Prof. Upinder S. Bhalla - Electronic data sources
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 | |
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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 | |
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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 | |
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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). |