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 a software ontology initiative and meeting minutes that were led by Ivo Dinov from the Center for Computational Biology. These data have been incorporated in the draft protege document (Daniel Rubin and Mark Musen)

Meetings

• 07/18/06
• 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:
• NCBC Ontology Classification:
• 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 NCBC Software Classification Simbios Template

NCBC Tool Classification and Ontology

The initial NCBC Software Tool Ontology is available in OWL/Protege here

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NA-MIC

Software Organization of the NA-MIC Kit

• NAMIC Examples of Tool Metadata and Tool Classification

Applications
  Slicer2 and Slicer 3

Toolkits
  Insight Toolkit (itk)
  itk Ontology
  Visualization Toolkit (vtk)
  KWWidgets

Software Engineering Tools
  Testing
    CDash
    CTest
  Cross-Platform Build
    CMake
  Cross-Platform Distribution
    CPack
  Cross-Language Wrapping
    CableSWIG

Simbios

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

• 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 CCB is available at these three links:

• CCB Examples of Tool Metadata and Tool Classification
• CCB Ontology Classification
• Class & Function Definitions
• Protege Ontology (Thanks to Daniel Rubin from NCBO)
• NCBC Ontology TCon discussions 11/08/05
• Ontology Draft Documents

I2B2

HERE IS OUR DRAFT SCHEMA:

• 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: 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: Tools and Resources registration site

This is an example of the new format for the same information: 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).

• 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

• NCBO Examples of Tool Metadata and Tool Classification
• Protege
• OBO-EDIT

Ontology Diff and Alignment

• PROMPT

Ontology Visualization

• Jambalaya
• OntoViz
• PromptViz
• TGViz

Biomedical Data Annotation

• OBO-EDIT

Progammatic Access to Ontologies

• Protege Script Tab

Web Access to Ontologies

• 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

• 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. File:The Internet Analysis Tools Registry revised.doc

A little picture of the schema appears here: File:Iatr 2.jpg

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

IATR Tool Vocabulary

• 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.