OpenOntologyRepository: Architecture & API Workshop-X - Tue 2012_01_31    (33TG)

Topic: "OOR Architecture & API Specification Development Workshop-X"    (33OD)

Session Co-chairs: Dr. ToddSchneider & Professor KenBaclawski    (33TH)

Conference Call Details:    (33TI)

Attendees    (33U9)

Session Abstract & Resources:    (33UK)

With this workshop we'll start reviewing the BioPortal build 3253 source code (from November 2011) to see how it fits into the current OOR (draft) architecture and identify changes or additions that need to made to the source code or the architecture.    (33UL)

The review will be based on an HTML report from the Enterprise Architect (EA) UML model of the (reverse engineered) BioPortal source code build 3253 (circa November 2011).    (33UM)

The EA HTML report can be found at    (33UN)

See also: OpenOntologyRepository_Architecture & OpenOntologyRepository_Architecture/Candidate03    (33UT)

In addition, there is an API of the core services that was obtained from anearlier implementation BioPortal, which is not entirely compatible with the straw man architecture, but furnishes a starting point. This API will also be discussed and modified as needed.    (33OE)

Finally, we need to agree on a plan for completing the development of the specification.    (33OH)

Here is the proposed organizing plan: OpenOntologyRepository_Architecture/GettingOrganized    (33OI)

We encourage all participants to update your candidate contributions to ensure your ideas are known and understood.    (33OJ)

The following are relevant prior meetings:    (33OK)

Agenda Ideas:    (33UO)

Agenda & Proceedings:    (33UR)

Archives:    (33US)

1. Meeting called to order:    (33P5)

2. Roll Call & Adoption of last meeting's minutes:    (33P9)

3. Key items for review and discussion today:    (33PC)

... items below are mostly from the previous workshop, and will be updated as this session progresses.    (33PE)

 --- Chat transcript begin: ---    (33QO)
	PeterYim: Welcome to the    (33V5)
	 = OpenOntologyRepository: Architecture & API Workshop-X - Tue 2012_01_31 =    (33V6)
	Topic: "OOR Architecture & API Specification Development Workshop-X"    (33V7)
	Session Co-chairs: Dr. ToddSchneider & Professor KenBaclawski    (33V8)
	Conference Call Details:    (33V9)
	* Date: Tuesday, 31-Jan-2012 
	* Start Time: 8:30am PST / 11:30am EST / 5:30pm CET / 16:30 UTC 
	* Expected Call Duration: ~1.5 hours    (33VA)
	Session page:    (33VB)
	Can't find Skype Dial pad? ... it's under the "Call" dropdown menu as "Show Dial pad"    (33VC)
	 == Proceedings: == 
         .    (33VD)
	PeterYim: The EA HTML report Todd has just produced can be found at    (33VF)
	Todd: ref.    (33VG)
	ToddSchneider:    (33VH)
	Todd: the xml file is at:    (33VI)
	Todd / Ken: ref. MikeDean's question: "are javadoc's available?" ... answer: seemingly "no!"    (33VJ)
	PeterYim: [consensus] our approach toward code contribution (/extension from the BioPortal codebase): 
                   (a) KenBaclawski-ToddSchneider to focus on "gatekeeping"; 
                   (b) MikeDean on "federation", and 
                   (c) MichaelGruninger on "metadata" then "mapping"    (33VK)
	ToddSchneider: Action Plan: Michael and his team will focus on metadata (and then mapping); Mike Dean will focus on federation capabilities; Ken and Todd will focus on workflow    (33VL)
	MikeDean: like idea of an OOR service layer that includes OOR-specific services (e.g.  Find) and 
                  can be easily adapted to new BioPortal releases    (33VM)
	PeterYim: as far as ncbo-RayFergerson is concerned, he'd appreciate all code extensions to be implemented on "tabs"    (33VN)
	MikeDean: it's easy to add new tabs to the UI    (33VO)
	MikeDean:    (33VP)
	ToddSchneider: The three 'action items' will have there own tabs: adjuncts to the current BioPortal UI    (33VQ)
	ToddSchneider: Need to find out if BioPortal data model supports 'location' (i.e., repository location/id) information    (33VR)
	ToddSchneider: How will access control across federates be handled?    (33VS)
	ToddSchneider: There may be additional fields from OMV that OOR will need.    (33VT)
	ToddSchneider: Can the OMV interface be generated dynamically from the OMV ontology? This may break some existing BioPortal code.    (33VU)
	ToddSchneider: Each of items of the 'action plan' will be added as a new tab (on the current UI).    (33VV)
	ToddSchneider: The federation tab will be labeled 'Federation' (this may only be visible to administrators); 
                       The workflow tab will initially expose the uploading capability of the gatekeeper functionality. 
                       Other gatekeeper capabilities/functionalities will be exposed on other tabs.    (33VW)
	ToddSchneider: Another action item is to agree on tab labels for the 'upload' and 'metadata' tabs.    (33VX)
	PeterYim: [action] targeting this - Mike, Ken & Michael will all try to have a prototype tab 
                  (even just a "hello world" tab) done by our next workshop    (33VY)
	KenBaclawski: Subject: [oor-dev] Problem with extending the UI 
	  I am trying to extend the BioPortal Rails UI on oor-03 using
	  It seems one must use
	  cd /srv/ncbo/rails/BioPortal/current
	  rather than
	  cd /var/rails/BioPortal/current
	  There is a script/generate, but when I try running it, I get
	  /usr/bin/env: ruby: No such file or directory
	  Does anyone have some idea of how this can be fixed?
	  -- Ken    (33VZ)
	PeterYim: Ken has fired the above question to Paul Alexander -    (33W0)
	PeterYim: MikeDean gave a brief report on the SOCoP-OOR at the INTEROP NSF PI meeting    (33W1)
	ToddSchneider: Can we pose a question to BioPortal to see if they would be open to moving 
                       the 'Submit New Ontology' functionality to a new tab, called 'Submit'?    (33W2)
	ToddSchneider: Have to go.    (33W3)
	KenBaclawski: I will continue to find out how to fix the captcha feature. Until it is fixed, captcha is off.    (33W4)
	PeterYim: who is anonymous?    (33W5)
	PeterYim: let's talk about the next workshops at next Tuesday's regular OOR team meeting    (33W6)
	PeterYim: MikeDean: I'll probably be missing next week's meeting, because i'll be traveling    (33W7)
	PeterYim: good meeting ... got a lot done ... bye!    (33W8)
	PeterYim: -- session ended: 10:14am PST --    (33W9)
 --- Chat transcript end: ---    (33QP)

Consensus, Conclusions & Follow-up Actions:    (33QQ)

4. Any Other Business:    (33QR)

5. Action items:    (33QS)

6. Schedule Next Meeting & Adjourn:    (33QT)

 notes taken by: PeterYim / 2012.01.31-11:01am PST
 All participants, please review and edit to enhance accuracy and granularity of the documented proceedings.    (33QY)

Resources    (33QZ)