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Metabolic network data | Pathway analysis

Metabolic pathways are series of enzymatic reactions that convert an initial substrate to the final end-products and are connected by their intermediates.

BiGG Models
Dataset

BiGG Models

A completely redesigned Biochemical, Genetic and Genomic knowledge base. BiGG…

A completely redesigned Biochemical, Genetic and Genomic knowledge base. BiGG Models contains more than 75 high-quality, manually-curated genome-scale metabolic models. On the website, users can…

Reactome
Dataset

Reactome

Allows to navigate pathway knowledge and provides bioinformatics tools for the…

Allows to navigate pathway knowledge and provides bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge. Reactome is a manually curated and peer-reviewed…

HRGRN
Dataset

HRGRN

Offers a way to search and discover the relationships among genes, proteins,…

Offers a way to search and discover the relationships among genes, proteins, compounds and small RNAs in plant signal transduction, metabolism and gene regulatory networks. HRGRN models the…

Transpath
Dataset

Transpath

Contains cellular events in humans, mice, and rats, collected from over 31,500…

Contains cellular events in humans, mice, and rats, collected from over 31,500 publications. Transpath offers information about the intracellular signaling pathways. It allows the user to see details…

MEMOSys
Dataset

MEMOSys MEtabolic MOdel research and development System

A versatile database for the management, storage and development of…

A versatile database for the management, storage and development of genome-scale models (GEMs). Since its initial release, the database has undergone major improvements, and the new version…

PathCaseMAW
Web

PathCaseMAW PathCase Metabolomics Analysis Workbench

Provides a database-enabled framework and Web-based computational tools for…

Provides a database-enabled framework and Web-based computational tools for browsing, querying, analyzing and visualizing stored metabolic networks. PathCaseMAW is easy to work with by design, and is…

PATRIC
Dataset

PATRIC Pathosystems Resource Integration Center

Aims to assist scientists in infectious-disease research. PATRIC is a National…

Aims to assist scientists in infectious-disease research. PATRIC is a National Institute of Health (NIH) supported bioinformatics resource center that has been built to enable comparative genomic…

IRMA
Dataset

IRMA In vivo “benchmarking” of Reverse-engineering and Modeling Approaches

Assesses and benchmarks modeling and reverse-engineering strategies. IRMA is a…

Assesses and benchmarks modeling and reverse-engineering strategies. IRMA is a synthetic network of five genes regulating each other for in vivo reverse-engineering and modeling assessment. This…

SubtiWiki
Dataset

SubtiWiki

A free collaborative resource for the Bacillus community. It is based on the…

A free collaborative resource for the Bacillus community. It is based on the idea that a community of experts that produces new knowledge every day is the best suited group for keeping a data…

MODOMICS
Dataset

MODOMICS

A database of RNA modifications that provides comprehensive information…

A database of RNA modifications that provides comprehensive information concerning the chemical structures of modified ribonucleosides, their biosynthetic pathways, RNA-modifying enzymes and location…

ECMDB
Dataset

ECMDB EColi Metabolome DataBase

An expertly curated database containing extensive metabolomic data and…

An expertly curated database containing extensive metabolomic data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655). This database includes significant quantities of…

TriTrypDB
Dataset

TriTrypDB

Provides information about Trypanosomatidae. Tritrypdb is a collective database…

Provides information about Trypanosomatidae. Tritrypdb is a collective database which intends to gather annotation, curation and access to tools enabling sophisticated queries against genomic scale…

CGD
Dataset

CGD Cucurbit Genomics Database

A database which offers gene annotation of cucurbit. This base offers the…

A database which offers gene annotation of cucurbit. This base offers the genome of Melon (Cucumis melo), Cucumber (Cucumis sativus), Watermelon (Citrullus lanatus), Pumpkin (Cucurbita maxima). The…

Pathway Commons
Dataset

Pathway Commons

Enables biologists to browse and search a comprehensive collection of pathways…

Enables biologists to browse and search a comprehensive collection of pathways from multiple sources represented in a common language, the BioPAX format. Data providers can share their pathway data…

KEGG PATHWAY
Dataset

KEGG PATHWAY

Consists in a collection of manually drawn pathway maps. KEGG PATHWAY concerns…

Consists in a collection of manually drawn pathway maps. KEGG PATHWAY concerns mainly molecular interaction, reaction and relation networks for: (1) drug development; (2) human diseases; (3)…

KEGG MODULE
Dataset

KEGG MODULE

Defines functional units. KEGG MODULE provides a collection of manually defined…

Defines functional units. KEGG MODULE provides a collection of manually defined functional units identified by the M numbers and used for annotation and biological interpretation of sequenced…

MetaCyc
Web

MetaCyc

A comprehensive and freely accessible database describing metabolic pathways…

A comprehensive and freely accessible database describing metabolic pathways and enzymes from all domains of life. MetaCyc pathways are experimentally determined, mostly small-molecule metabolic…

AraCyc
Dataset

AraCyc

Contains biochemical pathways of Arabidopsis, developed at The Arabidopsis…

Contains biochemical pathways of Arabidopsis, developed at The Arabidopsis Information Resource. The aim of AraCyc is to represent Arabidopsis metabolism as completely as possible with a…

PID
Desktop

PID Pathway Interaction Database

Deals with two issues affecting the representation of biological processes: the…

Deals with two issues affecting the representation of biological processes: the arbitrariness of pathway boundaries and the need to capture knowledge at different levels of detail. PID is a growing…

RGD
Dataset

RGD Rat Genome Database

Provides a comprehensive data repository and informatics platform related to…

Provides a comprehensive data repository and informatics platform related to the laboratory rat, one of the most important model organisms for disease studies. Rat Genome Database (RGD) maintains and…

Plant Reactome
Dataset

Plant Reactome

A network of plant proteins linked to their molecular functions and interactors…

A network of plant proteins linked to their molecular functions and interactors in the context of their locations within the plant cell. Plant Reactome provides intuitive bioinformatics tools for the…

HumanCyc
Dataset

HumanCyc

Provides a genome-based view of human nutrition that associates the essential…

Provides a genome-based view of human nutrition that associates the essential dietary requirements of humans with a set of metabolic pathways whose existence is supported by the human genome. The…

KaPPA-View
Dataset

KaPPA-View

A metabolic pathway database which is able to overlay gene-to-gene and/or…

A metabolic pathway database which is able to overlay gene-to-gene and/or metabolite-to-metabolite relationships as curves on a metabolic pathway map, or on a combination of up to four maps. This…

ToxoDB
Dataset

ToxoDB

A genome and functional genomic database for the protozoan parasite Toxoplasma…

A genome and functional genomic database for the protozoan parasite Toxoplasma gondii.

AHD
Dataset

AHD Arabidopsis Hormone Database

Provides a large collection of Arabidopsis hormone related genes (AHRGs). AHD…

Provides a large collection of Arabidopsis hormone related genes (AHRGs). AHD integrates detailed gene information and a phenotype ontology that is developed to precisely describe myriad…

HepatoNet1
Dataset

HepatoNet1

Represents a genome-scale metabolic network of human hepatocytes. The…

Represents a genome-scale metabolic network of human hepatocytes. The HepatoNet1 database enables the application of constraint-based modeling techniques to perceive allowable metabolic states in…

NCBI BioSystems
Dataset

NCBI BioSystems

Provides integrated access to biological systems and their component genes,…

Provides integrated access to biological systems and their component genes, proteins, and small molecules, as well as literature describing those biosystems and other related data throughout Entrez.…

YeastCyc
Dataset

YeastCyc

A Pathway/Genome Database of the model eukaryote Saccharomyces cerevisiae…

A Pathway/Genome Database of the model eukaryote Saccharomyces cerevisiae S288c. YeastCyc contains, in addition to genomic information, metabolic pathway, reaction, enzyme, and compound information,…

MouseCyc
Dataset

MouseCyc

Linking biochemical genetic data to the reference genome for the laboratory…

Linking biochemical genetic data to the reference genome for the laboratory mouse is important for comparative physiology and for developing mouse models of human biology and disease. MouseCyc is a…

CCDB
Dataset

CCDB CyberCell DataBase

A comprehensive collection of detailed enzymatic, biological, chemical,…

A comprehensive collection of detailed enzymatic, biological, chemical, genetic, and molecular biological data about E. coli (strain K12, MG1655).

KEGG
Dataset

KEGG

An integrated database resource consisting of 16 main databases, which are…

An integrated database resource consisting of 16 main databases, which are categorized into systems, genomic, chemical and health information. The PATHWAY, BRITE and MODULE databases in the systems…

Nematode.net
Dataset

Nematode.net

Disseminates diverse bioinformatic data sets and provide analysis tools to the…

Disseminates diverse bioinformatic data sets and provide analysis tools to the broad scientific community in a useful and user-friendly manner. Next-generation data has been added to the various…

PeroxisomeDB
Dataset

PeroxisomeDB Peroxisome DataBase

Aims to organise and integrate curated information on peroxisomal genes, their…

Aims to organise and integrate curated information on peroxisomal genes, their encoded proteins, their molecular function and metabolic pathway they belong to, and their related disorders. Additional…

PMAP
Dataset

PMAP Proteolysis MAP

A user-friendly website intended to aid the scientific community in reasoning…

A user-friendly website intended to aid the scientific community in reasoning about proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. The…

Interactive Fly
Dataset

Interactive Fly

Provides information about Drosophila development and metazoan evolution.…

Provides information about Drosophila development and metazoan evolution. Interactive Fly is a web resource that documents developmentally relevant genes, their function, expression and interactions,…

MetaNetX
Dataset

MetaNetX

A repository of genome-scale metabolic networks (GSMNs) and biochemical…

A repository of genome-scale metabolic networks (GSMNs) and biochemical pathways from a number of major resources imported into a common namespace of chemical compounds, reactions, cellular…

Arabidopsis…
Dataset

Arabidopsis Reactome

A knowledgebase of biological processes in Arabidopsis. It covers biological…

A knowledgebase of biological processes in Arabidopsis. It covers biological pathways ranging from the basic processes of metabolism to high-level processes such as cell cycle regulation. While…

hiPathDB
Dataset

hiPathDB

An integrated pathway database that combines the curated human pathway data of…

An integrated pathway database that combines the curated human pathway data of NCI-Nature PID, Reactome, BioCarta and KEGG. hiPathDB provides two different types of integration. The pathway-level…

PMN
Dataset

PMN Plant Metabolic Network

Metabolic networks reconstructed from sequenced genomes or transcriptomes can…

Metabolic networks reconstructed from sequenced genomes or transcriptomes can help visualize and analyze large-scale experimental data, predict metabolic phenotypes, discover enzymes, engineer…

LAMP
Dataset

LAMP Library of Apicomplexan Metabolic Pathways

A web database that provides near complete mapping from genes to the central…

A web database that provides near complete mapping from genes to the central metabolic functions for some of the prominent intracellular parasites of the phylum Apicomplexa. This phylum includes the…

MetaCrop
Dataset

MetaCrop

A manually curated repository of high-quality data about plant metabolism,…

A manually curated repository of high-quality data about plant metabolism, providing different levels of detail from overview maps of primary metabolism to kinetic data of enzymes. MetaCrop contains…

MaizeCyc
Dataset

MaizeCyc

A catalog of known and/or predicted metabolic and transport pathways from maize…

A catalog of known and/or predicted metabolic and transport pathways from maize (Zea mays ssp. mays). Pathways and genes presented in this catalog are based on the electronic and manual annotations…

metaTIGER
Web

metaTIGER

It has been created, using genomic information from 121 eukaryotes and 404…

It has been created, using genomic information from 121 eukaryotes and 404 prokaryotes and sensitive sequence search techniques to predict the presence of metabolic enzymes. These enzyme sequences…

iPAVS
Web

iPAVS integrated Pathway resources, Analysis and Visualization System

An integrated biological pathway database designed to support pathway discovery…

An integrated biological pathway database designed to support pathway discovery in the fields of proteomics, transcriptomics, metabolomics and systems biology. The key goal of IPAVS is to provide…

Plantmetabolomi…
Dataset

Plantmetabolomics.org

Contains comprehensive targeted and untargeted mass spectrum metabolomics data…

Contains comprehensive targeted and untargeted mass spectrum metabolomics data for Arabidopsis mutants across a variety of metabolomics platforms. The database allows users to generate hypotheses…

MMMDB
Dataset

MMMDB Mouse Multiple tissue Metabolome DataBase

Provides comprehensive and quantitative metabolomic information for multiple…

Provides comprehensive and quantitative metabolomic information for multiple tissues from single mice. MMMDB is designed to normalize users' data, which can be submitted online and used to…

TrypanoCyc
Dataset

TrypanoCyc

A dynamic database which describes the generic and condition-specific metabolic…

A dynamic database which describes the generic and condition-specific metabolic network of Trypanosoma brucei, a parasitic protozoan responsible for human and animal African trypanosomiasis. In…

CathaCyc
Dataset

CathaCyc

A detailed metabolic pathway database, from C. roseus RNA-Seq data sets.…

A detailed metabolic pathway database, from C. roseus RNA-Seq data sets. CathaCyc contains 390 pathways with 1,347 assigned enzymes and spans primary and secondary metabolism. Curation of the…

MODEM
Dataset

MODEM Multi-Omics Data Envelopment and Mining in maize

A comprehensive database to collect maize multidimensional omics data including…

A comprehensive database to collect maize multidimensional omics data including genomic variation, transcriptomic quantification, metabolic identification and phenotypic traits from cellular to…

MGI
Dataset

MGI Mouse Genome Informatics

Provides access to integrated genetic, genomic, and biological data about the…

Provides access to integrated genetic, genomic, and biological data about the laboratory mouse to facilitate study of human health and disease. MGI is an international mouse knowledgebase that…

HMA
Dataset

HMA Human Metabolic Atlas

Organizes and provides comprehensive human metabolic information as models and…

Organizes and provides comprehensive human metabolic information as models and a database. HMA is an online resource that consists of three services: Repository, Human REaction Entities Database…

MetNetDB
Dataset

MetNetDB MetNet database

Contains information on networks of metabolic and regulatory and interactions…

Contains information on networks of metabolic and regulatory and interactions in Arabidopsis. This information is based on input from biologists in their area of expertise. In addition to the…

SSER
Dataset

SSER Species-Specific Essential Reactions

Represents a species-specific essential reactions database. SSER includes…

Represents a species-specific essential reactions database. SSER includes essential biochemical and transport reactions obtained by applying flux balance analysis (FBA) on experimentally validated…

RiceGeneThreshe…
Dataset

RiceGeneThresher

A public online resource for mining genes underlying genome regions of interest…

A public online resource for mining genes underlying genome regions of interest or quantitative trait loci (QTL) in rice genome.

AtIPD
Dataset

AtIPD Arabidopsis thaliana Isoprenoid Pathway Database

Provides access to manually curated list of Arabidopsis isoprenoid pathways and…

Provides access to manually curated list of Arabidopsis isoprenoid pathways and genes, and allows to visualize pathway topology. The database was compiled using information on pathways and pathway…

HPD
Web

HPD Human Pathway Database

Developed the by integrating heterogeneous human pathway data that are either…

Developed the by integrating heterogeneous human pathway data that are either curated at the NCI Pathway Interaction Database (PID), Reactome, BioCarta, KEGG or indexed from the Protein Lounge Web…

FragariaCyc
Dataset

FragariaCyc

A strawberry-specific cellular metabolic network based on the annotated genome…

A strawberry-specific cellular metabolic network based on the annotated genome sequence of Fragaria vesca L. ssp. vesca, accession Hawaii 4. FragariaCyc was built on the Pathway-Tools platform using…

IPAD
Web

IPAD Integrated Pathway Analysis Database

A comprehensive database covering about 22,498 genes, 25,469 proteins, 1956…

A comprehensive database covering about 22,498 genes, 25,469 proteins, 1956 pathways, 6704 diseases, 5615 diseases, and 52 organs integrated from databases including the BioCarta, KEGG, NCI-Nature…

UniVIO
Dataset

UniVIO Uniformed Viewer for Integrative Omics

Provides an integrated data set of hormonome and transcriptome analyses in 14…

Provides an integrated data set of hormonome and transcriptome analyses in 14 organs of the rice plant at the reproductive stage and in gibberellin-related mutants. UniVIO allows users to search…

IntPath
Web

IntPath

A pathway gene relationship database that integrates data from KEGG,…

A pathway gene relationship database that integrates data from KEGG, WikiPathways, BioCyc. Currently, the following organisms are included: Homo sapiens, Mus musculus, Saccharomyces cerevisiae and…

BESC…
Dataset

BESC Knowledgebase

Serves as a centralized repository for experimentally generated data and to…

Serves as a centralized repository for experimentally generated data and to provide an integrated, interactive and user-friendly analysis framework. The Portal makes available tools for…

METscout
Dataset

METscout Metabolites Enzymes and Transporters scout

Gathers metabolic pathway maps with the expression patterns of about 1500…

Gathers metabolic pathway maps with the expression patterns of about 1500 metabolic enzyme genes and 350 metabolite transporter genes. METscout is a gene-centric database with an almost full coverage…

RiceCyc
Dataset

RiceCyc

A catalog of known and/or predicted biochemical pathways from rice (Oryza…

A catalog of known and/or predicted biochemical pathways from rice (Oryza sativa). Pathways and genes presented in this catalog are primarily based on the annotations carried out by Gramene database…

RNApathwaysDB
Dataset

RNApathwaysDB

Contains components involved in the RNA metabolic pathways of three main RNA…

Contains components involved in the RNA metabolic pathways of three main RNA classes (mRNA, tRNA and rRNA). RNApathwaysDB can be queried with keywords, and sequences of protein enzymes involved in…

MetSigDis
Dataset

MetSigDis

Gives access to information about metabolite alterations in various diseases.…

Gives access to information about metabolite alterations in various diseases. MetSigDis is a database that provides comprehensive public resources and perspective for understanding the causes of…

ECC2
Dataset

ECC2 EColiCore2

Describes several key properties of iJO1366, an E. coli genome-scale…

Describes several key properties of iJO1366, an E. coli genome-scale reconstruction. ECC2 contains 499 reactions (thereof 198 reversible) and 486 internal as well as 33 external metabolites. It…

CeCon
Dataset

CeCon C. Elegans metabolic reCONstruction

Provides a C. elegans genome-scale metabolic model. CeCon was generated by…

Provides a C. elegans genome-scale metabolic model. CeCon was generated by using C. elegans specific gene annotations obtained from UniProt and Wormbase. It was enriched with gene annotations for…

BioCyc
Dataset

BioCyc

Allows users to search information about pathway/genomes. BioCyc is a database…

Allows users to search information about pathway/genomes. BioCyc is a database that mixes thousands of genomes with additional information curated from the biomedical literature by biologist…

Cell ML Tools
Format

Cell ML Tools

An open standard based on the XML markup language. The purpose of CellML is to…

An open standard based on the XML markup language. The purpose of CellML is to store and exchange computer-based mathematical models. CellML allows scientists to share models even if they are using…

IMID
Dataset

IMID Integrated Molecular Interaction Database

Molecular interaction information can be searched using the search function…

Molecular interaction information can be searched using the search function below, where you may enter specific keywords according to your search criteria. You can limit your search by pathways,…

Meta-All
Dataset

Meta-All

Allows management of several types of information. Meta-All is designed for…

Allows management of several types of information. Meta-All is designed for administration of detailed information about metabolic pathways, including reactions, translocations, substances, pathways,…

SABIO-RK
Web

SABIO-RK

A curated database that contains information about biochemical reactions, their…

A curated database that contains information about biochemical reactions, their kinetic rate equations with parameters and experimental conditions. All the data are manually curated and annotated by…

ArthropodaCyc
Dataset

ArthropodaCyc

A collection of databases dedicated to the arthropod metabolism reconstruction.…

A collection of databases dedicated to the arthropod metabolism reconstruction. ArthropodaCyc allows researchers to perform reliable metabolism comparisons of fully sequenced arthropods genomes.…

DEOP
Dataset

DEOP Dragon Explorer of Osmoprotection Pathways

Focuses on the information related to osmoprotection. DEOP is an online…

Focuses on the information related to osmoprotection. DEOP is an online resource that contains curated information on compounds that were reported as osmoprotectants in scientific literature. This…

metabolicMine
Dataset

metabolicMine

Integrates data sets from a range of experiments and model organisms alongside…

Integrates data sets from a range of experiments and model organisms alongside tools for exploring them. The current version brings together information covering genes, proteins, orthologues,…

kpath
Dataset

kpath

Integrates information related to metabolic pathways. kpath also provides a…

Integrates information related to metabolic pathways. kpath also provides a navigational interface that enables not only the browsing, but also the deep use of the integrated data to build metabolic…

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The L.…
Dataset

The L. monocytogenes 10403S BioCyc database

A resource for researchers studying Listeria and related organisms. The L.…

A resource for researchers studying Listeria and related organisms. The L. monocytogenes 10403S BioCyc database allows users to (i) have a comprehensive view of all reactions and pathways predicted…

IUBMB-Nicholson…
Dataset

IUBMB-Nicholson maps

A collection of metabolic pathway diagrams curated by Donald Nicholson at the…

A collection of metabolic pathway diagrams curated by Donald Nicholson at the University of Leeds, England.

BioPath
Dataset

BioPath

A database of biochemical pathways that provides access to metabolic…

A database of biochemical pathways that provides access to metabolic transformations and cellular regulations derived from the Roche Applied Science "Biochemical Pathways" wall chart. In…

FUNGIpath
Dataset

FUNGIpath

A tool built using a two-stage approach. Groups of orthologous proteins…

A tool built using a two-stage approach. Groups of orthologous proteins predicted using complementary methods of detection were collected in a relational database. Each group was further mapped on to…

LmTDRM
Dataset

LmTDRM Thiol Disulphide Redox Metabolic

A comprehensive web-based database on thiol proteins and their functions. It…

A comprehensive web-based database on thiol proteins and their functions. It includes: Description, Search, TDRM analysis, and genome viewer. The quality of these data has been evaluated before they…

LeishCyc
Dataset

LeishCyc

Describes Leishmania major genes, gene products, metabolites, their…

Describes Leishmania major genes, gene products, metabolites, their relationships and biochemical organization into metabolic pathways. LeishCyc provides a systematic approach to organizing the…

SPDBS
Dataset

SPDBS SBML-based Biochemical Pathway Database System

Integrates information about Biochemical Pathway. SPDBS is an online resource…

Integrates information about Biochemical Pathway. SPDBS is an online resource that: (1) imports/exports SBML documents; (2) builds networks at different levels of representation starting from the…

KEGG Reaction…
Dataset

KEGG Reaction Module

Provides type of module defined from purely chemical data without incorporating…

Provides type of module defined from purely chemical data without incorporating any enzyme data. KEGG Reaction Module offers sequence of chemical structure transformation patterns defined by a set of…

RIKEN Plant…
Dataset

RIKEN Plant Hormone Research Network

Provides several information about the research activities in RIKEN. RIKEN…

Provides several information about the research activities in RIKEN. RIKEN Plant Hormone Research Network contains also a technical platform allowing hormone analysis, and a basic knowledge for…

The Banana…
Dataset

The Banana Genome Hub

Aggregates for unified access various information systems and analytical tools…

Aggregates for unified access various information systems and analytical tools that were not developed for one specific crop. The Banana Genome Hub is based on Tripal (a construction toolkit for…

BacillOndex
Desktop

BacillOndex

A semantically annotated, integrated knowledge database for the model…

A semantically annotated, integrated knowledge database for the model Gram-positive bacterium Bacillus subtilis. This application allows a user to mine a variety of Bacillus subtilis data sources,…

ProcessDB
Dataset

ProcessDB

Helps molecular cell biologists manage and test their increasingly complex…

Helps molecular cell biologists manage and test their increasingly complex mechanistic hypotheses. ProcessDB does this with a graphical user interface that helps users formulate, visualize, compare,…

Malaria…
Dataset

Malaria Parasite Metabolic Pathways

The genome project of Plasmodium falciparum has been completed and other…

The genome project of Plasmodium falciparum has been completed and other plasmodia species are on the line. The metabolic pathways of Plasmodium were extracted from the Kyoto University Encyclopedia…

FlyReactome
Dataset

FlyReactome

A curated repository for Drosophila melanogaster pathways and reactions. The…

A curated repository for Drosophila melanogaster pathways and reactions. The information in this database is authored by biological researchers with expertise in their fields, maintained by the…

PlasmoDB
Dataset

PlasmoDB

Provides a resource for data analysis and visualization in a gene-by-gene or…

Provides a resource for data analysis and visualization in a gene-by-gene or genome-wide scale. PlasmoDB is a functional genomic database for Plasmodium spp. It belongs to a family of genomic…

GiardiaDB
Dataset

GiardiaDB

A genomic database for Giardia lamblia. GiardiaDB is based on the genome of the…

A genomic database for Giardia lamblia. GiardiaDB is based on the genome of the WBC6 clinical isolate of G. lamblia. It is accessed via the standard EuPathDB web interface, providing a wide variety…

CryptoDB
Dataset

CryptoDB

A community bioinformatics resource for the AIDS-related apicomplexan-parasite,…

A community bioinformatics resource for the AIDS-related apicomplexan-parasite, Cryptosporidium.

FungiDB
Dataset

FungiDB

A functional genomic resource for pan-fungal genomes that was developed in…

A functional genomic resource for pan-fungal genomes that was developed in partnership with the Eukaryotic Pathogen Bioinformatic resource center.

UniPathway
Dataset

UniPathway

Provides explicit biochemical description of each reaction. UniPathway is a…

Provides explicit biochemical description of each reaction. UniPathway is a resource for the representation and annotation of enzymatic reactions and metabolic pathways. It allows individual…

AmoebaDB
Dataset

AmoebaDB

Functional genomic databases serving the amoebozoa research communities.

Functional genomic databases serving the amoebozoa research communities.

MicrosporidiaDB
Dataset

MicrosporidiaDB

Functional genomic databases serving the microsporidia research communities.

Functional genomic databases serving the microsporidia research communities.

UM-BBD
Dataset

UM-BBD University of Minnesota Biocatalysis/Biodegradation Database

Indicates range of microbial transformations. UM-BBD is an online database that…

Indicates range of microbial transformations. UM-BBD is an online database that catalogues information on microbial biocatalytic reactions and biodegradation pathways, primarily for xenobiotic…

EcID
Dataset

EcID Escherichia coli Interaction Database

Provides specific features that facilitate the detection of protein…

Provides specific features that facilitate the detection of protein interactions and the generation of species-specific hypothesis on biological functions. EcID is an online database that integrates…

Biozon
Dataset

Biozon

A unified biological database that integrates heterogeneous data types such as…

A unified biological database that integrates heterogeneous data types such as proteins, structures, domain families, protein-protein interactions and cellular pathways, and establishes the…

SchistoDB
Dataset

SchistoDB

Provides a rich resource of genomic data for key blood flukes (genus…

Provides a rich resource of genomic data for key blood flukes (genus Schistosoma) which cause disease in hundreds of millions of people worldwide.

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SYSTOMONAS
Dataset

SYSTOMONAS

Compiles data about the pseudomonas. SYSTOMONAS registers information on eight…

Compiles data about the pseudomonas. SYSTOMONAS registers information on eight different Pseudomonas species and strains, which genomes have been completely sequenced and functionally annotated. The…

DESM
Dataset

DESM

A platform for discovery, analysis and exploration of information from a number…

A platform for discovery, analysis and exploration of information from a number of topic-specific microbial knowledgebases. The knowledgebases include integrated information from published scientific…

PATIKA
Dataset

PATIKA Pathway Analysis Tools for Integration and Knowledge Acquisition

It is composed of a server-side, scalable, object-oriented database and…

It is composed of a server-side, scalable, object-oriented database and client-side editors to provide an integrated, multi-user environment for visualizing and manipulating network of cellular…

MedicCyc
Dataset

MedicCyc

A biochemical pathway database for Medicago truncatula. MedicCyc was assembled…

A biochemical pathway database for Medicago truncatula. MedicCyc was assembled based on new genomic sequence data and over 225,000 Medicago truncatula ESTs. The initial compilation was manually…

SFGD
Dataset

SFGD Soybean Functional Genomics Database

A comprehensive database integrating genome and transcriptome data, and also…

A comprehensive database integrating genome and transcriptome data, and also for soybean acyl-lipid metabolism pathways. SFGD provides useful toolboxes for biologists to improve the accuracy and…

PAGED
Dataset

PAGED Pathway And Gene Enrichment Database

Enables comprehensive searches for disease-specific pathways, gene signatures,…

Enables comprehensive searches for disease-specific pathways, gene signatures, microRNA targets, and network modules by integrating gene-set-based prior knowledge as molecular patterns from multiple…

PiroplasmaDB
Dataset

PiroplasmaDB

A genome database for the genus Piroplasma. PiroplasmaDB is a member of…

A genome database for the genus Piroplasma. PiroplasmaDB is a member of pathogen-databases that are housed under the NIAID-funded EuPathDB Bioinformatics Resource Center (BRC) umbrella.

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The aMAZE…
Dataset

The aMAZE LightBench

A web interface to the aMAZE relational database, which contains information on…

A web interface to the aMAZE relational database, which contains information on gene expression, catalysed chemical reactions, regulatory interactions, protein assembly, as well as metabolic and…

MetRxn
Dataset

MetRxn

A knowledgebase that includes standardized metabolite and reaction descriptions…

A knowledgebase that includes standardized metabolite and reaction descriptions by integrating information from BRENDA, KEGG, MetaCyc, Reactome.org and 44 metabolic models into a single unified data…

MRAD
Dataset

MRAD Metabolic Reaction Analysis Database

A relational database based on the entity-relationship (ER) model which…

A relational database based on the entity-relationship (ER) model which combines information about organisms, biochemical pathways, reactions, enzymes, substrates, products and genes. MRAD describes…

BIOBASE…
Dataset

BIOBASE PROTEOME

A knowledgebase containing data on genes and miRNAs, the diseases they are…

A knowledgebase containing data on genes and miRNAs, the diseases they are associated with, the drugs they are targeted by, and the pathways and networks they act within. Based on its extensive…

GON
Dataset

GON Genomic Object Net

Collects information related to biological pathway modeling. The GON website…

Collects information related to biological pathway modeling. The GON website provides pathway models of hybrid functional Petri net (HFPN) as well as the detailed explanation about these pathways.…

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