View source for SDIWG: NCBC Resource Yellow Pages and Software Ontologies

This is the main page for the NIH Roadmap National Centers for Biomedical Computing (NCBC) Working Group titled: '''Biositemaps, Resource Yellow Pages and Biomedical Software Classification'''

[http://www.ncbcs.org/ Top page of ncbcs.org web site which is maintained by the NCBCs themselves]

[[SDIWG:Software_and_Data_Integration_Working_Group|Top page of SDIWG web site]]

[http://www.na-mic.org/Wiki/index.php/SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers NCBC Working Group Discussion threads, tcons, Breeze/Access minutes]

=== The leads for this Working Group are [http://www.loni.ucla.edu/~dinov/ Ivo Dinov] ([http://www.loni.ucla.edu/CCB CCB]) and [http://smi-web.stanford.edu/people/rubin/ Daniel Rubin] ([http://bioontology.org NCBO]) ===

=== Mission Statement=== 
'''Biositemaps''': The goals of this working group (lead by the [[Tiger_team_biositemaps|Tiger Team]]) are: (1) Develop a Visualization interface (iTools) to enable query and browsing of the NCBC tools, and potentially access to a broad range of biomedical software tools; (2) Develop a software classification scheme that can be used broadly to enable query tools (such as iTools) and tagging of biomedical software tools; (3) Develop technologies that will enable convenient and rapid application development and pipelines across diverse heterogeneous hardware and software environments.

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<b>Latest works is focusing on the Biositemaps effort.</b> You can go to [http://www.Biositemaps.org www.Biositemaps.org] for further information.

<b>[http://www.loni.ucla.edu/iToolssvc/ncbc_iTools.html Click here to use PROTOTYPE iTools:]</b>  This will allow you to visually browse tools according to their classifications, or to search keywords and other descriptors.  Note there there are two kinds of views: (1) the visual Hyperbolic viewer, and (2) the more traditional hierarchical interface.

<b>[http://iTools.loni.ucla.edu/ NCBC iTools Development Page:]</b>  This is the main developers page for the iTools project, which is a visualization interface to enable query and browsing of the NCBC tools, and potentially access to a broad range of biomedical software tools.

<b>[http://bioontology.org/projects/ontologies/SoftwareOntology/ Software Classification Development Page:]</b>  This is the main developers page for the project to develop a common Software Tools Ontology that can be used to improve query and browsing in the iTools project and for more general efforts at classifying biomedical software tools.

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=== Archive Activies ===

* [[SDIWG:NCBC_Software_Classification|NCBC DRAFT Software Classification and Ontologies Page]]
* [http://www.loni.ucla.edu/twiki/bin/view/CCB/NCBC_ToolIntegration_XMLtology_Meeting_071806_RequiredFields Required/Minimal] & [http://www.loni.ucla.edu/twiki/bin/view/CCB/NCBC_ToolIntegration_XMLtology_Meeting_071806_ToolSpecificFields Optional and Resource-specific] Resource Description Fields
* [http://www.loni.ucla.edu/twiki/bin/view/CCB/NCBC_ToolIntegration_XMLtology_2006_OtherArchives Other Efforts to develop archives of resources]

=== Update on Biomedical Resource Ontology (BRO) ===
The ontology of software tools and resources ("Biomedical Resource Ontology (BRO)") has been attracting interest not only amongst NCBCs, but from other NIH programs and related external projects (such as BIRN, ICBP, and IATR). The current ontology is available in read-only format (http://bioontology.org/projects/ontologies/SoftwareOntology/).
A core group of individuals interested in developing the ontology into a more robust resource recently came together to begin developing the Software Ontology collaboratively: Daniel Rubin, Ivo Dinov, William Bug, Mayrann Martone, and David Kennedy.  They are editing the ontology using Protege in collaborative mode, enabling multiple people to edit the ontology.
If other people in the community are interested in participating in developing the Software Ontology and gaining edit access, please contact Daniel Rubin.  The meeting minutes (below) has the latest news on this thread...

=== Biositemaps Archive Meeting Minutes ===
Top level sites

[[SDIWG:Software_and_Data_Integration_Working_Group|Top page of SDIWG web site]]

[http://www.na-mic.org/Wiki/index.php/SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers NCBC Working Group Discussion threads, tcons, Breeze/Access minutes]

Specific Minutes relating to Biositemaps Development

* [[SDIWG:Action_Items_20090529 | Status and Action Items (05-29-2009)]]
* [[SDIWG:Action_Items_20090318 | Status and Action Items (03-18-2009)]]
* [[SDIWG:Action_Items_20090212 | Status and Action Items (02-12-2009)]]
* [[SDIWG:Action_Items_20090116 | Status and Action Items (01-16-2009)]]
* [[SDIWG:Action_Items_20081219 | Status and Action Items (12-19-2008)]]
* [[SDIWG:Action_Items_20081203 | Status and Action Items (12-3-2008)]]
* [[SDIWG:Action_Items_20081121 | Status and Action Items (11-21-2008)]]
* [[SDIWG:Meeting_Minutes_20081001|Biomedical Resource Ontology and Biositemaps: Tiger Team Subprojects and Biositemaps Shakeout (10/1/08)]]
* [[SDIWG:Meeting_Minutes_20080919|Biomedical Resource Ontology and Biositemaps: NCBC working group minutes (9/19/08)]]
* [[SDIWG:Meeting_Minutes_20080716|Biomedical Resource Ontology and Biositemaps: Four Activities Description (7/16/08)]]
* [[SDIWG:Meeting_Minutes_20080530|Biomedical Resource Ontology and Biositemaps Development Path Tcon (5/30/08)]]
* [[SDIWG:Meeting_Minutes_20080416|Biomedical Resource Ontology (BRO) Tcon (4/16/08)]]
* [[SDIWG:Meeting_Minutes_20061117|Joint NCBC Working Group TCon (11/17/06)]]
* [http://www.loni.ucla.edu/twiki/bin/view/CCB/NCBC_ToolIntegration_XMLtology_Meeting_103106 TCon 10/31/06]
* [[SDIWG:Meeting_Minutes_20060818|NCBC SDIWG/Working-Group TCon (Fri., 08/18/06)]]
* [http://www.loni.ucla.edu/twiki/bin/view/CCB/NCBC_ToolIntegration_XMLtology_Meeting_071806PM Tue 07/18/06, PM] - [http://www.bisti.nih.gov/ahm2006/agenda.htm NCBC Workgroup Reports (20 minutes per group), 1-2 PM]
* [http://www.loni.ucla.edu/twiki/bin/view/CCB/NCBC_ToolIntegration_XMLtology_Meeting_071806AM Tue 07/18/06, AM] - [http://www.bisti.nih.gov/ahm2006/agenda.htm Concurrent NCBC Workgroup Meetings, 10AM - 12PM]
* [[SDIWG:Meeting_Minutes_20060616|Fri 06/16/06]] -- Includes examples of Meta-data and XMLTology descriptions of 1-5 SW Tools from all 7 NCBCs
* [http://www.loni.ucla.edu/twiki/bin/view/CCB/NCBC_ToolIntegration_XMLtology_Meeting_061506 Fri 06/15/06]
* [http://www.loni.ucla.edu/twiki/bin/view/CCB/NCBC_ToolIntegration_XMLtology_Meeting_042806 Fri 04/28/06]