2013-07-17 VIVO Ontology Call

Updates

• Brown (Steve) – no recent changes to the ontology except adding some document classes that individual faculty members wanted to see – e.g., Engineering faculty wanted to see workshop papers to be a sibling of conference paper.
  
  • Looking ahead to the presentation at the Conference and ongoing humanities work is trying to distill main points:
    
    • the notion of a new class for some kind of canonical work that is distinct from a standard document (drawing on the idea of a canonical course as it relates to individual semester courses as events)
      
      • for example, to handle works that have gone through multiple editions or been updated over time
      • should the most recent edition be the reference point for the canonical work
      • a central concern, and more immediate because some faculty members asked a very good question about presentations that get given repeatedly over time, and where a common link is desired as a way to tie all those presentations together
    • can we take advantage of the provenance ontology (Prov-o by the W3C)? Steve has been looking at that and is interested in it for other
      
      • what about physical works? are they still information resources?
      • entities and artifacts created by agents, with predecessor-successor
      • both the VIVO and the prov-o ontology skirt the issue of
        
        • as long as a resource has some sort of representation
        • but how do we represent the abstract concept – implicitly through the stand-in as a web page is the stand-in for the person
        • the canonical course is the only place where we've addressed the concept of a canonical thing
        • would be on firmer ground if we come up with something that makes sense with the Basic Formal Ontology
• Florida
• Johns Hopkins (Jing) – not many changes in ontology either; looking at other sources, and suddenly quite a few ontologies floating around
  
  • W3C organization ontology is in a candidate recommendation now
  • also the Semantic Web Conference Ontology – conferences and presentations, but dates back to 2009
  • has been looking at Web Protege site – a sandbox set up by Stanford that can sign up for an upload to
  • with respect to the Prov-o ontology – has some notion of abstract concepts, and usage as well as derivative works
    
    • has a question about processes 
• Scripps
• Virginia Tech (Gail) – first meeting of the VIVO pilot team yesterday – 7 people from systems, data management, and data informatics
  • will be piloting with people from the Institute for Creativity, Arts, and Technology and the Virginia Bioinformatics Institute, plus some other possible additional faculty
  • about 125 faculty
  • 1.5 year time frame leading to a report
  • about to hire to hire a systems analyst/programmer for the VIVO project
  • Julie Speer and Tyler Walters will be at the Conference
• Weill Cornell
• others

Formalizing an ISF/VIVO Ontology Working Group

Representatives of each of the organizations sponsoring VIVO (see http://vivoweb.org/sponsorship) will be meeting on Wednesday afternoon, August 14, at the VIVO Conference for the first official VIVO Sponsors Meeting. One item on the agenda is to formalize a set of working groups, with the current and potential activities of this group and listserv providing one example.

Working groups will continue to be open to all and to encourage participation by individuals and organizations regardless of their sponsorship status.

With release 1.6, VIVO will be adopting a larger ontology derived from the VIVO and eagle-i ontologies and addressing broader needs in research representation including research resources and clinical expertise. The ontology will be promoted going forward as the Integrated Semantic Framework or ISF, but will continue to be managed by members of the VIVO community together with participants in the CTSAconnect project representing eagle-i and the biomedical research community more generally.

It will be helpful to have a conversation on this call and the next call (July 31) about how people would like to conduct this group in the future and what its goals could and should be for the remainder of the VIVO Project incubation period, through the end of calendar 2014.  Ideas might include:

• more explicitly developing and prioritizing issues for upcoming releases
• establishing sub-groups to work on specific areas of interest such as provenance
• working with members of the development team to design and test improvements to the VIVO ontology editor and/or features of VIVO to better manage and reflect ontology-related requirements, including VIVO's additional operational ontologies including the application configuration ontology, display model ontology, authentication and authorization ontology
• working with the Vitro code base as an ontology-driven application platform for projects unrelated to VIVO including Semantic Web education and training
• adapting and extending the VIVO/Integrated Semantic Framework (ISF) ontology for new domains, preferably by evaluating and adopting existing ontology efforts by other parties but also by targeted new ontology work
• working with members of other VIVO Working Groups to improve the ontology to support multi-site search, including issues such as sameAs assertions, shared instance data, and linkages to externally-managed terminologies and authoritative name services for people, organizations, geographic locations, events, or projects
• working with representatives of non-academic organizations to better understand the needs of labs, government or non-profit organizations, or consortia adopting VIVO
• evaluating existing and new tools to support ontology creation, editing, change management, release, and evaluation, ideally in a networked rather than single-user environment
• participating as representatives for VIVO in ontology projects with the W3C or other groups
• establishing a more formal process for moving the Integrated Semantic Framework forward through public releases, in coordination with the eagle-i community and other interested parties and not necessarily strictly tied to VIVO software releases

Your thoughts are very much appreciated, and feel free to add comments on a wiki discussion page for the VIVO-ISF Ontology Working Group even if you can't attend these two meetings.

Feedback from today's meeting:

• (Jing) – a need for more training on the ontology, and for a common working space
• (Steve) – identifying needs but also helping people out
  
  • learning about ontologies
  • sees the priorities as the first two bullets above, with then outreach into new domains
  • sees cross-pollination across groups and various VIVO implementers as very important
• (Gail) – training is also important
  
  • also relates to the 3rd bullet from the bottom (evaluating existing and new tools to support ontology creation, editing, change management, release, and evaluation, ideally in a networked rather than single-user environment)
• (Steve) – learning more about the ISF and BFO to see where the VIVO project is going and being able to help incorporate new domains into VIVO as well as learn more about how to create an ontology that is consistent with an upper level ontology
• (Jon) – we could have more focused calls, such as the first week of the month for training, the second for prioritizing changes for the next release, 3rd for topical discussions or invited speakers, etc.
  • Gail – endorses that idea