View source for SDIWG:NCBC Software Classification

'''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/projects/ontologies/SoftwareOntology/ draft protege document] (Daniel Rubin and Mark Musen)

=== Meetings ===

* [http://www.loni.ucla.edu/twiki/bin/view/CCB/NCBC_ToolIntegration_XMLtology_Meeting_071806AM 07/18/06]
* [[SDIWG:Meeting_Minutes_20060616|06/16/2006]]

=== NCBC Tool Meta-data ===

Here are the ''initial'' set of meta-data that will be saved for each of the NCBC software tools, when these are entered in the Protege's Ontology, IATR, Simbiome, etc.

* Tool Name:
* [http://bioontology.org/projects/ontologies/SoftwareOntology/ NCBC Ontology Classification]<nowiki>: </nowiki>
* Description:
* Input (parameters & Data Types):
* Output Data (parameters & Data Types):
* Implementation Language:
* Version, Date, Stage:
* Authors:
* License:
* Keywords:
* NCBC:
* URL:
* Other Info:

Also, see the [[SDIWG:NCBC_Software_Classification_SimbiosTemplate|NCBC Software Classification Simbios Template]]

=== NCBC Tool Classification and Ontology ===

The ''initial'' NCBC Software Tool Ontology is available in [http://bioontology.org/projects/ontologies/SoftwareOntology/ OWL/Protege here]

----

=== NA-MIC ===

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

* [[SDIWG:NCBC_Software_Classification_NAMIC_Examples|NAMIC Examples of Tool Metadata and Tool Classification]]

 Applications
   [http://www.slicer.org Slicer2 and Slicer 3]

 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

* [[SDIWG:NCBC_Software_Classification_Simbios_Examples|Simbios Examples of Tool Metadata and Tool Classification]]

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:

* [[SDIWG:NCBC_Software_Classification_CCB_Examples|CCB Examples of Tool Metadata and Tool Classification]]
* [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/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]

=== I2B2 ===

HERE IS OUR DRAFT SCHEMA:

* [[SDIWG:NCBC_Software_Classification_I2B2_Examples|I2B2 Examples of Tool Metadata and Tool Classification]]

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 ===

The current version of our interactive tools and resources site is here: [http://www.ncibi.org/toolreg/toolreg_list Tools and Resources review site]

The site for contributing new records (and editing records that you have contributed), which requires that you be registered, is here: [http://collab.ncibi.org/toolreg Tools and Resources registration site]

This is an example of the new format for the same information: [[SDIWG:NCBC_Software_Classification_NCIBI_Examples|NCIBI Examples of Tool Metadata and Tool Classification]]

=== 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).

* [[SDIWG:NCBC_Software_Classification_MAGNet_Examples|MAGNet Examples of Tool Metadata and Tool Classification]]

'''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'''

* [[SDIWG:NCBC_Software_Classification_NCBO_Examples|NCBO Examples of Tool Metadata and Tool Classification]]
* [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.