NAMIC Wiki - User contributions [en]

SDIWG: NCBC Resource Yellow Pages and Software Ontologies

2007-07-03T20:29:02Z

Dlrubin: /* Update on Software Ontology */

This is the main page for the NIH Roadmap National Centers for Biomedical Computing (NCBC) Working Group titled: 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]]

=== 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===
The goals of this working group 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.

----

[http://netulla.loni.ucla.edu:8080/itools/ncbc_iTools.html Click here to use PROTOTYPE iTools:] 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.

[http://www.loni.ucla.edu/twiki/bin/view/CCB/iTools NCBC iTools Development Page:] 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.

[http://bioontology.org/projects/ontologies/SoftwareOntology/ Software Classification Development Page:] 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.

----

=== 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 Software Ontology ===
The ontology of software tools and resources ("Software Ontology") 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.

=== Archive Meeting Minutes ===

* [[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]

SDIWG: NCBC Resource Yellow Pages and Software Ontologies

2007-07-03T20:05:28Z

Dlrubin:

This is the main page for the NIH Roadmap National Centers for Biomedical Computing (NCBC) Working Group titled: 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]]

=== 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===
The goals of this working group 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.

----

[http://netulla.loni.ucla.edu:8080/itools/ncbc_iTools.html Click here to use PROTOTYPE iTools:] 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.

[http://www.loni.ucla.edu/twiki/bin/view/CCB/iTools NCBC iTools Development Page:] 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.

[http://bioontology.org/projects/ontologies/SoftwareOntology/ Software Classification Development Page:] 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.

----

=== 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 Software Ontology ===
The ontology of software tools and resources ("Software Ontology") 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
* Mayrann Martone
* David Kennedy

=== Archive Meeting Minutes ===

* [[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]

SDIWG:Meeting Minutes 20070518

2007-05-19T04:10:16Z

Dlrubin: /* Minutes */

'''Agenda: NCBC Joint Working Group Meeting'''

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

===Notes===
''Friday, May 18, 2007: 2:30 -- 3:30 PM EST'' 
''Please contact Peter Lyster for information [mailto:lysterp@mail.nih.gov Peter Lyster]'' 
''[http://na-mic.org/Wiki/index.php/SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers SDIWG Meetings Page]'' 

=== TCon Agenda ===

* Roll Call/Note-taker (Rubin) (5 min)

* Minutes from most recent SDIWG tcon [[SDIWG:Meeting_Minutes_20070216|February 16, 2007]] (5 min)

* Progress in three working groups
** '''[[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]]''' (Zak Kohane, Mark Musen, and Suzi Lewis, 15 min)
*** enter draft agenda items here
** '''[[SDIWG:_NCBC_Resource_Yellow_Pages_and_Software_Ontologies|Yellow Pages and Resourceome]]''' (Ivo Dinov, Daniel Rubin, Will Schroeder, Jonathan Dugan, 15 min)
*** Status of [http://www.loni.ucla.edu/twiki/bin/view/CCB/iTools iTools]
*** [http://www.loni.ucla.edu/twiki/bin/view/CCB/NCBC_ToolIntegration_iTools_Usage iTools Usage]
*** [http://netulla.loni.ucla.edu:8080/itools/ncbc_iTools.html Use iTools Now]
** '''[[SDIWG:_NCBC_DBP_Interactions_and_Impact|NCBC Driving Biological Projects Interactions and Impact]]''' (Aris Floratos, Brian Athey, Russ Altman, 15 min)
*** enter draft agenda items here

=== Minutes ===

Note taker: (Daniel Rubin)

* Review of [[SDIWG:Meeting_Minutes_20070216|February 16, 2007 Minutes]]
*
#Attending: Peter Lyster, Ivo Dinov, Aris Floratos, Arthus Castle, Zohara Cohen, Daniel Rubin, David States, Jeanette Schmidt, Karen Skinner, Mark Musen, Michael Montegut, Shawn Murphy, Terry Weymouth, Brian Athey, Will Schroeder, David Kennedy, Zak Kohane
#iTools and Ontology of Software Tools (Ivo Dinov)
#*We have populated iTools with the metadata for each of the NCBC tools. Right now, this presents a center-specific view of tools. This will be changed to display according to the software tools ontology.
#*At this point, each NCBC should review the software tool ontology to make sure they are happy with it.
#*Tools will appear in multiple places in the taxonomy
#*The current content of iTools has not yet been vetted. The content should be labeled "prototype" and representatives at each NCBC should review the current content.
#*Users can update the software tools metadata directly in iTools or send requests to Ivo
#*The iTools site has documentation and screen shots
#Scientific Ontologies (Zak Kohane)
#*The effort was inteneded to be pragmatic. Results of initial work is a spreadsheet that lists curated ontologies that are endorsed, used and critiqued, and those not quite ready for prime time.
#*Zak is writing a paper on this. People can contribute use cases.
#*Action items for everyone: review the spreadsheet and make sure you agree. Contribute use cases to Zak for the manuscript.
#*This effort isn't an "endorsement" activity. This is more akin to a "Consumer Reports" in which each ontology is described according to various criteria.
#DBP Interactions (Brian Athey)
#*Had recent meeting on March 16. Discussion was about how via a new web site and future meetings, we coud form parternships related to NCBCs.
#*We should set up a web site where people could find out which meetings people will be attending. We should be connecting at these meetings to work together.
#*Created a draft taxonomy of the DBPs. It's important to put a broad map of DBPs across all the NCBCs that would be available to reviewers. Will be posting an updated taxonomy of DBPs and invite all NCBCs to review this.
#*It would help researchers looking for collaborations if all DBPs could be found in a central place.
#Other issues
#*Upcoming review: The NCBCs will be reviewed in a whole in the upcoming review. We could use ncbcs.org to post material at a high level shows the work NCBCs are doing--Highlights, bullets, powerpoints to show off the best of the NCBCs and of the whole program.
#*Suggestion was made to update the web site with this additional information. Emails to update the site should be Jim Cavicoli. Reps from each center should send any updated paragraph description of their center: Ivo for CCB, Daniel for NCBO, Jeanette for SIMBIOS, Brian and Will for NA-MIC, and Aris for MAGNET, and Zak for I2B2.

=== Attendees ===

*
* Note-taker: [Suggested order of note takers for future meetings: Rubin (this one); Jags; Dinov; Chueh; Sherman; Schroeder; Floratos]

=== Action Items ===
*
*

SDIWG:Software Engineering At NCBO

2007-05-09T18:14:45Z

Dlrubin:

== [[SDIWG:NCBC_Software_Classification#NCBO|Summary of the NCBO Software Tools]] ==

Additional information about the [http://bioontology.org/ National Center for Biomedical Ontology] web pages that pertain to the Center's software and Data are available at the following URL: [http://www.bioontology.org/tools.html NCBO Software].

NCBO Terms of Use is available at: [http://www.bioontology.org/terms.html this link].

Michael Montegut (mmontegut@stanford.edu) is the contact for the software development group at NCBO. We look forward to working with everyone.

SDIWG:Software Engineering At NCBO

2007-05-09T18:10:14Z

Dlrubin:

== [[SDIWG:NCBC_Software_Classification#CCB|Summary of the CCB Software Tools]] ==

Additional information about the [http://www.ccb.ucla.edu/ Center for Computational Biology] web pages that pertain to the center's SW and Data issues are available at the following URLs: [http://www.loni.ucla.edu/CCB/Software/ CCB Software], [https://services.loni.ucla.edu/ida/login.jsp?search=true CCB Databases] [http://www.loni.ucla.edu/CCB/Resources/ CCB Data].

CCB Software License is available at: [http://www.loni.ucla.edu/Policies/LONI_SoftwareAgreement.shtml this link].