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NCBC XMLtology for Tool Integration
Overarching Goals
The goals of this initiative is to generate an integrated pipeline of tools from all seven NCBCs.Preliminaries
- iTools
- http://na-mic.org/Wiki/index.php/SDIWG:_NCBC_Resource_Yellow_Pages_and_Software_Ontologies
- Where we started (Nov. 17, 2005) & The NCBC SDIWG Meetings Page
- NCBC XMLtology Charter Statement
- Ivo Dinov's PPT slides & First draft of SW Ontology Hierarchy
- Other Attempts at SW Tool Archives
- Completeness and consistency of Ontological Systems
Specifications
- Biomedical Resourceome Ontology (BRO) (Aug 01, 2008)
- Definition of Biomedical Resources
- Required Resource Description Fields
- Optional Resource Description Fields
- Current Ontological Description of the NCBC Resources
- NCBC Center's 3-6 Resource descriptions
Meetings (General NCBC SDIWG Meetings)
- Nov 16, 2007
- Joint NCBC Working Group TCon (09/21/07)
- Joint NCBC Working Group TCon (05/18/07)
- Joint NCBC Working Group TCon (02/16/07)
- Joint NCBC Working Group TCon (11/17/06)
- Tue 10/31/06 NCBC YPR WG TCon
- NCBC SDIWG + WorkingGroup TCon (Fri., Aug. 18, 2006)
- Tue 07/18/06, PM - NCBC Workgroup Reports (20 minutes per group), 1-2 PM
- Tue 07/18/06, AM - Concurrent NCBC Workgroup Meetings, 10AM - 12PM
- Fri 06/16/06 -- Includes examples of Meta-data and XMLTology descriptions of 1-5 SW Tools from all 7 NCBCs
- Fri 06/15/06
- Fri 04/28/06
- Ontologies of Images (Stanford Workshop, March 24-25, 2006)
- NCBC Ontology of Resources
| Centers, contacts and available tools | NCBC Geo-Map  | NCBC Pipeline  | NCBC Common DBP-related Research  |
| NCBC Center | SW Tools Page | Contact Person | Tool Description | Status |
|---|---|---|---|---|
| CCB | SW Tools | IvoDinov | IDA + Shape Modeling, Analysis and Viz tools | Available |
| I2B2 | SW Tools | Henry Chueh (hcchueh@partners.org) & Shawn Murphy (snmurphy@partners.org), 617-726-3909 | Genotype Analysis and DB | TBD |
| SimBios | SimBiome & SimTK | JoyKu@stanford.edu, Jon Dugan dugan@biocontact.org | LAPACK linear algebra library. Finite element method for nonlinear solid mechanics with discontinuous Galerkin (viscous warping) | TBD |
| NA-MIC | SW Tools | Will Schroeder | Image Seg/Reg tools | Available |
| NCBO | SW Tools | Daniel Rubin (650) 725-5693 rubin@smi.stanford.edu | ontology editing and annotation tools | TBD |
| NCIBI | SW Tools | Terry E. Weymouth weymouth@umich.edu 734 355-6802 & H.V. Jagadish | Timber/MiMI XML databases. Oncomine analysis of tumor gene expression maps | TBD |
| MAGNet (C2B2) | SW Tools | [[][Aris Floratos]] (212) 851-5139 af2202@columbia.edu | geWorkbench tools (e.g., molecular classification of brain tumors) | TBD |