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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Functional Annotation Resource Report Resource Website 1+ mentions |
Functional Annotation (RRID:SCR_017519) | service resource | MGI GO project provides functional annotations for mouse gene products using Gene Ontology. Functional annotation using Gene Ontology (GO). | MGI, GO, functional, annotation, mouse, gene, product, Gene Ontology |
uses: Gene Ontology has parent organization: Mouse Genome Informatics (MGI) |
Free, Freely available | SCR_017519 | 2026-08-01 12:06:07 | 4 | ||||||||||
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Avadis Resource Report Resource Website 1+ mentions Rating or validation data |
Avadis (RRID:SCR_000644) | Avadis | software library, software toolkit, software resource | Software integrated platform that provides analysis, management and visualization tools for next-generation sequencing data. It supports workflows for RNA-Seq, DNA-Seq, ChIP-Seq and small RNA-Seq experiments. Avadis has a built-in Gene Ontology browser to view ontology hierarchies. There are common ontology paths for multiple genes. Platform has collection of data / text mining algorithms, data visualization libraries, workflow/application automation layers, and enterprise data organization functions. These functions are available as libraries that allow developers to rapidly build software prototypes, applications and off-the-shelf products. The collection of algorithms and visualizations in AVADIS grows as new applications using the platform are developed. Currently, the algorithms that AVADIS platform contains range from general purpose statistical mining and modelling algorithms, to text mining algorithms, to very application-specific algorithms for microarray / NGS data analysis, QSAR modelling and biological networks analysis. AVADIS has a collection of powerful mining algorithms like PCA, ANOVA, T-test, clustering, classification and regression methods. The range of visualizations includes most statistical and data modelling related graphing views, and very application-specific visualizations. Some of the statistical views include 2D/3D scatter plots, profile plots, heat maps, histograms and matrix plot; data modelling relevant views include dendrograms, cluster profiles, similarity images and SOM U-matrices. Application-specific views in AVADIS include pathway network views, genome browsers, chemical structure views and pipe-line views. Platform: Windows compatible, Mac OS X compatible, Linux compatible, | pathway network views, genome browsers, chemical structure views, pipe-line views, next-generation sequencing data, integrated platform, view ontology hierarchies, statistical mining and modelling, collection of data, text mining algorithms collection, data visualization libraries, |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01120, nlx_149208 | http://www.strandls.com/Avadis | SCR_000644 | Access Visualize Analyze Discover, Avadis NGS | 2026-08-02 09:02:55 | 2 | ||||||
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PhenoM - Phenomics of yeast Mutants Resource Report Resource Website |
PhenoM - Phenomics of yeast Mutants (RRID:SCR_006970) | PhenoM | image collection, production service resource, data analysis service, service resource, database, analysis service resource, data or information resource | Database of morphological phenotypes caused by mutation of essential genes in Saccharomyces cerevisiae, it allows storing, retrieving, visualizing and data mining the quantitative single-cell measurements extracted from micrographs of the temperature-sensitive (ts) mutant cells. PhenoM allows users to rapidly search and retrieve raw images and their quantified morphological data for genes of interest. The database also provides several data-mining tools, including a PhenoBlast module for phenotypic comparison between mutant strains and a Gene Ontology module for functional enrichment analysis of gene sets showing similar morphological alterations. About one-fifth of the genes in the budding yeast are essential for haploid viability and cannot be functionally assessed using standard genetic approaches such as gene deletion. To facilitate genetic analysis of essential genes, we and others have assembled collections of yeast strains expressing temperature-sensitive (ts) alleles of essential genes. To explore the phenotypes caused by essential gene mutation we used a panel of genetically engineered fluorescent markers to explore the morphology of cells in the ts strain collection using high-throughput microscopy. The database contains quantitative measurements of 1,909,914 cells and 78,194 morphological images for 775 temperature-sensitive mutants spanning 491 different essential genes in permissive temperature (26* C) and restrictive temperature (32* C). The morphological images were generated by high-content screening (HCS) technology. | phenomics, phenotype, yeast, mutant, cell, morphology, essential gene, gene, high-content screening, microscopy, micrograph, mutant cell, temperature-sensitive allele, allele, genetic analysis, blast, mutation, orf, actin, dna damage, nucleus, mitochondria, plasma membrane, mitotic spindle, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: University of Toronto; Ontario; Canada |
Ontario Research Fund ; Fudan University - University of Toronto Exchange Scholarship ; Canadian Institutes of Health Research GMX-201237; Canadian Institutes of Health Research GMX-211012; Canadian Foundation for Innovation LEF-21475 |
PMID:22009677 | Free | nlx_151489, biotools:phenom, r3d100012722 | https://bio.tools/phenom, https://doi.org/10.17616/R3GJ5J | SCR_006970 | Phenomics of yeast Mutants, Phenomics of yeast Mutants (PhenoM) | 2026-08-03 09:33:13 | 0 | ||||
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FunNet - Transcriptional Networks Analysis Resource Report Resource Website 10+ mentions |
FunNet - Transcriptional Networks Analysis (RRID:SCR_006968) | FunNet | production service resource, data analysis service, software application, data processing software, analysis service resource, service resource, software resource | Functional Analysis of Transcriptional Networks (FunNet) is designed as an integrative tool for analyzing gene co-expression networks built from microarray expression data. The analytical model implemented in this tool involves two abstraction layers: transcriptional (i.e. gene expression profiles) and functional (i.e. biological themes indicating the roles of the analyzed transcripts). A functional analysis technique, which relies on Gene Ontology and KEGG annotations, is applied to extract a list of relevant biological themes from microarray gene expression data. Afterwards multiple-instance representations are built to relate relevant biological themes to their annotated transcripts. An original non-linear dynamical model is used to quantify the contextual proximity of relevant genomic themes based on their patterns of propagation in the gene co-expression network (i.e. capturing the similarity of the expression profiles of the transcriptional instances of annotating themes). In the end an unsupervised multiple-instance spectral clustering procedure is used to explore the modular architecture of the co-expression network by grouping together biological themes demonstrating a significant relationship in the co-expression network. Functional and transcriptional representations of the co-expression network are provided, together with detailed information on the contextual centrality of related transcripts and genomic themes. FunNet is provided both as a web-based tool and as a standalone R package. The standalone R implementation can be run on any operating system for which an R environment implementation is available (Windows, Mac OS, various flavors of Linux and Unix) and can be downloaded from the FunNet website, or from the worldwide mirrors of CRAN. Both implementations of the FunNet tool are provided freely under the GNU General Public License 2.0. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | genome, transcriptional interaction, microarray, gene expression, statistical analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: KEGG has parent organization: Cordelier Research Center |
PMID:18208606 | Free for academic use, GNU General Public License, v2 | nlx_149243 | SCR_006968 | Functional Analysis of Transcriptional Networks, Functional Analysis of Transcriptional Networks (FunNet) | 2026-08-03 09:33:14 | 16 | ||||||
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GOblet Resource Report Resource Website 1+ mentions |
GOblet (RRID:SCR_006998) | GOblet | production service resource, data analysis service, software application, analysis service resource, service resource, software resource | Tool that performs annotation based on GO and pathway terms for anonymous cDNA or protein sequences. It uses the species independent GO structure and vocabulary together with a series of protein databases collected from various sites, to perform a detailed GO annotation by sequence similarity searches. The sensitivity and the reference protein sets can be selected by the user. GOblet runs automatically and is available as a public service on our web server. GOblet expects query sequences to be in FASTA-Format (with header-lines). Protein and nucleotide sequences are accepted. Total size of all sequences submitted per request should not be larger than 50kb currently. For security reasons: Larger post's will be rejected. Due to limited capacities the queries may be processed in batches depending on the server load. The output of the BLAST job is filtered automatically and the relevant hits are displayed. In addition, the respective GO-terms are shown together with the complete GO-hierarchy of parent terms., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, sequence, cdna, ontology or annotation browser, pathway, term enrichment, clustering, virus, genomic, protein, nucleotide |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology has parent organization: Max Planck Institute for Molecular Genetics; Berlin; Germany |
BMBF | PMID:20134064 PMID:15215401 PMID:12824400 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30624, OMICS_02271 | http://goblet.molgen.mpg.de | SCR_006998 | 2026-08-03 09:33:15 | 6 | |||||
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agriGO Resource Report Resource Website 1000+ mentions |
agriGO (RRID:SCR_006989) | agriGO | production service resource, data analysis service, data or information resource, database, analysis service resource, service resource | A web-based tool and database for the gene ontology analysis. Its focus is on agricultural species and is user-friendly. The agriGO is designed to provide deep support to agricultural community in the realm of ontology analysis. Compared to other available GO analysis tools, unique advantages and features of agriGO are: # The agriGO especially focuses on agricultural species. It supports 45 species and 292 datatypes currently. And agriGO is designed as an user-friendly web server. # New tools including PAGE (Parametric Analysis of Gene set Enrichment), BLAST4ID (Transfer IDs by BLAST) and SEACOMPARE (Cross comparison of SEA) were developed. The arrival of these tools provides users with possibilities for data mining and systematic result exploration and will allow better data analysis and interpretation. # The exploratory capability and result visualization are enhanced. Results are provided in different formats: HTML tables, tabulated text files, hierarchical tree graphs, and flash bar graphs. # In agriGO, PAGE and SEACOMPARE can be used to carry out cross-comparisons of results derived from different data sets, which is very important when studying multiple groups of experiments, such as in time-course research. Platform: Online tool, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | browser, gene, online tool, visualization, statistical analysis, term enrichment, text mining, ontology or annotation browser, ontology or annotation visualization, database or data warehouse, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: China Agricultural University; Beijing; China |
Ministry of Science and Technology of China 90817006; Ministry of Science and Technology of China 2006CB100105 |
PMID:20435677 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149099, OMICS_02265, biotools:agrigo | https://bio.tools/agrigo | SCR_006989 | agriGO -- GO Analysis Toolkit and Database for Agricultural Community | 2026-08-03 09:33:15 | 1716 | ||||
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YeTFaSCo Resource Report Resource Website 10+ mentions |
YeTFaSCo (RRID:SCR_006893) | YeTFaSCo | data repository, production service resource, data analysis service, service resource, database, storage service resource, analysis service resource, data or information resource | Collection of all available transcription factor (TF) specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats. The specificities are evaluated for quality using several metrics. With this website, you can scan sequences with the motifs to find where potential binding sites lie, inspect precomputed genome-wide binding sites, find which TFs have similar motifs to one you have found, and download the collection of motifs. Submissions are welcome. | transcription factor, binding site, sequence, yeast, motif, gene, genome, protein, protein complex |
is listed by: OMICtools is related to: Gene Ontology has parent organization: University of Toronto; Ontario; Canada |
Ontario Graduate Scholarship awards ; Canadian Institutes of Health Research Operating Grant MOP-490425; Canadian Institutes of Health Research Operating Grant MOP-86705 |
PMID:22102575 | Acknowledgement requested | nlx_151611, OMICS_01861 | SCR_006893 | Yeast Transcription Factor Specificity Compendium, YeTFaSCo: The Yeast Transcription Factor Specificity Compendium | 2026-08-03 09:33:12 | 34 | |||||
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OBO Resource Report Resource Website 100+ mentions |
OBO (RRID:SCR_007083) | OBO | knowledge environment, standard specification, ontology, narrative resource, controlled vocabulary, data or information resource | A collaboration involving developers of science-based ontologies who are establishing a set of principles for ontology development with the goal of creating a suite of orthogonal interoperable reference ontologies in the biomedical domain. In addition to a listing of OBO ontologies, this site provides a statement of the OBO Foundry principles, discussion fora, technical infrastructure, and other services to facilitate ontology development. Feedback is welcome and participation encouraged. | biomedical, metadata standard, gold standard, FASEB list |
lists: CHEBI lists: NCI Thesaurus lists: Porifera Ontology lists: Gazetteer lists: Human Disease Ontology lists: Information Artifact Ontology lists: Teleost Anatomy Ontology lists: Gene Ontology lists: Spider Ontology lists: Mental Functioning Ontology lists: Ascomycete Phenotype Ontology lists: Beta Cell Genomics Ontology lists: Biological Collections Ontology lists: Emotion Ontology lists: Chemical Methods Ontology lists: Chemical Information Ontology lists: Clinical Measurement Ontology lists: Common Anatomy Reference Ontology lists: Experimental Conditions Ontology lists: Dictyostelium Discoideum Anatomy Ontology lists: Fission Yeast Phenotype Ontology lists: Fly Taxonomy lists: FlyBase Controlled Vocabulary lists: Hymenoptera Anatomy Ontology lists: Influenza Ontology lists: Lipid Ontology lists: Kinetic Simulation Algorithm Ontology lists: Malaria Ontology lists: Measurement Method Ontology lists: Minimal Anatomical Terminology lists: Ontology for Genetic Interval lists: Ontology for Parasite LifeCycle lists: Ontology of Adverse Events lists: Ontology of Medically Related Social Entities lists: Ontology of Vaccine Adverse Events lists: Rat Strain Ontology lists: Plant Environmental Conditions lists: Plant Trait Ontology lists: Population and Community Ontology lists: RNA Ontology lists: Rat Strain Ontology lists: Subcellular Anatomy Ontology lists: Software Ontology lists: Suggested Ontology for Pharmacogenomics lists: Vertebrate Taxonomy Ontology lists: Physico-Chemical Process lists: Adverse Event Reporting Ontology lists: Xenopus Anatomy Ontology lists: Cell Line Ontology lists: Human Phenotype Ontology lists: Neurobehavior Ontology lists: Ontology for Biomedical Investigations lists: Comparative Data Analysis Ontology lists: Ontology for General Medical Science lists: Physico-Chemical Methods and Properties lists: Gene Regulation Ontology is listed by: FORCE11 is related to: MeGO is related to: Drosophila anatomy and development ontologies is related to: Cell Type Ontology is related to: OBO-Edit is related to: go-perl is related to: OWLTools is related to: Zebrafish Anatomical Ontology is related to: OBO Tracker: Plant Ontology (PO) TERM requests is related to: eVOC is related to: OnEx - Ontology Evolution Explorer is related to: BioPerl is related to: dkCOIN is related to: Standards-based Infrastructure with Distributed Resources is related to: OntoVisT is related to: COBrA is related to: Wandora is related to: ONTO-PERL is related to: Genomic Standards Consortium is related to: Ontology Lookup Service is related to: LexGrid is related to: SBO is related to: RIKEN integrated database of mammals is related to: DOAF is related to: Gene Ontology is related to: African Population Ontology has parent organization: Berkeley Bioinformatics Open-Source Projects is parent organization of: OBO Relation Ontology is parent organization of: SO is parent organization of: PATO is parent organization of: MPO is parent organization of: AEO is parent organization of: UBERON |
PMID:17989687 | nlx_22892 | SCR_007083 | The Open Biomedical Ontologies, OBO Foundry, Open Biological and Biomedical Ontologies, Open Biological and Biomedical Ontology Foundry | 2026-08-03 09:33:21 | 169 | |||||||
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Organelle DB Resource Report Resource Website 1+ mentions |
Organelle DB (RRID:SCR_007837) | Organelle DB | image collection, data repository, d spatial image, data or information resource, database, storage service resource, service resource | Database of organelle proteins, and subcellular structures / complexes from compiled protein localization data from organisms spanning the eukaryotic kingdom. All data may be downloaded as a tab-delimited text file and new localization data (and localization images, etc) for any organism relevant to the data sets currently contained in Organelle DB is welcomed. The data sets in Organelle DB encompass 138 organisms with emphasis on the major model systems: S. cerevisiae, A. thaliana, D. melanogaster, C. elegans, M. musculus, and human proteins as well. In particular, Organelle DB is a central repository of yeast protein localization data, incorporating results from both previous and current (ongoing) large-scale studies of protein localization in Saccharomyces cerevisiae. In addition, we have manually curated several recent subcellular proteomic studies for incorporation in Organelle DB. In total, Organelle DB is a singular resource consolidating our knowledge of the protein composition of eukaryotic organelles and subcellular structures. When available, we have included terms from the Gene Ontologies: the cellular component, molecular function, and biological process fields are discussed more fully in GO. Additionally, when available, we have included fluorescent micrographs (principally of yeast cells) visualizing the described protein localization. Organelle View is a visualization tool for yeast protein localization. It is a visually engaging way for high school and undergraduate students to learn about genetics or for visually-inclined researchers to explore Organelle DB. By revealing the data through a colorful, dimensional model, we believe that different kinds of information will come to light. | gene, fly, vertebrate, human, mouse, plant, worm, yeast, protein, k-12, organelle, protein localization, function, subcellular structure, protein complex, sequence, annotation, micrograph, visualization, data analysis service |
is related to: Gene Ontology has parent organization: University of Michigan; Ann Arbor; USA |
American Cancer Society Research Scholar Grant RSG-06-179-01-MBC; March of Dimes Basil O'Connor Starter Scholar Research award 5-FY05-1224; NSF DBI-0543017 |
PMID:17130152 PMID:15608270 |
Free, Acknowledgement requested | nif-0000-03226 | SCR_007837 | Organelle DB: A Database of Organelles and Protein Complexes | 2026-08-03 09:33:33 | 7 | |||||
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Network Analysis, Visualization and Graphing TORonto Resource Report Resource Website 50+ mentions |
Network Analysis, Visualization and Graphing TORonto (RRID:SCR_008373) | NAViGaTOR | software application, data processing software, d visualization software, software resource, data visualization software | A software package for visualizing and analyzing protein-protein interaction networks. NAViGaTOR can query OPHID / I2D - online databases of interaction data - and display networks in 2D or 3D. To improve scalability and performance, NAViGaTOR combines Java with OpenGL to provide a 2D/3D visualization system on multiple hardware platforms. NAViGaTOR also provides analytical capabilities and supports standard import and export formats such as GO and the Proteomics Standards Initiative (PSI). NAViGaTOR can be installed and run on Microsoft Windows, Linux / UNIX, and Mac OS systems. NAViGaTOR is written in Java and uses JOGL (Java bindings for OpenGL) to support scalability, highlighting or suppressing of information, and other advanced graphic approaches. | fly, algorithm, capacity, graphical, graphing, human, interaction, interactome, intersection, mouse, network, node, protein, proteomic, rat, worm, yeast, graphing application, 2d visualization, 3d visualization, visualization, biological network, protein-protein interaction, gene, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: University of Toronto; Ontario; Canada |
Genome Canada ; Ontario Genomics Institute ; Canada Research Chair Program ; Ontario Research Fund Research Excellence ; Canada Foundation for Innovation 12301; Canada Foundation for Innovation 203383 |
PMID:19837718 | Freely-downloadable for academic and not-for-profit institutions | nif-0000-25610, biotools:navigator | https://bio.tools/navigator | SCR_008373 | NAViGaTOR - Network Analysis Visualization and Graphing TORonto, NAViGaTOR - Network Analysis Visualization & Graphing TORonto | 2026-08-03 09:34:01 | 52 | ||||
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OnEx - Ontology Evolution Explorer Resource Report Resource Website 1+ mentions |
OnEx - Ontology Evolution Explorer (RRID:SCR_000602) | OnEx | software resource, web application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Web-based application that integrates versions of 16 life science ontologies including the Gene Ontology, NCI Thesaurus and selected OBO ontologies with data leading back to 2002 in a common repository to explore ontology changes. It allows to study and apply the evolution of these integrated ontologies on three different levels. It provides global ontology evolution statistics and ontology-specific evolution trends for concepts and relationships and it allows the migration of annotations in case a new ontology version was released | ontology, gene, protein, function, process, component, ontology or annotation browser, evolution, trend, annotation, version |
is listed by: OMICtools is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: NCI Thesaurus is related to: OBO has parent organization: University of Leipzig; Saxony; Germany |
BMBF 01AK803E; DFG |
PMID:19678926 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02273, nlx_149129 | http://www.izbi.de/onex, http://aprilia.izbi.uni-leipzig.de:8080/onex/ | SCR_000602 | Ontology Evolution Explorer (OnEx), Ontology Evolution Explorer | 2026-08-03 09:31:06 | 1 | ||||
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categoryCompare Resource Report Resource Website 1+ mentions |
categoryCompare (RRID:SCR_001223) | categoryCompare | software resource, data processing software, software application, data analysis software | A software package for meta-analysis of high-throughput experiments using feature annotations. It calculates significant annotations (categories) in each of two (or more) feature (i.e. gene) lists, determines the overlap between the annotations, and returns graphical and tabular data about the significant annotations and which combinations of feature lists the annotations were found to be significant. Interactive exploration is facilitated through the use of RCytoscape (heavily suggested). | annotation, go, gene expression, multiple comparison, pathway, gene |
uses: Cytoscape is listed by: OMICtools is related to: Gene Ontology is related to: CRAN has parent organization: Bioconductor |
PMID:24808906 | Free, Available for download, Freely available | OMICS_02122 | SCR_001223 | categoryCompare - Meta-analysis of high-throughput experiments using feature annotations | 2026-08-03 09:31:19 | 9 | ||||||
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globaltest Resource Report Resource Website 10+ mentions |
globaltest (RRID:SCR_001256) | globaltest | sequence analysis software, software application, data processing software, data analysis software, software resource | A software package that tests groups of covariates (or features) for association with a response variable. The package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms. | differential expression, go, microarray, one channel, pathway, bio.tools |
uses: KEGG is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: Bioconductor |
PMID:34046931 | Free, Available for download, Freely available | biotools:globaltest, OMICS_02084 | https://bio.tools/globaltest | SCR_001256 | 2026-08-03 09:31:16 | 30 | ||||||
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CELDA Ontology Resource Report Resource Website |
CELDA Ontology (RRID:SCR_001601) | CELDA | controlled vocabulary, data or information resource, ontology | Structured vocabulary to organize cell-associated data and to place these data in clearly defined semantic relations to other biological facts. It describes cell types, their properties and origin and links this information to other existing ontologies like the Cell Ontology (CL), Foundational Model of Anatomy (FMA), Gene Ontology (GO), Mouse Anatomy and others using the top-level ontology BioTop. | cell, expression, localization, development, anatomy, cell type, development, organ, kidney, liver, skin |
is related to: Cell Type Ontology is related to: FMA is related to: Gene Ontology has parent organization: CellFinder |
Seoul National University; Seoul; South Korea ; Research Institute for Veterinary Science ; DFG KU 851/3-1; DFG LE 1428/3-1; DFG JA 1904/2-1 |
PMID:23865855 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153858 | SCR_001601 | Cell: Expression Localization Development Anatomy, CellFinder Ontology, CELDA Ontology | 2026-08-03 09:31:25 | 0 | |||||
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MatrixDB Resource Report Resource Website 50+ mentions |
MatrixDB (RRID:SCR_001727) | MatrixDB | service resource, data or information resource, database, production service resource | Freely available database focused on interactions established by extracellular proteins and polysaccharides, taking into account the multimeric nature of the extracellular proteins (e.g. collagens, laminins and thrombospondins are multimers). MatrixDB is an active member of the International Molecular Exchange (IMEx) consortium and has adopted the PSI-MI standards for annotating and exchanging interaction data. It includes interaction data extracted from the literature by manual curation, and offers access to relevant data involving extracellular proteins provided by the IMEx partner databases through the PSICQUIC webservice, as well as data from the Human Protein Reference Database. The database reports mammalian protein-protein and protein-carbohydrate interactions involving extracellular molecules. Interactions with lipids and cations are also reported. MatrixDB is focused on mammalian interactions, but aims to integrate interaction datasets of model organisms when available. MatrixDB provides direct links to databases recapitulating mutations in genes encoding extracellular proteins, to UniGene and to the Human Protein Atlas that shows expression and localization of proteins in a large variety of normal human tissues and cells. MatrixDB allows researchers to perform customized queries and to build tissue- and disease-specific interaction networks that can be visualized and analyzed with Cytoscape or Medusa. Statistics (2013): 2283 extracellular matrix interactions including 2095 protein-protein and 169 protein-glycosaminoglycan interactions. | extracellular, protein fragment, biomolecule, cation, cleavage, collagen, glycosaminoglycan, human, interaction, laminin, lipid, mammalian, matricryptin, matrikin, matrix, molecule, monomer, mulimerization, multimer, polysaccharide, protein, protein-carbohydrate interaction, protein-protein interaction, recognition, thrombospondin, interactome, extracellular protein, protein-polysaccharide interaction, extracellular interaction, molecular interaction, model organism, inorganic, small molecule-protein, small molecule, extracellular matrix protein, protein-glycosaminoglycan interaction, bio.tools, FASEB list |
is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: IMEx - The International Molecular Exchange Consortium is related to: Gene Ontology is related to: PSI-MI is related to: HPRD - Human Protein Reference Database is related to: Interaction Reference Index is related to: ConsensusPathDB is related to: IMEx - The International Molecular Exchange Consortium is related to: PSICQUIC Registry is related to: IntAct has parent organization: Claude Bernard University Lyon 1; Lyon; France |
European Union contract FP7-HEALTH-2007-223411 | PMID:20852260 PMID:19147664 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:matrixdb, r3d100010672, nif-0000-10226 | https://bio.tools/matrixdb, https://doi.org/10.17616/R3M03H | http://matrixdb.ibcp.fr/ | SCR_001727 | MatrixDB: Extracellular Matrix Interactions Database, Extracellular Matrix Interactions Database | 2026-08-03 09:31:25 | 86 | |||
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Kidney and Urinary Pathway Knowledge Base Resource Report Resource Website 1+ mentions |
Kidney and Urinary Pathway Knowledge Base (RRID:SCR_001746) | KUPKB | data repository, production service resource, data analysis service, service resource, storage service resource, analysis service resource, data or information resource, data set | A collection of omics datasets (mRNA, proteins and miRNA) that have been extracted from PubMed and other related renal databases, all related to kidney physiology and pathology giving KUP biologists the means to ask queries across many resources in order to aggregate knowledge that is necessary for answering biological questions. Some microarray raw datasets have also been downloaded from the Gene Expression Omnibus and analyzed by the open-source software GeneArmada. The Semantic Web technologies, together with the background knowledge from the domain's ontologies, allows both rapid conversion and integration of this knowledge base. SPARQL endpoint http://sparql.kupkb.org/sparql The KUPKB Network Explorer will help you visualize the relationships among molecules stored in the KUPKB. A simple spreadsheet template is available for users to submit data to the KUPKB. It aims to capture a minimal amount of information about the experiment and the observations made. | kidney, urinary, urine, pathway, molecule, visualizer, gene, protein, mirna, metabolite, mrna, microarray, ortholog, rdf, renal cell, anatomy, animal model, disease, sparql, proteomics, ontology, biomarker, gene expression, physiology, pathology |
is related to: NIDDK Information Network (dkNET) is related to: Gene Expression Omnibus is related to: Gene Ontology is related to: KEGG has parent organization: University of Manchester; Manchester; United Kingdom has parent organization: National Institute of Health and Medical Research; Rennes; France |
Kidney disease | European Union ; FP7 ; ICT-2007.4.4 e-LICO project |
PMID:21624162 | THIS RESOURCE IS NO LONGER IN SERVICE. | nlx_154134 | http://www.e-lico.eu/kupkb | SCR_001746 | Kidney & Urinary Pathway Knowledge Base | 2026-08-03 09:31:29 | 2 | |||
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MouseCyc Resource Report Resource Website 1+ mentions |
MouseCyc (RRID:SCR_001791) | MouseCyc | production service resource, data analysis service, service resource, database, analysis service resource, data or information resource | A manually curated database of both known and predicted metabolic pathways for the laboratory mouse. It has been integrated with genetic and genomic data for the laboratory mouse available from the Mouse Genome Informatics database and with pathway data from other organisms, including human. The database records for 1,060 genes in Mouse Genome Informatics (MGI) are linked directly to 294 pathways with 1,790 compounds and 1,122 enzymatic reactions in MouseCyc. (Aug. 2013) BLAST and other tools are available. The initial focus for the development of MouseCyc is on metabolism and includes such cell level processes as biosynthesis, degradation, energy production, and detoxification. MouseCyc differs from existing pathway databases and software tools because of the extent to which the pathway information in MouseCyc is integrated with the wealth of biological knowledge for the laboratory mouse that is available from the Mouse Genome Informatics (MGI) database. | energy production, biosynthesis, cell, cellular, degradation, detoxification, metabolism, mouse, physiological, enzymatic reaction, gene, disease, genome, metabolic pathway, pathway, compound, enzymatic reaction, protein, rna, reaction, blast, human, mammal, genetic, genomic |
is related to: Mouse Genome Informatics (MGI) is related to: Gene Ontology has parent organization: Jackson Laboratory |
NHGRI HG003622 | PMID:19682380 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10303 | SCR_001791 | MouseCyc database, Mouse Genome Informatics: MouseCyc database | 2026-08-03 09:31:30 | 9 | |||||
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Arabidopsis Hormone Database Resource Report Resource Website 10+ mentions |
Arabidopsis Hormone Database (RRID:SCR_001792) | AHD, AHD2.0 | data repository, ontology, service resource, database, storage service resource, controlled vocabulary, data or information resource | Database providing a systematic and comprehensive view of morphological phenotypes regulated by plant hormones, as well as regulatory genes participating in numerous plant hormone responses. By integrating the data from mutant studies, transgenic analysis and gene ontology annotation, genes related to the stimulus of eight plant hormones were identified, including abscisic acid, auxin, brassinosteroid, cytokinin, ethylene, gibberellin, jasmonic acid and salicylic acid. Another pronounced characteristics of this database is that a phenotype ontology was developed to precisely describe all kinds of morphological processes regulated by plant hormones with standardized vocabularies. To increase the coverage of phytohormone related genes, the database has been updated from AHD to AHD2.0 adding and integrating several pronounced features: (1) added 291 newly published Arabidopsis hormone related genes as well as corrected information (e.g. the arguable ABA receptors) based on the recent 2-year literature; (2) integrated orthologues of sequenced plants in OrthoMCLDB into each gene in the database; (3) integrated predicted miRNA splicing site in each gene in the database; (4) provided genetic relationship of these phytohormone related genes mining from literature, which represents the first effort to construct a relatively comprehensive and complex network of hormone related genes as shown in the home page of our database; (5) In convenience to in-time bioinformatics analysis, they also provided links to a powerful online analysis platform Weblab that they have recently developed, which will allow users to readily perform various sequence analysis with these phytohormone related genes retrieved from AHD2.0; (6) provided links to other protein databases as well as more expression profiling information that would facilitate users for a more systematic analysis related to phytohormone research. Please help to improve the database with your contributions. | arabidopsis thaliana, hormone, hormone function, hormone gene, phytohormone, abscisic acid, auxin, brassinosteroid, cytokinin, ethylene, gibberellin, jasmonic acid, salicylic acid, microarray, phenotype, gene, mirna prediction, expression, mutant, blast, orthologue, mirna splicing site, root, cotyledon, leaf, hypocotyl, stem, flower, silique, seed, embryo, stress, morphology, plant, hormone, regulatory gene, mutant, transgenic, annotation, data analysis service |
is related to: Gene Ontology has parent organization: Peking University; Beijing; China |
National Natural Science Foundation of China 30625003; National Natural Science Foundation of China 30730011; Ministry of Science and Technology of China 2009CB119101; Ministry of Education of China ED20060047 |
PMID:21045062 PMID:19015126 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02559 | SCR_001792 | Arabidopsis Hormone Database 2.0 | 2026-08-03 09:31:26 | 28 | |||||
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Diabetes Disease Portal Resource Report Resource Website |
Diabetes Disease Portal (RRID:SCR_001660) | Diabetes Disease Portal | portal, disease-related portal, topical portal, data or information resource, data set | An integrated resource for information on genes, QTLs and strains associated with diabetes. The portal provides easy acces to data related to both Type 1 and Type 2 Diabetes and Diabetes-related Obesity and Hypertension, as well as information on Diabetic Complications. View the results for all the included diabetes-related disease states or choose a disease category to get a pull-down list of diseases. A single click on a disease will provide a list of related genes, QTLs, and strains as well as a genome wide view of these via the GViewer tool. A link from GViewer to GBrowse shows the genes and QTLs within their genomic context. Additional pages for Phenotypes, Pathways and Biological Processes provide one-click access to data related to diabetes. Tools, Related Links and Rat Strain Models pages link to additional resources of interest to diabetes researchers. | gene, quantitative trait locus, strain, diabetic complication, genome, gviewer, genomic, phenotype, pathway, biological process, chromosome, visualization, molecular function, cellular component, synteny |
is related to: NIDDK Information Network (dkNET) is related to: Gene Ontology has parent organization: Rat Genome Database (RGD) |
Type 1 diabetes, Type 2 diabetes, Diabetes, Obesity, Hyperlipidemia, Metaboic disease, Hypertension | Free, Freely Available | nlx_153942 | http://rgd.mcw.edu/rgdCuration/?module=portal&func=show&name=diabetes | SCR_001660 | 2026-08-03 09:31:27 | 0 | ||||||
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Candida Genome Database Resource Report Resource Website 100+ mentions |
Candida Genome Database (RRID:SCR_002036) | CGD, CGD LOCUS, CGD REF | data repository, data or information resource, database, storage service resource, service resource | Database of genetic and molecular biological information about Candida albicans. Contains information about genes and proteins, descriptions and classifications of their biological roles, molecular functions, and subcellular localizations, gene, protein, and chromosome sequence information, tools for analysis and comparison of sequences and links to literature information. Each CGD gene or open reading frame has an individual Locus Page. Genetic loci that are not tied to DNA sequence also have Locus Pages. Provides Gene Ontology, GO, to all its users. Three ontologies that comprise GO (Molecular Function, Cellular Component, and Biological Process) are used by multiple databases to annotate gene products, so that this common vocabulary can be used to compare gene products across species. Development of ontologies is ongoing in order to incorporate new information. Data submissions are welcome. | protein, chromosome, classification, gene, genome, candidiasis, thrush, yeast, yeast gene, yeast genome, candida albicans, candida glabrata, data analysis service, biological role, molecular function, subcellular localization, chromosome sequence, bio.tools, FASEB list |
is used by: NIF Data Federation is listed by: bio.tools is listed by: Debian is related to: AmiGO is related to: ASPGD is related to: Gene Ontology has parent organization: Stanford University School of Medicine; California; USA |
NIDCR DE015873 | PMID:19808938 | Free, Available for download, Freely available | nif-0000-02634, biotools:cgd, r3d100010617 | https://bio.tools/cgd | SCR_002036 | 2026-08-03 09:31:31 | 472 |
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