NCBC Software/Tool/Algorithm Ontology Model, Yellow Pages and NIHForge

• Attendees: Michael Sherman (SimBios); Peter Highnam (NIH/NCRR); Bill Lorensen (NAMIC); Karen Skinner (NIH/NIDA); Henry Chueh (I2B2); Shawn Murphy (I2B2); Valentina Di Francesco (NIH/NIAID); Brian Athey (Michigan); David States (Michigan), Don Jenkins (NIH/NLM), Mark Musen (NCBO); Barry Smith (NCBO); Daniel Rubin (NCBO); Peter Good (NIH/NHGRI); Andrea Califano (MAGNet); Aristidis Floratos (C2B2); Dan Gallahan (NIH); Peter Lyster (NIH/NIGMS)'; Suzanna Lewis (MAGNet); John Haller (NIH/NIBIB); Ivo Dinov (CCB); Arthur Toga (CCB).

• Minutes and Action Items

• Over the past 2 months we've had a number of discussions regarding the development of NCBC (and beyond) Computational Software Tool Ontologies, Yellow-Pages and NIHForge environments.

• We are proposing to have a focused discussion over a Teleconference on Thu, 11/17/05, 11:00 AM - 12:00 Noon (Pacific Time). We've attempted to invite key personnel from all 7 NCBC's and NIH. Please distribute to and invite others from the NCBC community. Here are the logistics for the TCon:

• Please call in on 1-866-747-9489 passcode 4212569. Please be at a terminal and take your IE browser to http://nihbreeze.cit.nih.gov/r47348027/ sign into the guest field by typing your name and institution. Have another browser pointed to this WIKI page: http://www.loni.ucla.edu/twiki/bin/view/CCB/CCB_NCBC_11_17_05_TCon

• Attached are some drafts of documents that summarize some of our prior discussions. Also, we include here several pertinent online resources. It would be helpful if we all browse through these resources to get a feeling of the current state-of-the-art approaches for algorithm and tool ontologies and the complexity of the problem we're embarking on.
  • http://www.openmicroscopy.org/api/xml/OME/
  • http://www.dmoz.org/Science/Software/
  • http://www.gforge.org/
  • http://www.daml.org/ontologies/
  • http://www.daml.org/ontologies/67
  • http://www.cma.mgh.harvard.edu/iatr/
  • http://www.cma.mgh.harvard.edu/iatr/vocabulary.php
  • BIRNLex Ontology of Names

• Initial comments from Suzanna Lewis:
  • Where are editors? Visualization is passive, and too restrictive.
  • What differentiates Grid/Portals/WebServices?
  • Visualization (a top node) has 2 kinds of children. Those differentiated by class of data being viewed (e.g. sequence/clinical) and a type of display (graphs)
  • I would say there is a considerable amount of work still to be done just to get a top-level.

• Barry Smith, NCBO, had suggested:
  • Dividing things at high levels into processes, functions, tools and data.
  • Using singular nouns throughout the draft of the Tool Ontology Diagram (e.g., changing integration to integration tool).

• Please note that there is a regular SDIWG TCon on Fri 11/18/05 11:30 AM (Pacific), and some of our discussions on Thursday may be reiterated on Friday. Peter Lyster, SDIWG Chair, will send out a separate email with agenda for the Friday TCon.

• Additional Documents
  • NCBC_SWO_TopLevelDiagram.ppt: NCBC SWO Top-Level Diagram PPT
  • NCBC_ToolOntologyModel.doc: NCBC Tool Ontology Model Specification Document
  • NIH_YellowPagesModel.doc: NCBC Yellow-Page-to-Knowledge-Management Model
  • Picture1.emf: Draft of Top-Level Ontology
  • Lee_Bioinformatics_03.pdf: Kohane_Integration_Genetics_Tools

Attachment	Action	Size	Date	Who	Comment
NCBC_SWO_TopLevelDiagram.ppt	manage	196.0 K	20 Nov 2005 - 02:55	Main.ccb	NCBC SWO Top-Level Diagram PPT
NCBC_ToolOntologyModel.doc	manage	73.0 K	15 Nov 2005 - 01:22	Main.ccb	NCBC Tool Ontology Model Specification Document
NIH_YellowPagesModel.doc	manage	27.0 K	15 Nov 2005 - 01:23	Main.ccb	NCBC Yellow-Page-to-Knowledge-Management Model
Picture1.emf	manage	268.9 K	15 Nov 2005 - 01:26	Main.ccb	Draft of Top-Level Ontology
Lee_Bioinformatics_03.pdf	manage	34.2 K	18 Nov 2005 - 05:46	Main.ccb	Kohane_Integration_Genetics_Tools