111101
** view-only password: "ontolog"


* '''RSVP''' '' to [mailto:peter.yim@cim3.com peter.yim@cim3.com] appreciated,'' ... or simply just by adding yourself to the "Expected Attendee" list below (if you are a member of the team.)  
* '''RSVP''' '' to [mailto:peter.yim@cim3.com peter.yim@cim3.com] appreciated,'' ... or simply just by adding yourself to the "Expected Attendee" list below (if you are a member of the team.)  


* This session, like all other Ontolog events, is open to the public. Information relating to this session is shared on this wiki page: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_10_18
* This session, like all other Ontolog events, is open to the public. Information relating to this session is shared on this wiki page: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_11_01


* Please note that this session may be recorded, and if so, the audio archive is expected to be made available as open content, along with the proceedings of the call to our community membership and the public at-large under [[WikiHomePage#Intellectual_Property_Rights_.28IPR.29_Policy|our prevailing open IPR policy]].  
* Please note that this session may be recorded, and if so, the audio archive is expected to be made available as open content, along with the proceedings of the call to our community membership and the public at-large under [[WikiHomePage#Intellectual_Property_Rights_.28IPR.29_Policy|our prevailing open IPR policy]].  
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* Attended:  
* Attended:  
** [[MichaelGruninger|Michael Grüninger]] (chair)  
** [[User:KennethBaclawski|Ken Baclawski]] (chair)  
** [[PeterYim|Peter P. Yim]]  
** [[PeterYim|Peter P. Yim]]  
** [[TerryLongstreth|Terry Longstreth]]
** [[MichaelGruninger|Michael Grüninger]]  
** [[User:KennethBaclawski|Ken Baclawski]]
** [[NikkiaAnderson|Nikkia Anderson]] (for GailHodge)
** [[TimWilson|Tim Wilson]]
** [[TimDarr|Tim Darr]]  
** [[ToddSchneider|Todd Schneider]]  
** [[ToddSchneider|Todd Schneider]]  
** [[AliHashemi|Ali Hashemi]]
** [[MikeBennett|Mike Bennett]]  
** [[XingfangLi|Xingfang Li]]  


* Expecting:  
* Expecting:  
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* Regrets:  
* Regrets:  
** [[MikeBennett|Mike Bennett]]
** [[MikeDean|Mike Dean]]  
** [[MikeDean|Mike Dean]]  
** [[TimDarr|Tim Darr]]
** [[LeoObrst|Leo Obrst]]  
** [[LeoObrst|Leo Obrst]]  


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''please insert any additional items below (along with your name for follow-up purposes)''  
''please insert any additional items below (along with your name for follow-up purposes)''  


* [[MichaelGruninger|Michael Grüninger]]: continuing from previous sessions ...
* OOR-sandbox and OOR-devbox status update
** Our goal is to evaluate the adequacy of OMV for OOR metadata.
* Member activities updates
** Our current objective is to determine the different relationships among ontologies within OOR.  
* planning and coordination on upcoming OOR events
** We will discuss use cases, especially two potential areas that can supply candidate ontologies -- time ontologies and geospatial ontologies.
** OOR Architecture-API sessions, OOR Metadata sessions, Standards sessions, next regular team meeting, ... more
* Peter: continue to explore what resources are needed to define a minimal set of metadata requirements for implementation into OOR-gatekeeping (so we can move from OOR-sandbox to OOR-production, and be able to stand up both servers); then we can start soliciting volunteers to upload their ontologies.  
* action planning for facilitating code contribution (organizing ourselves so various teams can actually get to work on coding)
 
* Getting us to a stage when we can run a OOR-production box
== References  ==
* action planning for "soliciting" content (getting people to upload ontologies)
* ...  
* [[PeterYim|Peter P. Yim]]: after we are done with the regular OOR team agenda, we need help from everyone who can stay to test an alternate conference bridge as well


* Proceedings of '''[http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_03_18 OOR Metadata Workshop-I]''' and MichaelGruninger's opening [http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-metadata-workshop/metafuture--MichaelGruninger_20110318.pdf slides] from that session
* ...  
* Proceedings of '''[http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_05_13 OOR Metadata Workshop-II]'''
* Proceedings of '''[http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_05_27 OOR Metadata Workshop-III]'''
* Metadata for Ontologies - [[OntologySummit2008_Communique|from the [[OntologySummit2008_Communique]]]]
* Metadata requirement - [[OpenOntologyRepository_IPR|as stipulated in the OOR IPR Policy]]
* Ontology Metadata Vocabulary - [[OMV]]
** Brief Description of OMV (with diagram) - http://omv2.sourceforge.net/description.html
** "OMV - Ontology Metadata Vocabulary for the SemanticWeb" - [http://ontolog.cim3.net/file/resource/OOR/OMV/OMV-Reportv2.4.1.pdf OMV v2.4.1 (final)] (Mar-2009)
* The Joint [[OpenOntologyRepository]]-OntologySummit2008 Panel Discussion Session - ConferenceCall_2008_04_10
** Presentation by [[PeterHaase|Peter Haase]] "[[ConferenceCall_2008_04_10|The OMV Ontology Metadata Vocabulary]]" at that session
* [[OpenOntologyRepository_Architecture]]
* [[OpenOntologyRepository_UseCases]] - http://www.ccs.neu.edu/home/kenb/ontologies/


== Agenda & Proceedings  ==
== Agenda & Proceedings  ==


1. Meeting called to order:  
'''[http://ontolog.cim3.net/file/work/OpenOntologyRepository/MeetingsCalls/ Archives]:'''


* [[MichaelGruninger|Michael Grüninger]] takes the chair and welcome everyone
* [http://ontolog.cim3.net/file/work/OpenOntologyRepository/MeetingsCalls/OOR-team-conf-call_20111101b.mp3 audio recording of the session]  
* Review and adopt agenda
* [http://ontolog.cim3.net/file/work/OpenOntologyRepository/MeetingsCalls/chat-transcript_oor-team_20111101b.txt chat-transcript of this session] ''(lightly edited)''
* [[PeterYim|Peter P. Yim]] volunteered to keep a record of the proceedings


2. Roll Call:  
1. Meeting called to order:  


* see [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_10_18#nid2XWP above]  
* [[User:KennethBaclawski|Ken Baclawski]] takes the chair and welcome everyone
* review and adopt agenda
* [[PeterYim|Peter P. Yim]] volunteered to take notes


* new participant introduction (as required)  
* the first conference bridge we were planning to test (FZM) did not work out (we hit full capacity after a few connections), therefore, moved directly to testing the alternate conference bridge (ITS2).


* Announcements (as required)
2. Roll Call:  
** 2011_10_20 - Thursday: Joint IAOA-OOR-Ontolog "Ontologies and Standards" mini-series session-1: Introducing the ISO/WD 17347 "Ontology Integration and Interoperability ([[OntoIOp]])" Standardization Effort - Co-chairs: [[JohnBateman|John Bateman]] & [[MichaelGruninger|Michael Grüninger]] - ConferenceCall_2011_10_20
** 2011_11_03 - Thursday: Joint IAOA-OOR-Ontolog "Ontologies and Standards" mini-series session-2: Invited Speaker: [[ElisaKendall|Elisa Kendall]] on ISO 19763 "Metamodel Framework for Interoperability (MFI)" - Co-chairs: [[MichaelGruninger|Michael Grüninger]] & [[JohnBateman|John Bateman]] - ConferenceCall_2011_11_03
* 
** we will be transitioning to another conference bridge provider (within the next couple of weeks). Need help from people to help test the new platform.
 
3. Key items for review and discussion today:
 
3.1 '''Opening:''' -  by [[MichaelGruninger|Michael Grüninger]]
 
Today's (2011.10.18) agenda:
 
* Claim 1: For specifying properties of ontologies, OMV is sufficient for OOR use cases.
 
* Claim 2: OMV is not sufficient for specifying the relationships between ontologies within an
ontology repository.
 
* Existing relations between ontologies within [http://ontolog.cim3.net/file/resource/OOR/OMV/OMV-Reportv2.4.1.pdf OMV (v2.4.1)]: (ref. pp. 13, 29 30)
** <nowiki>useImports</nowiki>
** <nowiki>hasPriorVersion</nowiki>
** <nowiki>isIncompatibleWith</nowiki>
** <nowiki>isBackwardsCompatible</nowiki>
 
* The last three relationships focus on different versions of an ontology rather than the
relationship between different ontologies.
 
* Is useImports defined if the ontologies are axiomatized in different languages?
 
* Heterogeneous ontologies -- ontologies that import other ontologies which are axiomatized
in different languages.
 
* What is the distinction between metalogical relations between ontologies that are required for an ontology repository and relations that are needed to support the software functionality of the repository?
 
* What notion of modularity do we use within OOR? What constitutes an ontology within OOR?
 
3.2 '''Discussion:'''
 
* see [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_10_18#nid2Y20 archives above]
 
* continued discussion and exploration of the above (today's main agenda items) ...
 
* continue to explore what resources are needed to define a minimal set of metadata requirements for implementation into OOR-gatekeeping (so we can move from OOR-sandbox to OOR-production, and be able to stand up both servers); and solicit volunteers
 
3.3 ===IM Chat Transcript captured during the session===
 
see raw transcript [http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-metadata-workshop/oor-metadata-04_chat-transcript_unedited_20111018a.txt here].
 
(for better clarity, the version below is a [http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-metadata-workshop/oor-metadata-04_chat-transcript_edited_20111018b.txt re-organized and lightly edited chat-transcript].)
 
Participants are welcome to make light edits to their own contributions as they see fit.
 
-- begin in-session chat-transcript --
 
[[PeterYim|Peter P. Yim]]: Welcome to the
 
''' open ontology repository (oor) session - tue 2011_10_18 '''
 
Topic: OOR Metadata Workshop-IV
 
Session Chair: [[MichaelGruninger|Michael Gr&uuml;ninger]]
 
Session page: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_10_18
 
''' proceedings: '''
 
anonymous morphed into [[TimWilson|Tim Wilson]]
 
[[TimWilson|Tim Wilson]]: Hi, this is Tim Wilson.  I am having work done in my basement, it is very noisy.
 
[[MichaelGruninger|Michael Gr&uuml;ninger]]: I am having trouble connecting by phone
 
Tim Darr: Joining ...
 
[[PeterYim|Peter P. Yim]]: are you trying to connect via skype?
 
[[PeterYim|Peter P. Yim]]: Michael got in!
 
[[ToddSchneider|Todd Schneider]]: Michael, What's a 'module'?
 
anonymous morphed into [[NikkiaAnderson|Nikkia Anderson]]
 
anonymous morphed into [[AliHashemi|Ali Hashemi]]
 
[[ToddSchneider|Todd Schneider]] / [[MichaelGruninger|Michael Gr&uuml;ninger]]: Manchester's TONES repository - http://owl.cs.manchester.ac.uk/repository/browser
 
[[MichaelGruninger|Michael Gr&uuml;ninger]]: how ontologies relate to one another elevates OOR from being
 
"just a library of ontologies" (e.g. if you look at TONES from Manchester, that
 
is a large list of ontologies with no interaction between them)
 
[[AliHashemi|Ali Hashemi]]: Scenario:
 
Given:
 
Ontology O1 in OWL (in OOR)
 
Ontology O2 in CL (not in OOR)
 
Ontology O3 in CL (in OOR) <-- (previously: "ORR" - typo corrected)
 
Declare in OMV:
 
O3 hasImport O1
 
O3 hasImport O2
 
O1 hasLanguage OWL
 
O2 hasLanguage CL
 
O3 hasLanguage CL
 
--- ---
 
[[AliHashemi|Ali Hashemi]]: ORR is a typo meant OOR
 
[[TimWilson|Tim Wilson]]: At my work, ORR is Operational Readiness Review.
 
[[PeterYim|Peter P. Yim]]: There is actually an "ORR" - the MMI project's Ontology Registry and Repository
 
(which is also [[BioPortal]] based) - see: http://mmisw.org/orr/#b
 
If ontologies are located externally to OOR
 
How to handle this in a workflow tool?
 
Speak to a need to differentiate between Ontologies that are registered
 
(and axioms are available on OOR)
 
[[MichaelGruninger|Michael Gr&uuml;ninger]]: Using the notion of importing ontologies, there will exist
 
a set of ontologies that are imported by other ontologies but which do not themselves
 
import any others. Such ontologies would be "building block" modules, and we would
 
require them to be registered in the repository.  
 
[[AliHashemi|Ali Hashemi]]: hasImport --> useImports*


[[TimWilson|Tim Wilson]]: (Very interesting discussion, but I need to go.)
* see [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_11_01#nid2Y0M above]


[[TerryLongstreth|Terry Longstreth]]: The notion of imports entrains a responsibility on the part of the OOR services to validate the imported items
* welcome and intro of new member(s) (as needed)


[[TerryLongstreth|Terry Longstreth]]: Once validated, the imported ontology module is presumed to be an invariant
3. Status Review and Discussion:  


[[ToddSchneider|Todd Schneider]]: OOR will automatically parse import statements and check for
* '''Review and update our "Most Critical Task(s) At Hand" list''' ...(''we will skip this stock agenda item at today's call.)''
** ref. http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository#nid17YH


the presence of the ontologies to be imported in OORs.  
=== 4. Key items for review and discussion today  ===


[[ToddSchneider|Todd Schneider]]: Terry, invariant? With respect to what?  
* OOR-sandbox and OOR-devbox status update - see [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_11_01#nid2YDX below]


[[TerryLongstreth|Terry Longstreth]]: With respect to the importing object
* planning and coordination on upcoming OOR events - see [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_11_01#nid2YE5 below]  
** OOR Architecture-API sessions, OOR Metadata sessions, Standards sessions, next regular team meeting, ... more


[[AliHashemi|Ali Hashemi]]: If you're building services in the OOR to exploit elements of an ontology,
* Member activities updates - see [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_11_01#nid2YG7 below] ... ''(discussion postponed)''  


if it is not in (or transparent to) the system you can't really deploy the services
* action planning for facilitating code contribution (organizing ourselves so various teams can actually get to work on coding) ... ''(discussion postponed)''  


[[TerryLongstreth|Terry Longstreth]]: If the imported, validated module can change, than everything that
* Getting us to a stage when we can run a OOR-production box ... ''(discussion postponed)''


imports it can be invalidated
* action planning for "soliciting" content (getting people to upload ontologies) ... ''(discussion postponed)''


[[AliHashemi|Ali Hashemi]]: (I've got to run. Bye.)
* we need help from everyone who can stay to test an alternate conference bridge "ITS2" as a candidate for future calls


[[TerryLongstreth|Terry Longstreth]]: ...at some arbitrary time in the future
* OOR-sandbox and OOR-devbox status update
** new OOR logo now on the OOR-Sandbox - see: http://sandbox.oor.net
** NCBO [[BioPortal]] v3.3 released on 2011.10.19 - ref. http://ontolog.cim3.net/forum/oor-forum/2011-10/msg00027.html
** Xen vm image of the latest NCBO Appliance almost ready (as of our 2011.10.31 communication with the NCBO team)
** <support@oor.net> mail forwarder created:
*** people can just mail this address or enter into "Send Feedback" form on the OOR Sandbox
*** which currently gets forwarded to: [[TejasParikh|Tejas Parikh]], [[User:KennethBaclawski|Ken Baclawski]], [[MikeDean|Mike Dean]], [[PeterYim|Peter P. Yim]] and <oor-users@ontolog.cim3.net>  ''(--PeterYim/2011.10.14)''
*** remember to tweak this too, after the new vm image is in place - ref. http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR_SandBox_Customization#nid2X3C


[[ToddSchneider|Todd Schneider]]: (Sorry, but have to go.)  
* planning and coordination on upcoming OOR events - workshop plans
** Michael: ISO 19763 - Thu Nov-3 (12:30 EDT)
*** Peter will get a reminder out (after this meeting) based on prelim material received from [[ElisaKendall|Elisa Kendall]] (at least as a placeholder)
** Session on "Getting OOR Development going on Eclipse" - aim for Tue 2011.11.08 (if not then Tue 2011.11.22)
*** candidate panel: [[MikeDean|Mike Dean]], [[CameronRoss|Cameron Ross]], [[EricChan|Eric Chan]], [[PaulAlexander|Paul Alexander]]
** Ken / Todd - OOR-Architecture-API IX - "NCBO-OOR architectural considerations and synergies" + "creating [[BioPortal]] Tabs" - Tue 2011.11.29 (RayFergerson is ok with this date; he is not available on 2011.11.22)
** Michael: OOR-Metadata V - ??? ... [[MikeBennett|Mike Bennett]] will send something he will contribute to Michael;
** [[OntologiesAndStandards]] III - on "Common Logic" - tentative Thu 2011.12.15 ... - candidate panel: [[FabianNeuhaus|Fabian Neuhaus]], [[LeoObrst|Leo Obrst]], ... - Chair: [[MichaelGruninger|Michael Gr&uuml;ninger]] & [[JohnBateman|John Bateman]]
*** ... then, [[OntologiesAndStandards]] IV a session on IDIOM
** [[FactGuru|Fact Guru]] incorporation & integration?
** more on SIO ...?
** other sessions of interest ???
** next regular OOR team meeting Tue 2011.12.06 (11:30 EDT)  


[[MichaelGruninger|Michael Gr&uuml;ninger]]: How does [[BioPortal]] capture the notion of different ontology versions and the possibility of new  versions being used which are not part of BioPortal?
... ''Notes below are from previous meeting(s), and will be updated as this meeting progresses.''


[[TerryLongstreth|Terry Longstreth]]: How does Bioportal reflect changes in semantics of medical ideas?
* assessing a strengthened OOR-NCBO collaborative relationship
* OOR-sandbox and OOR-devbox status update
** http://oor-01.cim3.net/ - now: http://sandbox.oor.net/ --> to become our OOR-devbox (OOR development server)
** http://oor-02.cim3.net/ - to be designated: http://sandbox.oor.net/


[[User:KennethBaclawski|Ken Baclawski]]: There are two different notions of import.  One can import an ontology with
* Discussion: the [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_07_15#nid2VYW newly adopted dual-track OOR approach]
** action planning
*** we run (for now) 2 instances - a sandbox instance[1] on the OOR-01 vm, and an experimental instance[2] on the OOR-02 vm
**** [1] this will be a straight forward, and updated [[BioPortal]] code install, with customization only for: the logo, the IP / License statement, categories.
**** [2] this will be the instance we use to continue the current work of further development in Architecture, API, metadata, CL support, etc.
**** consensus: both instances would use the same database (so ontologies uploaded are accessible by both instances, and are obviously "in sync" ... saving us the need to "import" as we ad discussed at the last meeting)
*** Peter: the next things to push is to have "gatekeeping" in place so we can stand up a "production" OOR


no specification of which version is being imported. One could also have a strict import
* updating "categories"
** Peter: the ICOM people suggests adding the categories of "standards" and "collaboration" (the latter probably belongs under "Cultural"
** Mike: something like Dublin Core should go under "metadata" - we are adding this category, "process" too
** discussed - see updated "category" list at: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_08_05#nid2W6B
** one can select multiple categories by doing a "ctrl-click" (or "cmd" for Mac users)
** Ken: the software stores "categories" in an OMV ontology, and support a hierarchy of nested categories
*** Mike: there is a GUI interface for adding categories
** All: we probably want to leave it simple (one level) and support "addition of categories" on demand
** Todd: For some categories, e.g., science, subcategories will be needed. Since the provided listing is linear, subcategories could be listed as pairs or triples: Science, Science - Biology, Science-Physics, Science-Physics-Gravitation, etc.
** Leo: we might consider adopting some standard categorization, like what the Library of Congress has put out (maybe not the entire hierarchy, but only the very upper level(s)
* Category list (based on MikeDean's list): (updated 2011.08.05)
** Upper Ontologies
** Standards (for example, Measurement)
** Science (for example, Biomedical)
** Financial
** Government
** Cultural (for example, Social Networking, People)
** Geospatial
** Commercial
** Literature
** Technology
** Provenance
** Defense
** Metadata (for example, OMV, Dublin Core)
** Process (for example, PSL)
** Other


that requires the imported ontology to be a specific version. One can enforce
* Status and action review: OOR-dev box - http://oor-03.cim3.net


a strict import by specifying a checksum.  
* Status and action review: SOCoP presentation box - http://socop.oor.net (at BBN?)


[[MichaelGruninger|Michael Gr&uuml;ninger]]: Find examples within [[BioPortal]] of one ontology importing another ontology,  
* Getting us to a stage when members can contribute code ... how, ETA?
** ''(discussion 2011.05.06):''
*** an adopted Architecture & API is definitely crucial, but that's not all
** All team members are encouraged to mull over how we can get to that state effectively
*** in particular ... how do we make this a "successful" community-driven, open source project!?
** (discussion 2011.06.03)'' ...


either internal or external to [[BioPortal]]
* Code repository - considering "git" or github?


[[PeterYim|Peter P. Yim]]: [[MichaelGruninger|Michael Gr&uuml;ninger]]: at the next workshop, we can put some focus on "versioning"  
* getting the OOR code repository at semwebcentral started (for real!) - http://oor.semwebcentral.org/
** [[OOR_SandBox]] - http://sandbox.oor.net/ontologies (previously http://oor-01.cim3.net/ontologies)
** OOR code-repository and re-assessing the 'branch instead of fork' (what does that mean?) [MikeDean, [[User:KennethBaclawski|Ken Baclawski]], et al.]  
** categories - ref. MikeDean's msg - http://ontolog.cim3.net/forum/oor-dev/2011-02/msg00012.html
** 2011.02.18: *'''Important Note'''* - we will start afresh on the OOR sandbox content (i.e. uploaded ontologies) after the update install - everyone who has uploaded ontologies so far should note
*** those who are "using" the OOR sandbox content now, should note down the ontologies they need, and may need to contact the authors to upload them again if they don't show up. (presumably, those content relating to biomedicine, previously federated from [[BioPortal]], will not be there any more, at least not automatically.) Also, links to ontologies or elements within ontologies established previously will no longer be valid after the content gets re-populated - Ken will make a post about this on [oor-forum]
** workplan:
*** update codebase to appropriate oor install code
**** The consensus is that we should use a uniform language in each component to make it easier for people to contribute code and add extensions.
**** customize banner/logo
**** customize IPR statement
**** re-establish categories - ref. [http://ontolog.cim3.net/forum/oor-dev/2011-02/msg00012.html MikeDean's input]


[[MichaelGruninger|Michael Gr&uuml;ninger]]: Action Item (for everyone): find papers on ontology versioning
* Getting us to a stage when we can run a OOR-production box ... what's still needed, ETA?
** ...


[[PeterYim|Peter P. Yim]]: -- session ended: 10:05 am PDT --
'''Member activities updates:'''


-- end of in-session chat-transcript --  
* Review: members and OOR-related activities (2011.11.01)
** OOR-sandbox status
** code repository status
** NCBO
** NEU
** Raytheon-BBN
*** [[MikeDean|Mike Dean]]: I am attending [http://ontolog.cim3.net/cgi-bin/wiki.pl?SocopWorkshops/Spatial_Semantics_And_Ontologies_2011 SSO 2011], sponsored by SOCoP and am making a brief presentation of OOR as a lightning talk.
** Bremen
** UToronto
** Ryerson
** Mathet
** [[SOCoP_INTEROP]]
** [[DataONE]]
** [[NeOn]] (KMi and STL)
** ONKI
** KBSI
** MMI
** Use Cases
** Architecture
** API
** Gatekeeping
** production OOR instance
** SIO
** Funding
** ICOM / DERI


4. Any Other Business:
''' Action planning for "soliciting" '''content''' (getting people to upload ontologies)


* [[PeterYim|Peter P. Yim]]: we will be transitioning to another conference bridge provider (within the next couple of weeks). Need help from to help test the new platform(s). Watch out for requests, and come help if you can.
5. '''Funding progress:'''


5. Action items:  
6. '''Any Other Business:'''


* [[MichaelGruninger|Michael Gr&uuml;ninger]]: Action Item (for everyone): find papers on ontology versioning
7. '''Action items:'''


6. Schedule Next Meeting & Adjourn:  
8. Schedule Next Meeting & Adjourn:  


* Next Meeting:  
* Next Meeting:  
** this coming Thu 2011.10.20 - the Joint IAOA-OOR-Ontolog "Ontologies and Standards" mini-series: session-1 - see: ConferenceCall_2011_10_20
** next session - Joint IAOA-OOR-Ontolog "Ontologies and Standards" mini-series: session-2 - Invited Speaker: [[ElisaKendall|Elisa Kendall]] on ISO 19763 - this Thursday ConferenceCall_2011_11_03
** we will then be having a regular OOR-team meeting -  
** next OOR-team meeting - Tue 2011.12.06 same time - [[ OOR/ConferenceCall_2011_12_06 ]]  
*** Date: Tue 2011.11.01 - Start time: 8:30am PDT / 11:30am EDT / 4:30pm CET / 15:30 UTC (ref. [http://www.timeanddate.com/worldclock/fixedtime.html?month=11&day=1&year=2011&hour=8&min=30&sec=0&p1=224 worldclock])
*** see developing session page is at [[OOR/ConferenceCall_2011_11_01]]  


* Call adjourned at: 10:05 am PDT  
* Call adjourned at: 9:37 am PDT  


--
--


notes taken by: [[PeterYim|Peter P. Yim]] / 2011.10.18-10:16am PDT
notes taken by: [[PeterYim|Peter P. Yim]] / 2011.11.01-9:38am PDT


All participants, please review and edit to enhance accuracy and granularity of the documented proceedings.  
All participants, please review and edit to enhance accuracy and granularity of the documented proceedings.  
Line 364: Line 286:
** 2011_06_17 - Friday: OOR - "Architecture & API Specification Development Workshop-VI" - Co-chairs: [[User:KennethBaclawski|Ken Baclawski]] & [[ToddSchneider|Todd Schneider]] - [[OOR/ConferenceCall_2011_06_17]]  
** 2011_06_17 - Friday: OOR - "Architecture & API Specification Development Workshop-VI" - Co-chairs: [[User:KennethBaclawski|Ken Baclawski]] & [[ToddSchneider|Todd Schneider]] - [[OOR/ConferenceCall_2011_06_17]]  
** 2011_09_13 - Tuesday: Joint NCBO-OOR Team Meeting - "Kicking-off the Next Phase of Collaboration" - Co-chairs: [[RayFergerson|Ray Fergerson]] & [[PeterYim|Peter P. Yim]] - [[OOR/ConferenceCall_2011_09_13]]  
** 2011_09_13 - Tuesday: Joint NCBO-OOR Team Meeting - "Kicking-off the Next Phase of Collaboration" - Co-chairs: [[RayFergerson|Ray Fergerson]] & [[PeterYim|Peter P. Yim]] - [[OOR/ConferenceCall_2011_09_13]]  
** 2011_09_20 - Tuesday: OOR - "Architecture & API Specification Development Workshop-VII" - Chair: [[User:KennethBaclawski|Ken Baclawski]] - [[OOR/ConferenceCall_2011_09_20]]  
** 2011_09_20 - Tuesday: OOR - "Architecture & API Specification Development Workshop-VII" - Co-chairs: [[User:KennethBaclawski|Ken Baclawski]] & [[ToddSchneider|Todd Schneider]] - [[OOR/ConferenceCall_2011_09_20]]  
** 2011_10_11 - Tuesday: OOR - "Architecture & API Specification Development Workshop-VIII" - Chair: [[User:KennethBaclawski|Ken Baclawski]] & [[ToddSchneider|Todd Schneider]] - [[OOR/ConferenceCall_2011_10_11]]  
** 2011_10_11 - Tuesday: OOR - "Architecture & API Specification Development Workshop-VII" - Co-chairs: [[User:KennethBaclawski|Ken Baclawski]] & [[ToddSchneider|Todd Schneider]] - [[OOR/ConferenceCall_2011_10_11]]  
** 2011_10_18 - Tuesday: OOR Metadata Workshop-IV - Chair: [[MichaelGruninger|Michael Gr&uuml;ninger]] - [[OOR/ConferenceCall_2011_10_18]]  
** 2011_10_18 - Friday: OOR Metadata Workshop-IV - Chair: [[MichaelGruninger|Michael Gr&uuml;ninger]] - [[OOR/ConferenceCall_2011_10_18]]  
* the '''OOR-IPR mini-series''':  
* the '''OOR-IPR mini-series''':  
** 2010_09_09 - Thursday: Joint OOR-Ontolog-NCBO-CC-IAOA-OASIS Panel Discussion - "IPR issues in Ontology and the OOR" session-1: an exposition on relevant IPR regimes - Keynote speaker: [[GeorgeStrawn|George Strawn]] - Chair: [[PeterYim|Peter P. Yim]] - Panelists: [[JamieClark]], [[JohnWilbanks|John Wilbanks]], [[BrucePerens|Bruce Perens]] - ConferenceCall_2010_09_09  
** 2010_09_09 - Thursday: Joint OOR-Ontolog-NCBO-CC-IAOA-OASIS Panel Discussion - "IPR issues in Ontology and the OOR" session-1: an exposition on relevant IPR regimes - Keynote speaker: [[GeorgeStrawn|George Strawn]] - Chair: [[PeterYim|Peter P. Yim]] - Panelists: [[JamieClark]], [[JohnWilbanks|John Wilbanks]], [[BrucePerens|Bruce Perens]] - ConferenceCall_2010_09_09  
Line 395: Line 317:
* '''[[OOR/ActiveMemberContribution]]'''  
* '''[[OOR/ActiveMemberContribution]]'''  
* '''OOR Project site at [[SemWebCentral]]''' - http://oor.semwebcentral.org  
* '''OOR Project site at [[SemWebCentral]]''' - http://oor.semwebcentral.org  
* '''Public sandbox instance of OOR (OOR-sandbox) - http://sandbox.oor.net/ontologies''' (previously http://oor-02.cim3.net/ontologies)  
* '''Public instances of OOR - http://sandbox.oor.net/ontologies''' (previously http://oor-01.cim3.net/ontologies) ... we are in process to standing up:
** '''[[OOR_SandBox]]'''  
** '''[[OOR_SandBox]]''' - http://oor-03.cim3.net - http://sandbox.oor.net/
* '''Development instance of OOR (OOR-dev) - http://oor-01.cim3.net/''' - to browse: http://oor-01.cim3.net/ontologies - http://dev.oor.net/  
** '''[[OOR_DevBox]]''' - http://oor-01.cim3.net - http://devbox.oor.net/  
** '''[[OOR_DevBox]]'''
** [[NCBO]] - [http://bioportal.bioontology.org/ BioPortal]  
** [[NCBO]] - [http://bioportal.bioontology.org/ BioPortal]  
*** BioPortal's [bioontology-support] mailing list - see: https://mailman.stanford.edu/mailman/listinfo/bioontology-support  
*** BioPortal's [bioontology-support] mailing list - see: https://mailman.stanford.edu/mailman/listinfo/bioontology-support  

Latest revision as of 07:33, 9 January 2016

OpenOntologyRepository: OOR Team Conference Call - Tue 2011_11_01

This is a regular OOR Team meeting. ... please refer to proceedings from the last team meeting at OOR/ConferenceCall_2011_10_04

* * * Please pay special attention to the time of this event, as the US is still on Daylight Saving Time (summer time), while Europe is back to Standard Time (winter time) * * *

* * * Please also note that we are calling into a new conference bridge starting from this session, note the new dial-in information! * * *

Conference Call Details

  • Date: Tuesday, 1-Nov-2011
  • Start Time: 8:30am PDT / 11:30am EDT / 4:30pm CET / 15:30 UTC
  • Expected Call Duration: 1.0~1.5 hours
  • Dial-in:
    • Phone (US): +1 (206) 402-0100 (long distance cost will apply)
    • Skype: joinconference
    • when prompted enter PIN: 141184#
  • RSVP to peter.yim@cim3.com appreciated, ... or simply just by adding yourself to the "Expected Attendee" list below (if you are a member of the team.)
  • Please note that this session may be recorded, and if so, the audio archive is expected to be made available as open content, along with the proceedings of the call to our community membership and the public at-large under our prevailing open IPR policy.

Attendees

  • Expecting:
    • ... if you are coming to the meeting, please add your name above (plus your affiliation, if you aren't already a member of the community) above, or e-mail <peter.yim@cim3.com> so that we can reserve enough resources to support everyone's participation. ...

Agenda Ideas

please insert any additional items below (along with your name for follow-up purposes)

  • OOR-sandbox and OOR-devbox status update
  • Member activities updates
  • planning and coordination on upcoming OOR events
    • OOR Architecture-API sessions, OOR Metadata sessions, Standards sessions, next regular team meeting, ... more
  • action planning for facilitating code contribution (organizing ourselves so various teams can actually get to work on coding)
  • Getting us to a stage when we can run a OOR-production box
  • action planning for "soliciting" content (getting people to upload ontologies)
  • ...
  • Peter P. Yim: after we are done with the regular OOR team agenda, we need help from everyone who can stay to test an alternate conference bridge as well
  • ...

Agenda & Proceedings

Archives:

1. Meeting called to order:

  • the first conference bridge we were planning to test (FZM) did not work out (we hit full capacity after a few connections), therefore, moved directly to testing the alternate conference bridge (ITS2).

2. Roll Call:

  • welcome and intro of new member(s) (as needed)

3. Status Review and Discussion:

4. Key items for review and discussion today

  • OOR-sandbox and OOR-devbox status update - see below
  • planning and coordination on upcoming OOR events - see below
    • OOR Architecture-API sessions, OOR Metadata sessions, Standards sessions, next regular team meeting, ... more
  • Member activities updates - see below ... (discussion postponed)
  • action planning for facilitating code contribution (organizing ourselves so various teams can actually get to work on coding) ... (discussion postponed)
  • Getting us to a stage when we can run a OOR-production box ... (discussion postponed)
  • action planning for "soliciting" content (getting people to upload ontologies) ... (discussion postponed)
  • we need help from everyone who can stay to test an alternate conference bridge "ITS2" as a candidate for future calls
  • planning and coordination on upcoming OOR events - workshop plans
    • Michael: ISO 19763 - Thu Nov-3 (12:30 EDT)
      • Peter will get a reminder out (after this meeting) based on prelim material received from Elisa Kendall (at least as a placeholder)
    • Session on "Getting OOR Development going on Eclipse" - aim for Tue 2011.11.08 (if not then Tue 2011.11.22)
    • Ken / Todd - OOR-Architecture-API IX - "NCBO-OOR architectural considerations and synergies" + "creating BioPortal Tabs" - Tue 2011.11.29 (RayFergerson is ok with this date; he is not available on 2011.11.22)
    • Michael: OOR-Metadata V - ??? ... Mike Bennett will send something he will contribute to Michael;
    • OntologiesAndStandards III - on "Common Logic" - tentative Thu 2011.12.15 ... - candidate panel: Fabian Neuhaus, Leo Obrst, ... - Chair: Michael Grüninger & John Bateman
    • Fact Guru incorporation & integration?
    • more on SIO ...?
    • other sessions of interest ???
    • next regular OOR team meeting Tue 2011.12.06 (11:30 EDT)

... Notes below are from previous meeting(s), and will be updated as this meeting progresses.

  • Discussion: the newly adopted dual-track OOR approach
    • action planning
      • we run (for now) 2 instances - a sandbox instance[1] on the OOR-01 vm, and an experimental instance[2] on the OOR-02 vm
        • [1] this will be a straight forward, and updated BioPortal code install, with customization only for: the logo, the IP / License statement, categories.
        • [2] this will be the instance we use to continue the current work of further development in Architecture, API, metadata, CL support, etc.
        • consensus: both instances would use the same database (so ontologies uploaded are accessible by both instances, and are obviously "in sync" ... saving us the need to "import" as we ad discussed at the last meeting)
      • Peter: the next things to push is to have "gatekeeping" in place so we can stand up a "production" OOR
  • updating "categories"
    • Peter: the ICOM people suggests adding the categories of "standards" and "collaboration" (the latter probably belongs under "Cultural"
    • Mike: something like Dublin Core should go under "metadata" - we are adding this category, "process" too
    • discussed - see updated "category" list at: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_08_05#nid2W6B
    • one can select multiple categories by doing a "ctrl-click" (or "cmd" for Mac users)
    • Ken: the software stores "categories" in an OMV ontology, and support a hierarchy of nested categories
      • Mike: there is a GUI interface for adding categories
    • All: we probably want to leave it simple (one level) and support "addition of categories" on demand
    • Todd: For some categories, e.g., science, subcategories will be needed. Since the provided listing is linear, subcategories could be listed as pairs or triples: Science, Science - Biology, Science-Physics, Science-Physics-Gravitation, etc.
    • Leo: we might consider adopting some standard categorization, like what the Library of Congress has put out (maybe not the entire hierarchy, but only the very upper level(s)
  • Category list (based on MikeDean's list): (updated 2011.08.05)
    • Upper Ontologies
    • Standards (for example, Measurement)
    • Science (for example, Biomedical)
    • Financial
    • Government
    • Cultural (for example, Social Networking, People)
    • Geospatial
    • Commercial
    • Literature
    • Technology
    • Provenance
    • Defense
    • Metadata (for example, OMV, Dublin Core)
    • Process (for example, PSL)
    • Other
  • Getting us to a stage when members can contribute code ... how, ETA?
    • (discussion 2011.05.06):
      • an adopted Architecture & API is definitely crucial, but that's not all
    • All team members are encouraged to mull over how we can get to that state effectively
      • in particular ... how do we make this a "successful" community-driven, open source project!?
    • (discussion 2011.06.03) ...
  • Code repository - considering "git" or github?
  • getting the OOR code repository at semwebcentral started (for real!) - http://oor.semwebcentral.org/
    • OOR_SandBox - http://sandbox.oor.net/ontologies (previously http://oor-01.cim3.net/ontologies)
    • OOR code-repository and re-assessing the 'branch instead of fork' (what does that mean?) [MikeDean, Ken Baclawski, et al.]
    • categories - ref. MikeDean's msg - http://ontolog.cim3.net/forum/oor-dev/2011-02/msg00012.html
    • 2011.02.18: *Important Note* - we will start afresh on the OOR sandbox content (i.e. uploaded ontologies) after the update install - everyone who has uploaded ontologies so far should note
      • those who are "using" the OOR sandbox content now, should note down the ontologies they need, and may need to contact the authors to upload them again if they don't show up. (presumably, those content relating to biomedicine, previously federated from BioPortal, will not be there any more, at least not automatically.) Also, links to ontologies or elements within ontologies established previously will no longer be valid after the content gets re-populated - Ken will make a post about this on [oor-forum]
    • workplan:
      • update codebase to appropriate oor install code
        • The consensus is that we should use a uniform language in each component to make it easier for people to contribute code and add extensions.
        • customize banner/logo
        • customize IPR statement
        • re-establish categories - ref. MikeDean's input
  • Getting us to a stage when we can run a OOR-production box ... what's still needed, ETA?
    • ...

Member activities updates:

  • Review: members and OOR-related activities (2011.11.01)
    • OOR-sandbox status
    • code repository status
    • NCBO
    • NEU
    • Raytheon-BBN
      • Mike Dean: I am attending SSO 2011, sponsored by SOCoP and am making a brief presentation of OOR as a lightning talk.
    • Bremen
    • UToronto
    • Ryerson
    • Mathet
    • SOCoP_INTEROP
    • DataONE
    • NeOn (KMi and STL)
    • ONKI
    • KBSI
    • MMI
    • Use Cases
    • Architecture
    • API
    • Gatekeeping
    • production OOR instance
    • SIO
    • Funding
    • ICOM / DERI

Action planning for "soliciting" content (getting people to upload ontologies)

5. Funding progress:

6. Any Other Business:

7. Action items:

8. Schedule Next Meeting & Adjourn:

  • Next Meeting:
    • next session - Joint IAOA-OOR-Ontolog "Ontologies and Standards" mini-series: session-2 - Invited Speaker: Elisa Kendall on ISO 19763 - this Thursday ConferenceCall_2011_11_03
    • next OOR-team meeting - Tue 2011.12.06 same time - OOR/ConferenceCall_2011_12_06
  • Call adjourned at: 9:37 am PDT

--

notes taken by: Peter P. Yim / 2011.11.01-9:38am PDT

All participants, please review and edit to enhance accuracy and granularity of the documented proceedings.

Resources



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