SDIWG:NCBC Software Classification - Revision history

Will: /* NA-MIC */

2009-10-17T13:01:47Z

NA-MIC

Will: /* NA-MIC */

2009-10-17T13:01:32Z

NA-MIC

Kikinis: /* NA-MIC */

2007-04-12T00:41:57Z

NA-MIC

Kikinis: /* NA-MIC */

2007-04-12T00:38:48Z

NA-MIC

Lysterp at 20:55, 21 January 2007

2007-01-21T20:55:21Z

Lysterp at 20:54, 21 January 2007

2007-01-21T20:54:37Z

Lysterp at 20:49, 21 January 2007

2007-01-21T20:49:41Z

Andy: Update from Wiki

2006-12-18T13:23:23Z

Update from Wiki

Andy: Update from Wiki

2006-12-18T13:23:20Z

Update from Wiki

New page

'''NCBC Software Classification Page'''

Summary: The sections below are hierarchical classifications of biomedical computing software, currently focused on the NIH Roadmap National Centers for Biomedical Computing (NCBC). This effort stemmed out of [http://www.loni.ucla.edu/twiki/bin/view/CCB/CCB_NCBC_11_17_05_TCon a software ontology initiative] and [http://www.loni.ucla.edu/twiki/bin/view/CCB/CCB_NCBC_11_17_05_TCon_Minutes meeting minutes] that were led by Ivo Dinov from the Center for Computational Biology. These data have been incorporated in the [http://bioontology.org/ontologies/SoftwareOntology/ draft protege document] (Daniel Rubin and Mark Musen)

<br />

=== NA-MIC ===

Software Organization of the [[SoftwareInventory|NA-MIC Kit]]

Applications
[[Slicer|Slicer2]]
[[LONIPipelineSummary|LONI Pipeline]]
Toolkits
[[ITKSummary|Insight Toolkit]] (itk)
[http://www.itk.org/Insight/Doxygen/html/modules.html itk Ontology]
[[VTKSummary|Visualization Toolkit]] (vtk)
[[KWWidgetsSummary|KWWidgets]]

Software Engineering Tools
Testing
[[Dart2Summary|Dart2]]
[[CTestSummary|CTest]]
Cross-Platform Build
[[CmakeSummary|CMake]]
Cross-Platform Distribution
CPack
Cross-Language Wrapping
CableSWIG

=== Simbios ===

Preliminary Simbios Center software categories (non-hierarchical) 12/07/2005

Deliverable software modules

Applications
Models
Computational components
Model-building toolsets
Application-building toolsets
User and developer documentation

Application areas

Driving Biological Problems
RNA folding
Myosin dynamics
Cardiovascular fluid dynamics
Neuromuscular biomechanics
Molecule modeling
Electrostatics

User categories

Clinician
Experimentalist
Application developer
Modeler
Algorithm developer
SimTK software developer

Platform support

Shared memory multiprocessors
Clusters

Language support

Scripting languages (tcl, perl, python)
Java
C++, C, Fortran

Computation components

Linear Algebra (dense, sparse)
Numerical Integrators (ODE, DAE, PDE, Stochastic)
Monte Carlo simulation
Multibody dynamics
Contact modeling
Meshing
PDE solvers
Controllers
Optimizers/root finders
Molecular force field calculations
Computational geometry

Software development tools

Source control
Multiplatform build system
Regression test support
Document generation

Software dissemination tools

User interaction
Bug reporting
Feature requests
Mailing lists
News
Software and documentation delivery support
Installation
Download
Upgrade
Education
Tutorials
Course material and software
Online courses

=== CCB ===

The Software Tool Ontology envisioned by the [http://www.ccb.ucla.edu/ CCB] is available at these three links:

* [http://www.loni.ucla.edu/twiki/bin/view/Pipeline/OntologyClassDefinitions CCB Ontology Classification]
* [http://www.loni.ucla.edu/twiki/bin/view/Pipeline/ClassDefinitions Class & Function Definitions]
* [http://bioontology.org/ontologies/SoftwareOntology/ Protege Ontology] (Thanks to Daniel Rubin from [http://bioontology.org NCBO])
* [http://www.loni.ucla.edu/twiki/bin/view/CCB/CCB_NCBC_11_17_05_TCon NCBC Ontology TCon discussions] 11/08/05
* [http://www.loni.ucla.edu/twiki/bin/view/CCB/CCB_NCBC_11_17_05_TCon_Minutes Ontology Draft Documents]

=== I2B2 ===

HERE IS OUR DRAFT SCHEMA:

Computer Code

Source
Application Domain(s)
License
Tested on platforms
Binaries
Application Domain(s)
License
Tested on platforms

Documentation

Biological Experimentation Protocol
Algorithm Description
Publication
PUBMED ID or DOI
Human Cohort Description
Non-Human Experiment Description
Organism
Software/Technology protocols
Technology white papers

Application Domains (Software)

Clinical Information Systems

Natural Language Processing
Predictive modeling and classification
Extract, Transform, and Load
Database Schema
Ontology Management
Service Oriented Architecture
Biological Structure
Structure:function and structure:disease prediction
Protein interaction modeling
Expression studies
Disease classification/advanced histopathology
Outcome prediction
Pathway/gene identification for disease
Integration of expression w/DNA studies
DNA/Genomic studies
Population study type (association/linkage etc)
Scoring/predicting DNA variant functional and disease significance
Comparative genomics
Motif studies (TFBS/miRNA/protein domains, etc)

Experimental Data

Aggregate Human Data
DNA
RNA
Protein
Non-image Phenoty[e
Image
Individual Human Data
DNA (sequence and mapping)
RNA
Protein
Non-image Phenoty[e
Image
Usage
Non-human
DNA
RNA
Protein
Non-image Phenoty[e
Image

Equipment

Genomic Measurement
Imaging
Imaging Class

DNA (sequence and mapping)

Gene ID
Non-standard descriptor

RNA

Gene ID
Splice variant
Non-standard descriptor

Protein

ID or AA sequence?

Non-image Phenotype

UMLS or other vocabulary coded
Narrative text

Usage

Anonymity level
Consent level

Image

DICOM?
MIME type?

Reagents

Chemical
Organismal

=== NCIBI ===

[http://www.ncibi.org/resources tools and resources]

=== Magnet ===

Tools are broken down into 2 large categories: Analyses and Databases. Each category is further specified by functionality (analyses) or content (databases). Where available, URLs are provided. For analyses, the primary input data type is indicated in parentheses next to the name of the analytical tool. Databases are accompanied by associated querying tools (such tools are '''not''' listed here as separate entries).

'''Analyses: Regulatory/Signaling network reconstruction'''

* ARACNE (gene expression), http://amdec-bioinfo.cu-genome.org/html/ARACNE.htm
* GeneClass (gene expression), http://www1.cs.columbia.edu/compbio/robust-geneclass/download.html.

'''Analyses: Network characterization'''

* NetClass/NetBoost (molecular interactions networks), http://www.columbia.edu/~chw2/.
* InfoMod (molecular interactions networks), http://www.columbia.edu/~chw2/.

'''Analyses: Homology-based protein sequence classification'''

* Bio-Kernels (protein sequences), http://www1.cs.columbia.edu/compbio/string-kernels/.
* RankProp/MotifProp (protein sequences).

'''Analyses: Structured-based protein classification'''

* Protein function pipeline (protein structure).

'''Analyses: Prediction of regulatory (cis) elements'''

* REDUCE (gene expression), http://bussemaker.bio.columbia.edu:8080/reduce/.
* MEDUSA (gene expression), http://www1.cs.columbia.edu/compbio/medusa/download.html.

'''Analyses: Protein structure prediction'''

* Protein structure pipeline (protein sequence).
* META-server (protein sequence).
* Super-NEST (protein sequence).
* Protein cavity and binding site prediction (protein structure).

'''Databases: Molecular interactions'''

* GeneWays, http://geneways.genomecenter.columbia.edu/.
* Cellular Network KB.

'''Databases: Gene-phenotype associations'''

* PhenotypeML DB.

=== NCBO ===

'''Ontology Management'''

* [http://protege.stanford.edu Protege]
* [http://sourceforge.net/project/showfiles.php?group_id=36855 OBO-EDIT]

'''Ontology Diff and Alignment'''

* [http://protege.stanford.edu/plugins/prompt/prompt.html PROMPT]

'''Ontology Visualization'''

* [http://www.cs.uvic.ca/~chisel/projects/jambalaya/jambalaya.html Jambalaya]
* [http://protege.stanford.edu/plugins/ontoviz/ontoviz.html OntoViz]
* [http://www.thechiselgroup.org/~chisel/projects/promptviz/promptviz.html PromptViz]
* [http://www.ecs.soton.ac.uk/~ha/TGVizTab/TGVizTab.htm TGViz]

'''Biomedical Data Annotation'''

* OBO-EDIT

'''Progammatic Access to Ontologies'''

* [http://smi-web.stanford.edu/people/dameron/protegeScript/index.html Protege Script Tab]

'''Web Access to Ontologies'''

* [http://protege.cim3.net/cgi-bin/wiki.pl?WebProtege WebProtege]

=== IATR ===

The Internet Analysis Tool Registry (IATR) is a website dedicated to (trying to) provide a centrally available listing of all image analysis tools that are available to the neuroscience community in order to facilitate the development, identification, and sharing of tools that are of use to the general community. It is hoped that this helps the "tool developers" to get their tools to a larger user community and to reduce redundancy (or at least utilize tool redundancy to facilitate optimal tool design) in tool development.

'''IATR Site'''

* [http://www.cma.mgh.harvard.edu/iatr/index.php IATR]

As part of this effort, we have had users indicate software ''keywords'' to describe tool functionallity, funding source, interface options, operating platforms, etc. Through this collection of information, the following prototype image analysis software tool function ''vocabulary'' has been constructed.

'''Documentation'''

A recently accepted paper (to appear in Neuroinformatics) provides a lingthy description of the site and it's design. [[Image:The_Internet_Analysis_Tools_Registry_revised.doc|Image:The Internet Analysis Tools Registry revised.doc]]

A little picture of the schema appears here: [[Image:Iatr_2.jpg|[[Image:250px-Iatr_2.jpg.png]]]]

'''IATR as an example NCBC 'Yellow Pages''''

We have developed project-specific entry points into the registry. Thus, with one simple URL, one can come into the site at the result of a search for a specific set of tools. Examples of this include:

* http://www.cma.mgh.harvard.edu/iatr/display.php?spec=na-mic Shows NA-MIC Tools

* http://www.cma.mgh.harvard.edu/iatr/display.php?spec=magnet Shows MAGNet Tools

* http://www.cma.mgh.harvard.edu/iatr/display.php?spec=ncbc Shows all listed NCBC Tools

<br />

'''IATR Tool Vocabulary'''

* [http://www.cma.mgh.harvard.edu/iatr/vocabulary.php IATR Tool Vocabulary]

This vocabulary is a prototype, work-in-progress, suggestion, open for input and revision kind of thing. Feel free to provide (constructuve!) feedback in this effort, and it's interoperation with other similar efforts.

@@ Line 3: / Line 3: @@
 === Summary ===
-The sections below are hierarchical classifications of biomedical computing software, currently focused on the NIH Roadmap National Centers for Biomedical Computing (NCBC). This effort stemmed out of http://www.loni.ucla.edu/twiki/bin/view/CCB/CCB_NCBC_11_17_05_TCon a software ontology initiative] and [http://www.loni.ucla.edu/twiki/bin/view/CCB/CCB_NCBC_11_17_05_TCon_Minutes meeting minutes] that were led by Ivo Dinov from the Center for Computational Biology. These data have been incorporated in the [http://bioontology.org/projects/ontologies/SoftwareOntology/ draft protege document] (Daniel Rubin and Mark Musen)
+The sections below are hierarchical classifications of biomedical computing software, currently focused on the NIH Roadmap National Centers for Biomedical Computing (NCBC). This effort stemmed out of [http://www.loni.ucla.edu/twiki/bin/view/CCB/CCB_NCBC_11_17_05_TCon a software ontology initiative] and [http://www.loni.ucla.edu/twiki/bin/view/CCB/CCB_NCBC_11_17_05_TCon_Minutes meeting minutes] that were led by Ivo Dinov from the Center for Computational Biology. These data have been incorporated in the [http://bioontology.org/projects/ontologies/SoftwareOntology/ draft protege document] (Daniel Rubin and Mark Musen)
 === Meetings ===

@@ Line 3: / Line 3: @@
 === Summary ===
-The sections below are hierarchical classifications of biomedical computing software, currently focused on the NIH Roadmap National Centers for Biomedical Computing (NCBC). This effort stemmed out of [http://www.loni.ucla.edu/twiki/bin/view/CCB/CCB_NCBC_11_17_05_TCon a software ontology initiative] and [http://www.loni.ucla.edu/twiki/bin/view/CCB/CCB_NCBC_11_17_05_TCon_Minutes meeting minutes] that were led by Ivo Dinov from the Center for Computational Biology. These data have been incorporated in the [http://bioontology.org/projects/ontologies/SoftwareOntology/ draft protege document] (Daniel Rubin and Mark Musen)
+The sections below are hierarchical classifications of biomedical computing software, currently focused on the NIH Roadmap National Centers for Biomedical Computing (NCBC). This effort stemmed out of http://www.loni.ucla.edu/twiki/bin/view/CCB/CCB_NCBC_11_17_05_TCon a software ontology initiative] and [http://www.loni.ucla.edu/twiki/bin/view/CCB/CCB_NCBC_11_17_05_TCon_Minutes meeting minutes] that were led by Ivo Dinov from the Center for Computational Biology. These data have been incorporated in the [http://bioontology.org/projects/ontologies/SoftwareOntology/ draft protege document] (Daniel Rubin and Mark Musen)
 === Meetings ===

@@ Line 3: / Line 3: @@
 === Summary ===
-The sections below are hierarchical classifications of biomedical computing software, currently focused on the NIH Roadmap National Centers for Biomedical Computing (NCBC). This effort stemmed out of [http://www.loni.ucla.edu/twiki/bin/view/CCB/CCB_NCBC_11_17_05_TCon a software ontology initiative] and [http://www.loni.ucla.edu/twiki/bin/view/CCB/CCB_NCBC_11_17_05_TCon_Minutes meeting minutes] that were led by Ivo Dinov from the Center for Computational Biology. These data have been incorporated in the [http://bioontology.org/ontologies/SoftwareOntology/ draft protege document] (Daniel Rubin and Mark Musen)
+The sections below are hierarchical classifications of biomedical computing software, currently focused on the NIH Roadmap National Centers for Biomedical Computing (NCBC). This effort stemmed out of [http://www.loni.ucla.edu/twiki/bin/view/CCB/CCB_NCBC_11_17_05_TCon a software ontology initiative] and [http://www.loni.ucla.edu/twiki/bin/view/CCB/CCB_NCBC_11_17_05_TCon_Minutes meeting minutes] that were led by Ivo Dinov from the Center for Computational Biology. These data have been incorporated in the [http://bioontology.org/projects/ontologies/SoftwareOntology/ draft protege document] (Daniel Rubin and Mark Musen)
 === Meetings ===
@@ Line 15: / Line 15: @@
 * Tool Name:
-* [http://bioontology.org/ontologies/SoftwareOntology/ NCBC Ontology Classification]<nowiki>: </nowiki>
+* [http://bioontology.org/projects/ontologies/SoftwareOntology/ NCBC Ontology Classification]<nowiki>: </nowiki>
 * Description:
 * Input (parameters & Data Types):
@@ Line 32: / Line 32: @@
 === NCBC Tool Classification and Ontology ===
-The ''initial'' NCBC Software Tool Ontology is available in [http://bioontology.org/ontologies/SoftwareOntology/ OWL/Protege here]
+The ''initial'' NCBC Software Tool Ontology is available in [http://bioontology.org/projects/ontologies/SoftwareOntology/ OWL/Protege here]
 ----
@@ Line 152: / Line 152: @@
 * [http://www.loni.ucla.edu/twiki/bin/view/Pipeline/OntologyClassDefinitions CCB Ontology Classification]
 * [http://www.loni.ucla.edu/twiki/bin/view/Pipeline/ClassDefinitions Class & Function Definitions]
-* [http://bioontology.org/ontologies/SoftwareOntology/ Protege Ontology] (Thanks to Daniel Rubin from [http://bioontology.org NCBO])
+* [http://bioontology.org/projects/ontologies/SoftwareOntology/ Protege Ontology] (Thanks to Daniel Rubin from [http://bioontology.org NCBO])
 * [http://www.loni.ucla.edu/twiki/bin/view/CCB/CCB_NCBC_11_17_05_TCon NCBC Ontology TCon discussions] 11/08/05
 * [http://www.loni.ucla.edu/twiki/bin/view/CCB/CCB_NCBC_11_17_05_TCon_Minutes Ontology Draft Documents]

@@ Line 53: / Line 53: @@
   Software Engineering Tools
     Testing
-      [[CDashSummary|Dart2]]
+      [[CDashSummary|CDash]]
       [[CTestSummary|CTest]]
     Cross-Platform Build

@@ Line 39: / Line 39: @@
 Software Organization of the [[NA-MIC-Kit|NA-MIC Kit]]
 * [[SDIWG:NCBC_Software_Classification_NAMIC_Examples|NAMIC Examples of Tool Metadata and Tool Classification]]
-    [[Slicer|Slicer2]]
+ Applications
   Toolkits

@@ Line 38: / Line 38: @@
 === NA-MIC ===
-Software Organization of the [[SoftwareInventory|NA-MIC Kit]]
+Software Organization of the [[NA-MIC-Kit|NA-MIC Kit]]
   Applications
@@ Line 45: / Line 45: @@
     [[Slicer|Slicer2]]
-   [[LONIPipelineSummary|LONI Pipeline]]
   Toolkits
     [[ITKSummary|Insight Toolkit]] (itk)

@@ Line 1: / Line 1: @@
 '''NCBC Software Classification Page'''
-Summary: The sections below are hierarchical classifications of biomedical computing software, currently focused on the NIH Roadmap National Centers for Biomedical Computing (NCBC). This effort stemmed out of [http://www.loni.ucla.edu/twiki/bin/view/CCB/CCB_NCBC_11_17_05_TCon a software ontology initiative] and [http://www.loni.ucla.edu/twiki/bin/view/CCB/CCB_NCBC_11_17_05_TCon_Minutes meeting minutes] that were led by Ivo Dinov from the Center for Computational Biology. These data have been incorporated in the [http://bioontology.org/ontologies/SoftwareOntology/ draft protege document] (Daniel Rubin and Mark Musen)
+=== Summary ===
-<br />
+The sections below are hierarchical classifications of biomedical computing software, currently focused on the NIH Roadmap National Centers for Biomedical Computing (NCBC). This effort stemmed out of [http://www.loni.ucla.edu/twiki/bin/view/CCB/CCB_NCBC_11_17_05_TCon a software ontology initiative] and [http://www.loni.ucla.edu/twiki/bin/view/CCB/CCB_NCBC_11_17_05_TCon_Minutes meeting minutes] that were led by Ivo Dinov from the Center for Computational Biology. These data have been incorporated in the [http://bioontology.org/ontologies/SoftwareOntology/ draft protege document] (Daniel Rubin and Mark Musen)
 === NA-MIC ===
@@ Line 10: / Line 41: @@
   Applications
     [[Slicer|Slicer2]]
     [[LONIPipelineSummary|LONI Pipeline]]
@@ Line 32: / Line 66: @@
 Preliminary Simbios Center software categories (non-hierarchical) 12/07/2005
 Deliverable software modules
@@ Line 113: / Line 149: @@
 The Software Tool Ontology envisioned by the [http://www.ccb.ucla.edu/ CCB] is available at these three links:
 * [http://www.loni.ucla.edu/twiki/bin/view/Pipeline/OntologyClassDefinitions CCB Ontology Classification]
 * [http://www.loni.ucla.edu/twiki/bin/view/Pipeline/ClassDefinitions Class & Function Definitions]
@@ Line 122: / Line 159: @@
 HERE IS OUR DRAFT SCHEMA:
 Computer Code
@@ Line 148: / Line 187: @@
 Application Domains (Software)
-Clinical Information Systems
+  Clinical Information Systems
       Natural Language Processing
       Predictive modeling and classification
@@ Line 202: / Line 240: @@
    Gene ID
    Non-standard descriptor
 RNA
@@ Line 235: / Line 274: @@
 === NCIBI ===
-[http://www.ncibi.org/resources tools and resources]
+The current version of our interactive tools and resources site is here: [http://www.ncibi.org/toolreg/toolreg_list Tools and Resources review site]
 === Magnet ===
 Tools are broken down into 2 large categories: Analyses and Databases. Each category is further specified by functionality (analyses) or content (databases). Where available, URLs are provided. For analyses, the primary input data type is indicated in parentheses next to the name of the analytical tool. Databases are accompanied by associated querying tools (such tools are '''not''' listed here as separate entries).
 '''Analyses: Regulatory/Signaling network reconstruction'''
@@ Line 285: / Line 330: @@
 '''Ontology Management'''
 * [http://protege.stanford.edu Protege]
 * [http://sourceforge.net/project/showfiles.php?group_id=36855 OBO-EDIT]