Supplementary classification of databases for:
Electronic data sources for kinetic models of cell signaling
(J Biochem (Tokyo). 2005 Jun;137(6):653-7.)

Authors:

HarshaRani, G.V. National Centre for Biological Sciences
Vayttaden, S.J. National Centre for Biological Sciences and
Bhalla, U.S.* National Centre for Biological Sciences

*Corresponding author.

Diagram Resources
Model Depositories
Specialized Databanks
Searchable Model Depositories
Online Modeling Databases

Abstract

Functional understanding of signaling pathways requires detailed information about the constituent molecules and their interactions. Simulations of signaling pathways therefore build upon a great deal of data from various sources. We first survey electronic data resources for cell signaling modeling and then based on the type of data representation the data sources are broadly classified into five groups. None of the data sources surveyed provide all required data in a ready-to-be-modeled fashion. We then put forward a "wish list" for the desired attributes for an ideal modeling centric database. Finally, we close with perspectives on how electronic data sources for cell signaling modeling have developed. We suggest that future directions in such data sources are largely model-driven and are hinged on interoperability of data sources.

Diagram Resources

  Short Name Full Name URL
1 BBID Biological Biochemical Image Database http://bbid.grc.nia.nih.gov/
The BBID is a searchable database of images of putative biological pathways, macromolecular structures, gene families, and cellular relationships.
       
2 BioCarta BioCarta Proteomic Pathway Project (P3) http://www.biocarta.com/genes/index.asp
The BioCarta Proteomic Pathway Project (P3) on the BioCarta web site aims to make sense of the numerous important molecular interactions. The database has graphic depictions of molecular or cell-to-cell interactions.
       
3 Expasy Biochemical Pathway Boehringer Mannheim Biochemical Pathways Wall Chart http://www.expasy.org/cgi-bin/search-biochem-index
Boehringer Mannheim Biochemical Pathways Wall Chart on Expasy gives access to the digitized version of the Roche Applied Science "Biochemical Pathways" wall chart.
       
4 HPRD-Pathway Human Protein Reference Database-Pathway http://www.hprd.org/interactor_map
Human Protein Reference Database Interaction Map is a database of human proteins. A number of curated pathways created from the interaction data are available as images.
       
5 NOH Integrating Network Objects with Hierarchies http://www.inoh.org/
Integrating Network Objects with Hierarchies is a pathway database of model organisms including human, mouse, rat and others. Their Functional Relation Explorer System (FREX) provides keyword search for diagrams.
       
6 Malaria Parasite Malaria Parasite Metabolic Pathways http://sites.huji.ac.il/malaria
Malaria Parasite Metabolic Pathways is a database for Malaria biology, biochemistry and physiology. It contains pathway diagrams of metabolic pathways, cell-cell interactions, invasion of the erythrocyte by the parasite and transport functions.
       
7 MIPS-Pathway Munich Information Center for Protein Sequences-Pathway http://mips.gsf.de/proj/yeast/CYGD/db/pathway_index.html
The MIPS Comprehensive Yeast Genome Database (CYGD) aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. They have pathway diagrams among other information.
       
8 MIMminer Molecular Interaction Maps miner http://discover.nci.nih.gov/mim/index.jsp
MIMminer provides access to both the static and interactive Kohn Molecular Interaction maps.
       
9 Pathway Interaction Database Cancer Molecular Analysis Project's Pathway Interaction Database http://cmap.nci.nih.gov/PW
CMAP's Pathway Interaction Database is a database of pathway interactions, assembled by the National Cancer Institute's Center for Bioinformatics staff from publicly available sources of information primarily from from KEGG and BioCarta.
       
10 Connections Maps Science's STKE: The connections Maps Database http://stke.sciencemag.org/cm/
The Connections Maps are dynamically generated graphical interface to a database of information on the components of cellular signaling pathways and their relations to one another available on Science's STKE.

 

Model Depositories

  Short Name Full Name URL
1 Biomodels.Net Biomodels.Net http://www.biomodels.net/
Biomodels.Net project is an international effort to define common standards for model curation and annotation, coupled with a free, centralized, publicly-accessible database of annotated models. This resource is currently under development.
       
2 BioNetGen BioNetGen input files http://cellsignaling.lanl.gov/bionetgen/samples.shtml
BioNetGen is a software for generating mathematical/computational models. Their web site has a repository of samples model as BioNetGen input files.
       
3 Cellerator™ Cellerator™ Model Repository http://www-aig.jpl.nasa.gov/public/mls/cellerator/nb.html
Cellerator™ is a Mathematica® package designed to facilitate biological modeling via automated equation generation. The Cellerator™ model repository has a collection of freely available models.
       
4 CellML CellML Model Repository http://www.cellml.org/examples/repository/
CellML model repository contains models representative of several types of cellular level biological models - both signal transduction and electrophysiology models.
       
5 Cellular Models Cellular Models http://www.cds.caltech.edu/~hsauro/models.htm
Cellular Models is a collection of models maintained by Herbert M. Sauro. These models can be read by SBML Level 1 Compatible Simulation tools.
       
6 Genomic Object Net Genomic Object Net http://www.genomicobject.net/member3/index.html
Genomic Object Net is an enviroment for simulating and representing biological systems. There web site has a collection of model implemented by Genomic Object Net
       
7 Circadian Rhythm models Andrew J. Millar Circadian Rhythm model collection http://template.bio.warwick.ac.uk/staff/amillar/PEBrown/CircadianModelling/NewModels/NewModels.htm
The Millar Group model collection has Circadian Rhythm models from different systems.
       
8 Pathway Logic Demo Pathway Logic Demo http://mcs.une.edu.au/~iop/Bionet/index.html
Pathway Logic Demo webpage allows exploration of several Pathway Logic models using the Bionet viewer.
       
9 ReceptorDB ReceptorDB http://cellsignaling.lanl.gov/cgi-bin/database/index.cgi
ReceptorDB, a service of the CellSignaling Team of the Theoretical Biology and Biophysics Group at the Los Alamos National Lab, provides access to models of signal-transduction, developed with BioNetGen software.
       
10 SBML.org Systems Biology Markup Language http://sbml.org/models/
The SBML.org model repository is a collection of models in SBML format. The models have been developed by hand, not converted automatically from other sources, and most were validated by running simulations on them using the parameter and boundary values specified in the model.

 

Specialized Databanks

  Short Name Full Name URL
1 AfCS-nature The AfCS-Nature Signaling Gateway http://www.signaling-gateway.org/
The Alliance for Cellular Signaling has databases of molecules involved in signaling, a listing of relevant proteins proteins and signaling maps.
       
2 aMAZE aMAZE LightBench http://www.amaze.ulb.ac.be/
aMAZE LightBench is a WorkBench for the representation, management, annotation and analysis of information on networks of cellular processes: genetic regulation, biochemical pathways, signal transductions.
       
3 BIND Biomolecular Interaction Network Database http://www.bind.ca/
The BIND is a collection of records documenting molecular interactions. BIND has three classifications for molecular associations: molecules that associate with each other to form interactions, molecular complexes that are formed from one or more interaction(s) and pathways that are defined by a specific sequence of two or more interactions.
       
4 BRENDA Braunschweig Enzyme Database - The Comprehensive Enzyme Information System http://www.brenda.uni-koeln.de/
The Comprehensive Enzyme Information System (BRENDA) is an enzyme data information system. It is maintained and developed at the Institute of Biochemistry at the University of Cologne. Data on enzyme function are extracted directly from the primary literature.
       
5 CSNDB Cell Signaling Networks DataBase Cell Signaling Networks Data base http://athos.is.s.u-tokyo.ac.jp/ace/
CSNDB is a resource for signaling pathways of human cells. Signaling pathways are compiled as binary relationships of biomolecules and represented by graphs drawn automatically.
       
6 DIP Database of Interacting Proteins http://dip.doe-mbi.ucla.edu/
DIP™ database catalogs experimentally determined protein pair interactions.
       
7 Entrez Gene Entrez Gene http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene
Entrez Gene provides a unified query environment for genes defined by sequence and/or in NCBI's Map Viewer. The GeneRIF entry on Entrez Gene gives functional annotation relating the query gene to other genes.
       
8 Entrez PubMed Entrez PubMed http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed
Entrez PubMed provides free access to MEDLINE, NLM's database of more than 11 million bibliographic citations and abstracts in the fields of medicine, nursing, dentistry, veterinary medicine, health care systems, and preclinical sciences and also access to additional selected life sciences journals not in MEDLINE.
       
9 Gene Regulation Gene Regulation http://www.gene-regulation.com/index.html
Gene Regulation is a collection of freely available versions of Biobase databases viz. TRANSFAC®, Patho DB®, S/MARt DB™ Cytomer®, TRANSCompel® and TRANSPATH®
       
10 KDBI Kinetic Data of Biomolecular Interactions http://xin.cz3.nus.edu.sg/group/kdbi/kdbi.asp
KDBI provides experimentally determined kinetic data protein-protein, protein-RNA or reaction events described in the literature. KDBI contains information about binding or reaction event, participating molecules, binding or reaction equation, kinetic data and related references.
       
11 KEGG Kyoto Encyclopedia of Genes and Genomes http://www.genome.jp/kegg/pathway.html
KEGG Pathway Database is a collection of graphical diagrams (KEGG pathway maps) representing molecular interaction networks in various cellular processes.
       
12 MINT Molecular INTeraction http://mint.bio.uniroma2.it/mint/
MINT is a database of molecular interactions between biological molecules, it focuses on experimentally verified protein interactions with special emphasis on proteomes from mammalian organisms.
       
13 ProTherm Thermodynamic Database for Proteins and Mutants http://gibk26.bse.kyutech.ac.jp/jouhou/protherm/protherm.html
Thermodynamic Database for Proteins and Mutants is a collection of numerical data of the thermodynamic parameters of proteins.
       
14 ROSPath Reactive Oxygen Species related Signaling Pathway http://rospath.ewha.ac.kr/DefaultMain.jsp
ROSPath is an integrated database for proteins involved in ROS-mediated signaling pathways.
       
15 stkE SCIENCE's Signal Transduction knowledge Enviroment http://stke.sciencemag.org/
Large resource for signal transduction, needs subscription for full access.

 

Searchable Model Depositories

  Short Name Full Name URL
1 DOQCS Database of Quantitative Cellular Signaling http://doqcs.ncbs.res.in
The Database of Quantitative Cellular Signaling is a searchable repository of models of signaling pathways.
       
2 SigPath SigPath http://icb.med.cornell.edu/crt/SigPath/index.xml
SigPath is an information system designed to support quantitative studies on the signaling pathways and networks of the cell.

 

Online Modeling Databases

  Short Name Full Name URL
1 Budding Yeast Cell Cycle Homepage Budding Yeast Cell Cycle Homepage http://leibniz.biol.vt.edu/research/budding_yeast_model/pp/index.php
Budding Yeast Cell Cycle Database is a resource maintained by the John J. Tyson group at Virginia Tech. The resource has a collection of mathematical models of cell cycle and it also allows online simulation of these models.
       
2 Ecell E-cell Model Repository http://www.e-cell.org/research/model
E-Cell System is a software suite for modeling, simulation, and analysis of large scale complex systems such as biological cells. Sample models are available with the E-Cell package.
       
3 JWS Online: JWS Online: Cellular Systems Modelling http://jjj.biochem.sun.ac.za/index.html
JWS Online: Cellular Systems Modelling Model Database is a repository of kinetic models, describing biological systems, which can be interactively run and queried over the Internet.
       
4 ModelDB ModelDB http://senselab.med.yale.edu/senselab/ModelDB/default.asp
ModelDB is a modeling resource part of the SenseLab Project inititative. It is used for storing and efficiently retrieving computational neuron models.
       
5 Virtual Cell Portal Virtual Cell Portal http://www.nrcam.uchc.edu/vcellR3/login/login.jsp
Virtual Cell Portal is a remote user modeling and simulation environment created by The National Resource for Cell Analysis and Modeling (NRCAM).