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OpenOntologyRepository: OOR Infrastructure Meeting - Tue 2013_11_12     (1)

Topic: OOR Infrastructure Discussion: "SOCoP-OOR and related issues"     (1A)

Co-chairs: KenBaclawski, Mike Dean & TillMossakowski     (1B)

  • Dial-in:     (1C4)
    • Phone (US): +1 (206) 402-0100 ... Conference ID: 141184# ... (long distance cost may apply)     (1C4A)
    • in view of recently reported skype connection issues, this is not recommended (especially for speakers) although it may still work for some ... Skype: joinconference (i.e. make a skype call to the contact with skypeID="joinconference") ... (generally free-of-charge, when connecting from your computer ... ref.)     (1C4B)
      • when prompted enter Conference ID: 141184#     (1C4B1)
      • Unfamiliar with how to do this on Skype? ...     (1C4B2)
        • Add the contact "joinconference" to your skype contact list first. To participate in the teleconference, make a skype call to "joinconference", then open the dial pad (see platform-specific instructions below) and enter the Conference ID: 141184# when prompted.     (1C4B2A)
      • Can't find Skype Dial pad? ...     (1C4B3)
        • for Windows Skype users: Can't find Skype Dial pad? ... it's under the "Call" dropdown menu as "Show Dial pad"     (1C4B3A)
        • for Linux Skype users: please note that the dial-pad is only available on v4.1 (or later; or on the earlier Skype versions 2.x,) if the dialpad button is not shown in the call window you need to press the "d" hotkey to enable it. ... (ref.)     (1C4B3B)
      • if you are using skype and the connection to "joinconference" is not holding up, try using (your favorite POTS or VoIP line, etc.) either your phone, skype-out or google-voice and call the US dial-in number: +1 (206) 402-0100 ... when prompted enter Conference ID: 141184#     (1C4B4)
  • Discussions and Q & A:     (1C5)
    • Nominally, when a presentation is in progress, the moderator will mute everyone, except for the speaker.     (1C5A)
    • To un-mute, press "*7" ... To mute, press "*6" (please mute your phone, especially if you are in a noisy surrounding, or if you are introducing noise, echoes, etc. into the conference line.)     (1C5B)
    • we will usually save all questions and discussions till after all presentations are through. You are encouraged to jot down questions onto the chat-area in the mean time (that way, they get documented; and you might even get some answers in the interim, through the chat.)     (1C5C)
    • During the Q&A / discussion segment (when everyone is muted), If you want to speak or have questions or remarks to make, please raise your hand (virtually) by clicking on the "hand button" (lower right) on the chat session page. You may speak when acknowledged by the session moderator (again, press "*7" on your phone to un-mute). Test your voice and introduce yourself first before proceeding with your remarks, please. (Please remember to click on the "hand button" again (to lower your hand) and press "*6" on your phone to mute yourself after you are done speaking.)     (1C5D)
    • instructions: once you got access to the page, click on the "settings" button, and identify yourself (by modifying the Name field from "anonymous" to your real name, like "JaneDoe").     (1C6A)
    • You can indicate that you want to ask a question verbally by clicking on the "hand" button, and wait for the moderator to call on you; or, type and send your question into the chat window at the bottom of the screen.     (1C6B)
    • thanks to the soaphub.org folks, one can now use a jabber/xmpp client (e.g. gtalk) to join this chatroom. Just add the room as a buddy - (in our case here) oor_20131112@soaphub.org ... Handy for mobile devices!     (1C6C)
  • Shared-screen support (VNC session), if applicable, will be started 5 minutes before the call at: http://vnc2.cim3.net:5800/     (1C7)
    • view-only password: "ontolog"     (1C7A)
    • if you plan to be logging into this shared-screen option (which the speaker may be navigating), and you are not familiar with the process, please try to call in 5 minutes before the start of the session so that we can work out the connection logistics. Help on this will generally not be available once the presentation starts.     (1C7B)
    • people behind corporate firewalls may have difficulty accessing this. If that is the case, please download the [ slides] (where applicable) and running them locally. The speaker(s) will prompt you to advance the slides during the talk.     (1C7C)
  • 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.)     (1C9)
  • 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.     (1C11)

Attendees     (1D)

  • Expecting:     (1D2)
    • (please add yourself to the list above if you are a member of the community, or, rsvp to <peter.yim@cim3.com> with the event title/date and your name and affiliation)     (1D2B)

Agenda Ideas     (1D4)

Agenda & Proceedings     (1E)

1. Meeting called to order:     (1E4)

1.1 Roll Call:     (1E9)

2. Key discussion:     (1E12)

2.1 Discuss SOCoP-OOR and related issues     (1E13)

2.2 Scheduling of upcoming OOR Events     (1E21)

  • more OOR session plans ... from now through first half of Jan-2014.     (1E24)

most of the content below are inherited from the previous call(s), and will be edited/updated as this meeting progresses ...     (1E26)

  • there is general consensus we would change to a more bottom-up approach (rather than the "top-down" approach we have been taking) ...        (1E27)
    • we will encourage each oor node project to develop (colore, ontohub, socop, oor public instance, etc.) on their own, and coordinate the "team" effort through the use of a shared set of metadata, API and the UI (e.g. how people download (or even upload) ontologies, etc.)     (1E27A)
    • The key is to ensure that each of the ontology repository projects in OOR are interoperable from the software perspective, uniform in the GUI, and they use a shared approach to ontology metadata     (1E27B)
    • initially (prior to federation mechanisms being in place) we will make <oor.net> to be an ontology registry, which then links to the ontologies in the actual ontology repository where the ontology is described     (1E27C)
    • actions will be focused on developing three things (hopefully within the next 3 months): the set of metadata, the API, and some shared thoughts on the UI     (1E27D)
    • after that, we will focus on building up content with each OOR node tackling the domain(s) they are best with, and put in a concerted effort towards OOR adoption     (1E27E)

3.2 scheduling of OOR Events     (1E30)

4. Prior Discussions:     (1E33)

4.1 Discussion: tactically, what shall we be doing differently in the next 6 to 12 months     (1E34)

... to provide synergies for all.     (1E36)

4.2 Setting the metrics - what does "success" look like     (1E37)

4.3 Action planning for "content drive" (getting people to upload ontologies) ... (deferred discussion of this item)     (1E38)

  • (discussion 2011.05.06):     (1E39)
    • an adopted Architecture & API is definitely crucial, but that's not all     (1E39A)
  • All team members are encouraged to mull over how we can get to that state effectively     (1E40)
    • in particular ... how do we make this a "successful" community-driven, open source project!?     (1E40A)
  • (discussion 2011.08.07) ...     (1E41)
    • ref. IAOA Committee and SIG session at FOIS (2012.07.25) discussion:     (1E41A)
      • IAOA Ontology Registry and Repository Committee to put focus on contents     (1E41A1)
      • getting FOIS papers to be submitted with cited ontologies and their metadata, and have those ontologies hosted on OOR     (1E41A2)
  • 4.6 Getting us to a stage when we can run a OOR-production box ... (deferred discussion of this item)     (1E45)
    • we need a gatekeeping/policy module in place - [KenBaclawski]     (1E45A)

5. IM Chat Transcript captured during the session     (1F)

see raw transcript here.     (1F1)

(for better clarity, the version below is a re-organized and lightly edited chat-transcript.)     (1F2)

Participants are welcome to make light edits to their own contributions as they see fit.     (1F3)

-- begin in-session chat-transcript --     (1F4)


Chat transcript from room: oor_20131112     (1F5)

2013-11-12 GMT-08:00 [PST]     (1F6)


[6:55] Peter P. Yim: Welcome to the     (1F7)

OpenOntologyRepository: OOR Infrastructure Meeting - Tue 2013_11_12     (1F8)

Topic: OOR Infrastructure Discussion: "SOCoP-OOR and related issues"     (1F9)

Attendees: Ken Baclawski (co-chair), Mike Dean (co-chair), Till Mossakowski (co-chair),     (1F12)

Nancy Wiegand (on voice only; not in chat-room)     (1F14)

Proceedings:     (1F15)

[7:01] Peter P. Yim: Till: needs to leave in 30 minutes;     (1F17)

[7:01] Peter P. Yim: Ken: need to leave in an hour too     (1F18)

[7:06] Peter P. Yim: access to various OOR instances & SOCoP-OOR - see: http://oor.net/index1.html &     (1F20)

[7:11] Peter P. Yim: so far, we don't know what caused the Oct-22 SOCoP-OOR crashing (and another     (1F22)

subsequent crash after rebooting)     (1F23)

[7:14] GaryBergCross: Note that Stephen M Richard from Arizona loaded IUGS CGI Consolidation Degree     (1F24)

Term Vocabulary (consoldeg) in Pct. Also Simon Cox loaded his O & M ontology in Sept and got a     (1F25)

parsing error. These are people that I talked to about the OOR and so they tried to load things to     (1F26)

test it out.     (1F27)

[7:25] Mike Dean: The BioPortal version used for SOCoP still uses Protege 3 code. If you get a     (1F28)

loading error, try loading the ontology into Protege 3.     (1F29)

[7:09] GaryBergCross: @Peter, Does your retirement mean that CIM3 will no longer be involved?     (1F30)

[7:14] Peter P. Yim: @Gary - I am just starting to plan that (and is just giving people ample notice)     (1F31)

... nothing is assumed yet, and it is not happening in, at least, another 6 (or 12) months     (1F32)

[7:14] Till Mossakowski: (imported content of) BioPortal at Ontohub:     (1F33)

[7:17] Peter P. Yim: Till: we have imported all the BioPortal ontologies onto Ontohub already; we can do     (1F35)

that for the SOCoP-OOR content as well     (1F36)

[7:18] Peter P. Yim: Till: we plan to run multiple instances of Ontohub ... look under the     (1F37)

[7:19] Till Mossakowski: Note that there are multiple repositories *within* one instance of Ontohub     (1F39)

[7:20] Till Mossakowski: Is the BioPortal API available also for the SOCoP instance?     (1F40)

[7:26] Till Mossakowski: The BioPortal API is available under     (1F41)

How do I translate this into socop.oor.net ?     (1F43)

[7:28] Peter P. Yim: [action] Ken: I'll get back to you, Till     (1F44)

[7:30] GaryBergCross: Till Would your propose running the SOCoP repository as a separate instance?     (1F45)

[7:30] Till Mossakowski: sorry, have to leave now     (1F46)

[7:31] Peter P. Yim: question for the SOCoP principals - are you in touch with the ESIP people?     (1F47)

[7:30] GaryBergCross: No I haven't been in touch with Peter Fox.     (1F48)

[7:32] Peter P. Yim: ESIP = Earth Science International Partners     (1F50)

[7:33] Peter P. Yim: ESIP-Portal = the Federation of Earth Science Information Partnerss ESIP-Portal.     (1F51)

ESIP-Portal is a customized version of the National Center for Biomedical Ontologys BioPortal     (1F52)

application, and is used for accessing and sharing Earth Science ontologies. This is run by     (1F53)

Foundation for Earth Science     (1F54)

[7:40] Peter P. Yim: [answering question from Nancy on "what is the focus and scope of Ontohob" ...     (1F56)

(Till lready left the meeting)] as far as I undestand, one main focus of Ontohub is to implement     (1F57)

OntoIOp (Ontology, Model and Specification Integration and Interoperability) - see:     (1F58)

[7:44] Peter P. Yim: [action] GaryBergCross to work with MikDean (offline) to get access to the     (1F60)

SOCoP-OOR admin interface     (1F61)

[7:45] Peter P. Yim: [action] Ken will work with Till to mirror the SOCoP-OOR content over to Ontohub     (1F62)

(Nancy: don't want to go public with this yet) and "Observations and Measurements (OM)" (Gary: not while     (1F64)

it still has parsing error)     (1F65)

[7:47] Ken Baclawski: [ follow-up on [7:14] GaryBergCross' comment on SimonCox's parsing error:     (1F66)

validator error messages regarding the version of "Observations and Measurements (OM)" on the     (1F67)

SOCoP-OOR now ] Detailed report     (1F68)

Use of non-absolute IRI     (1F69)

Use of non-absolute IRI     (1F72)

Use of non-absolute IRI     (1F75)

[7:47] Ken Baclawski: These are the errors reported by OWL Validator.     (1F78)

[7:56] Ken Baclawski: I checked IUGS CGI Lithology ontology with OWL Validator and it is valid, so it     (1F79)

should not have a problem at OntoHub.     (1F80)

[7:53] Peter P. Yim: still need to address the IPR issues, and gatekeeper to enforce the OOR-IPR Policy     (1F81)

[7:58] Peter P. Yim: as a reference COLORE is now using: http://code.google.com/p/colore/ - Code     (1F83)

license: Apache License 2.0 ; Content license: Creative Commons 3.0 BY-SA     (1F84)

[7:58] Peter P. Yim: Ontohub, I believe, is on AGPL (for code)     (1F85)

[7:59] Peter P. Yim: I am negotiating with both Michael Grüninger and Till Mossakowski about the     (1F86)

possibility of changing their licenses to align with the OOR-IPR Policy     (1F87)

[8:00] Peter P. Yim: BioPortal has changed (from a Mozilla License) to be a fully OOR-IPR Policy     (1F88)

compliant set of licenses     (1F89)

[8:04] Peter P. Yim: from the outset (2008 Ontology Summit), the OOR Initiative does support both "open"     (1F90)

and "non-open" content ... so, we *need to be clear*     (1F91)

[8:08] Mike Dean: OOR should be able to (optionally) accommodate ontologies with different IPR rights     (1F92)

within a single repository.     (1F93)

[8:07] GaryBergCross: Mike...Nancy... We will have to address some of these issues/lessons learned     (1F94)

about maintenance and porting in our NSF report.     (1F95)

[8:13] GaryBergCross: Mike, Nancy et al., do you think that NSF would have any issues with some of     (1F96)

the products of their supported work going overseas???     (1F97)

[8:08] Peter P. Yim: Aleksandra: we will have the option on Ontohub to support ontologies that can be     (1F98)

openly accessed, and ones with "limited access" ... that should be in place in a week or two ...     (1F99)

this is part of the preparation for the FOIS competition too     (1F100)

[8:11] GaryBergCross: @Aleksandra This model of different domains for ontologies sounds very useful     (1F101)

and would accommodate a place for our geospatial topics.     (1F102)

[8:13] GaryBergCross: One question if we port our ontologies there would be how to help develop,     (1F103)

manage and administer our part - or would OntoHub assume all of these duties....     (1F104)

[8:23] Peter P. Yim: something else to think about: implementing the next ncbo-vm release     (1F105)

(triple-store-based; probably in the next month or so) on the Amazon cloud ... we should see whether     (1F106)

we can round up the resources to do it     (1F107)

[8:26] GaryBergCross: Peter / Mike when do you think the SOCoP OOR would go away do to lack of funding?     (1F108)

[8:27] GaryBergCross: I won't have time till December to consider some new work..     (1F109)

[8:28] Peter P. Yim: @Gary - if SOCoP-OOR is going away, it is not for lack of funding     (1F110)

(it is "not funded" already!)     (1F111)

[8:28] Peter P. Yim: good meeting!     (1F112)

[8:29] Mike Dean: Thanks everyone!     (1F113)

[8:55] Aleksandra Sojic: [in response to Nancy's question on whether Ontohub will be available and     (1F114)

stable while the team is still developing that infrastructure] an important point regarding     (1F115)

stability of Ontohub. Since Ontohub is built on a git structure, it has separate branches for     (1F116)

development and staging. So, nothing is submitted to the staging (and master, i.e. visible website)     (1F117)

unless it is stable to be merged to it. In that way, while the development is taking place on     (1F118)

develop.ontohub.org, the UI on the main page is always stable.     (1F119)

[8:29] Peter P. Yim: [action] Peter will follow-up with Ken & Till ref. the focus of next Tuesday's     (1F120)

OOR-Hackathon (n.05 - Tue 2013.11.19)     (1F121)

[8:30] Peter P. Yim: -- session ended: 8:29am PST --     (1F122)

-- end in-session chat-transcript --     (1F123)

6. Action items:     (1F124)

  • [7:28] Ken will get back to Till about the access to the socop-oor API     (1F126)

(Nancy: don't want to go public with this yet) and "Observations and Measurements (OM)" (Gary: while it still has parsing error)     (1F128)

  • [8:29] Peter will follow-up with Ken & Till ref. the focus of next Tuesday's OOR-Hackathon (n.05 - Tue 2013.11.19)     (1F129)

7. Any Other Business:     (1F130)

8. Schedule Next Meeting & Adjourn:     (1F132)

notes taken by: Peter P. Yim / 2013.11.12-8:33am PST     (1F136)

All participants, please review and edit to enhance accuracy and granularity of the documented proceedings.     (1F137)


Resources     (1G)

  • the Joint IAOA-OOR-Ontolog "Ontologies and Standards" mini-series:     (1G18)


This page has been migrated from the OntologWiki - Click here for original page     (1G27)