SDIWG:Meeting Minutes 20060120

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Agenda: Software and Data Integration Working Group (SDIWG)

Top page of SDIWG web site

Friday January 20, 2006: 2:30 -- 3:30 PM Eastern Time

Next SDIWG Friday February 17, 2:30 PM –- 3:30 PM ET: Pls contact Peter Lyster for information

Preliminary Agenda

  • Discuss ongoing progress of SDIWG, membership, agenda-setting, output of December 16 SDIWG discussion: Agenda, Minutes.
  • Add additional agenda items here...
  • Discussion of Software Classification and Ontologies. The source documents are:
  1. Minutes from the NCBC SW Tool Ontology TCon on 11/17/05, from the discussion led by Ivo Dinov CCB
  2. The draft software ontologies-classification can be found at
  3. Daniel Rubin draft protege document (based on the CCB classification) at
  • As an FYI here are slides on our efforts across 7 Centers that were prepared by Zohara Cohen and Peter Lyster and presented at the NA-MIC AHM on Jan 10 slides


Attendees: Brian Athey, Bill Lorensen, Don Jenkins, Michael Ackerman, Daniel Rubin, Peter Good, Jennifer Couch, Ivo Dinov, Steve Pieper, Suzanne Churchill, Mike Sherman, Karen Skinner, Cristina Thalhammer-Reyero. Note taker: Peter Lyster


Agenda: Each month Peter Lyster circulates a wiki link for the purpose of generating draft minutes--please check this out and bring up agenda items to help the SDIWG as a community effort.

Membership discussion: There is a suggestion to include contributors from outside the NCBCs. E.g., David Kennedy (creator and curator of Internet Analysis Tools Registry IATR, and Dan Gardner (PI on NIH Blueprint Neuroscience Information Framework contract). People are happy to include contributions from outside the NCBCs.

Today’s agenda: Yellow Pages-Software Ontology. This stems from the monthly SDIWG tcons last year and from the discussion at the New Hands meeting on Dec 16 The Yellow Pages was discussed as a mechanism for making the tools known and available to the respective user and developer communities, and could be usefully hosted on each NCBCs site. The Software Ontology effort is an enabling technology that can be used in a number of ways, e.g., enable the Yellow Pages to support query (computer-computer, human-computer)—it can also help organize the software.

From the Dec 16 meeting: The SDIWG considered its role in software development, and the effort may be compartmentalized (in order of increasing difficulty and sophistication) as (i) yellow pages, (ii) knowledge environment, and (iii) collaborative software development environment. All three should contribute to an environment that is useful to both developers and users. The SDIWG proposed to develop an ontology that may be used to categorize software. This could be used, say, as a basis of concept-based query of our tools and thus enable better access for outside users. It could also be useful for developers. In the best-case scenario, the NCBCs may generate critical mass (‘tipping point’) and galvanize the biomedical computing community. The ongoing activity can be viewed at the software classification-ontology page on this wiki (

One suggestion from Daniel Rubin for how to proceed is:

1) Identify one person at each NCBC who is interested in the issue of categorizing their software and who is willing to work with us in incorporating their taxonomy into Ivo Dinov's "top level" ontology (this is the one that has been incorporated in protege ( Each such person will look at this ontology and either (1) suggest changes needed in order to incorporate their ontology under it, or (2) incorporate it directly.

2) After everyone's software has been incorporated into one ontology, then we can look at developing a set of attributes to describe all software programs.

3) Finally, each NCBC creates an instance in the ontology to describe each of their software programs. These descriptions can be stored in OWL and hosted at the various NCBCs and updated as needed. They will also form the basis for a consistent description of all software in the NCBCs, and will facilitate search by users seeking to find software according to their needs

Bill Lorensen: NA-MIC has 600-700 classes in object oriented hierarchy. What is now on the wiki ( is a dump of the NA-MIC hierarchy. There is not much commonality with other hierarchies.

Daniel Rubin: propose that people may be willing to work to shape an upper level description of tools.

Bill: is top level intended for end user, customer, …?

Daniel: Audience is important. NCBC is producing tools. Want community to be aware. Needs to be better than Google. Use cases are good.

David States: need to anticipate many classes of user.

Ivo Dinov: Came about from Brain graph project. Want to find a way to connect various brain nomenclatures (anatomy, cytochemistry, …), i.e., same object viewed in different ways. Not just hierarchy but graph. Computational biology user is interested in finding tools and finding tools that are linked.

Bill: the term is ‘view’ or ‘perspective’.

Daniel: reference ontology is like Foundational Model of Anatomy (FMA) which is application neutral. A different perspective is use case. If we try to go for generalizability then will be difficult to converge.

Ivo: Agrees there will be trade off between generalizability and extensibility.

Daniel: create a top level that can encompass tools

Ivo: does there have to be a top level? Can every Center develop their own view?

Mike Sherman (Sherm): Altman group is just started working on Simbios yellow pages.

Brian Athey: Lead architect to participate in working group. Even if we don’t have it figured out. Endorses the idea of working group.

Daniel: Siemans has a related initiative.

Bill: From an Object Oriented perspective—not sure how to roll up what he is doing in overarching ontology. Is there is a workable high level to the putative overarching ontology?

Daniel: can do top down or bottom up.

Cristina: Develop relations you want to map.

Isaac Kohane (Zac): minimal set of high-level domain names in hierarchy that we can all agree on.

Bill: even ‘image’ has different meaning to different (overloaded concepts): Dan says that is a good thing.

Bill: Perhaps one of the uses of Ontologies/OWL/semantic web in this context is a way to ‘reason’ about our systems.

Daniel: it is useful and justified when it becomes a ‘batch’able.

Bill: If someone is looking for CT data then how will they enter?

Sherm: how would a user know to come to NA-MIC rather than CCB?

Daniel: it is bigger than our seven Centers. It is how to develop an infrastructure that will be generalizable.

Brian: maybe some of us can work with the NIF (Dan Gardner) … want to be interoperable with neuroscience Blueprint initiative.

Zac: is there forward motion on Yellow pages? Simbios is developing yellow pages.

Peter: The software ontology is an enabling technology for yellow pages (ok: I didn’t actually say that, but that is what I meant to say).

Zac: Fair enough, but will take time.

Daniel: how is the current Wiki different from ‘yellow pages’? Is this iteration completed. People can use it. Bill: the structures are very different for each Center—is there a level we can agree on the organization of it?

Zac: two ways: Google way, Yahoo way. We are proposing Yahoo way. Why not do Google way (no one disagrees)? Everyone takes hierarchy and links terms to actual objects. With tags. So search engine can find them. Can have each site maintain its own hierarchy?

Bill: They have Google search on NA-MIC wiki.

Zac: they can do combination. How to build Google search beyond NCBCs?

Bill: gut feeling it is useful. Good to do what Zac says.

Zac: encourages two efforts (1) low hanging fruit, everyone does their own vocabulary/content and develop their own yellow pages; (2) longer term (labor intensive) ontology-based effort.

Action Items

  • Reporting back on each Centers' Yellow Pages development progress
  • Joint working group to investigate/codify Software Ontology as enabling technology for extended Yellow Pages development (Ivo and Daniel)