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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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PAZAR Resource Report Resource Website 10+ mentions |
PAZAR (RRID:SCR_005410) | PAZAR | storage service resource, software resource, data repository, service resource, database, data or information resource | Database that unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. The flexible PAZAR schema permits the representation of diverse information derived from experiments ranging from biochemical protein-DNA binding to cellular reporter gene assays. Data collections can be made available to the public, or restricted to specific system users. The data ''boutiques'' within the shopping-mall-inspired system facilitate the analysis of genomics data and the creation of predictive models of gene regulation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | transcription factor, target gene, regulatory sequence, transcription factor profile, annotation, sequence, profile, transcription factor binding profile, chip, chip-seq, gene, cis-regulatory element, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of British Columbia; British Columbia; Canada has parent organization: SourceForge |
PMID:18971253 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00540, biotools:pazar | https://bio.tools/pazar | SCR_005410 | 2026-08-04 09:41:21 | 32 | ||||||
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MRC Mammalian Genetics Unit Resource Report Resource Website 100+ mentions |
MRC Mammalian Genetics Unit (RRID:SCR_005378) | MGU | topical portal, portal, data or information resource | It is now widely known that animals share many genes with humans and can suffer from the same diseases, for example diabetes or deafness. Investigating these diseases in animals can provide vital leads to understanding both their causes and ways to treat them in humans. This approach to medical research lies at the heart of work at the MRC Mammalian Genetics Unit (MGU) at Harwell in Oxfordshire. In 1995 the MRC Radiobiology Unit was reconstituted to form two new units, the Radiation and Genome Stability Unit and the MGU. These opened in January 1996, together with the UK Mouse Genome Centre which is now part of MGU, making MRC Harwell a unique campus for multi-disciplinary genetics research. Since MGU's Director Steve Brown took the reins in 1996, the unit has dramatically expanded its scientific scope and increased its personnel from 40 to over 100. It now has 13 research programs encompassing molecular genetics, genomics, genetic manipulation and data analysis at all levels, from single genes to the whole genome. With a combination of cutting-edge facilities and expertise unrivaled in Europe, MGU Harwell has become firmly established as one of the world's leading academic centres for mouse genetics. | mouse, genetics, gene |
is parent organization of: European Mouse Phenotyping Resource of Standardised Screens is parent organization of: Europhenome Mouse Phenotyping Resource is parent organization of: International Mouse Strain Resource |
nlx_144449 | http://www.mrc.ac.uk/Ourresearch/Unitscentresinstitutes/Profiles/MGU/index.htm | SCR_005378 | Medical Research Council Mammalian Genetics Unit, MGU Harwell, MRC MGU | 2026-08-04 09:41:20 | 236 | |||||||
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Synergizer Resource Report Resource Website 1+ mentions |
Synergizer (RRID:SCR_005308) | Synergizer | data analysis service, analysis service resource, web service, software resource, data access protocol, production service resource, service resource | The Synergizer database is a growing repository of gene and protein identifier synonym relationships. This tool facilitates the conversion of identifiers from one naming scheme (a.k.a namespace) to another. The Synergizer is a service for translating between sets of biological identifiers. It can, for example, translate Ensembl Gene IDs to Entrez Gene IDs, or IPI IDs to HGNC gene symbols, and much more. Unlike some other tools for this purpose, The Synergizer is simple and easy to learn. The Synergizer works via a web interface (for users who are not programmers) or through a web service (for programmatic access). | gene, protein, json | has parent organization: University of Toronto; Ontario; Canada | nlx_144380 | SCR_005308 | The Synergizer | 2026-08-04 09:41:20 | 9 | ||||||||
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Brain Basics Resource Report Resource Website |
Brain Basics (RRID:SCR_005606) | Brain Basics | narrative resource, data or information resource, training material, video resource | Brain Basics provides information on how the brain works, how mental illnesses are disorders of the brain, and ongoing research that helps us better understand and treat disorders. Mental disorders are common. You may have a friend, colleague, or relative with a mental disorder, or perhaps you have experienced one yourself at some point. Such disorders include depression, anxiety disorders, bipolar disorder, attention deficit hyperactivity disorder (ADHD), and many others. Some people who develop a mental illness may recover completely; others may have repeated episodes of illness with relatively stable periods in between. Still others live with symptoms of mental illness every day. They can be moderate, or serious and cause severe disability. Through research, we know that mental disorders are brain disorders. Evidence shows that they can be related to changes in the anatomy, physiology, and chemistry of the nervous system. When the brain cannot effectively coordinate the billions of cells in the body, the results can affect many aspects of life. Scientists are continually learning more about how the brain grows and works in healthy people, and how normal brain development and function can go awry, leading to mental illnesses. Brain Basics will introduce you to some of this science, such as: * How the brain develops * How genes and the environment affect the brain * The basic structure of the brain * How different parts of the brain communicate and work with each other * How changes in the brain can lead to mental disorders, such as depression. | brain, depression, anxiety disorder, bipolar disorder, attention deficit-hyperactivity disorder, depressive disorder, mental disease, gene, environment | has parent organization: NIMH Educational Resources | NIMH | nlx_146226 | SCR_005606 | NIMH Brain Basics | 2026-08-04 09:41:23 | 0 | |||||||
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CoPub Resource Report Resource Website 1+ mentions |
CoPub (RRID:SCR_005327) | CoPub | data access protocol, software resource, service resource, web service | Text mining tool that detects co-occuring biomedical concepts in abstracts from the MedLine literature database. It allows batch input of multiple human, mouse or rat genes and produces lists of keywords from several biomedical thesauri that are significantly correlated with the set of input genes. These lists link to Medline abstracts in which the co-occurring input genes and correlated keywords are highlighted. Furthermore, CoPub can graphically visualize differentially expressed genes and over-represented keywords in a network, providing detailed insight in the relationships between genes and keywords, and revealing the most influential genes as highly connected hubs. | microarray, gene, literature, enrich, annotate, network, database, differential expression, bio.tools |
uses: MEDLINE uses: Gene Ontology is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Netherlands Bioinformatics Centre |
Netherlands Bioinformatics Centre | PMID:18442992 | Free, Public, Acknowledgement requested | OMICS_01178, biotools:copub | https://bio.tools/copub | http://services.nbic.nl/cgi-bin/copub/CoPub.pl | SCR_005327 | 2026-08-04 09:41:20 | 5 | ||||
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Genetic Testing Registry Resource Report Resource Website 10+ mentions |
Genetic Testing Registry (RRID:SCR_005565) | GTR | storage service resource, data repository, service resource, database, data or information resource | Central location for voluntary submission of genetic test information by providers including the test''s purpose, methodology, validity, evidence of the test''s usefulness, and laboratory contacts and credentials. GTR aims to advance the public health and research into the genetic basis of health and disease. GTR is accepting registration of clinical tests for Mendelian disorders, complex tests and arrays, and pharmacogenetic tests. These tests may include multiple methods and may include multiple major method categories such as biochemical, cytogenetic, and molecular tests. GTR is not currently accepting registration of tests for somatic disorders, research tests or direct-to-consumer tests. | genetic, gene, clinical, genetic test, condition, phenotype, disease name, trait, drug, protein, analyte, disease, laboratory, molecular, clinical, genetics, people |
lists: MedGen is listed by: OMICtools has parent organization: NCBI |
The community can contribute to this resource | nlx_144654, OMICS_01541 | SCR_005565 | NIH Genetic Testing Registry, GTR: Genetic Testing Registry | 2026-08-04 09:41:23 | 35 | |||||||
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BrainStars Resource Report Resource Website 10+ mentions |
BrainStars (RRID:SCR_005810) | B* | web service, software resource, data access protocol, database, data or information resource | BrainStars (or B*) is a quantitative expression database of the adult mouse brain. The database has genome-wide expression profile at 51 adult mouse CNS regions. For 51 CNS regions, slices (0.5-mm thick) of mouse brain were cut on a Mouse Brain Matrix, frozen, and the specific regions were punched out bilaterally with a microdissecting needle (gauge 0.5 mm) under a stereomicroscope. For each region, we took samples every 4 hours, starting at ZT0 (Zeitgaber time 0; the time of lights on), for 24 hours (6 time-point samples for each region), and we pooled the samples from the different time points. We independently sampled each region twice (n=2). These samples were purified their RNA, and measured with Affymetrix GeneChip Mouse Genome 430 2.0 arrays. Expression values were then summarized with the RMA method. After several analysis with the expression data, the data and analysis results were stored in the BrainStars database. The database has a REST-like Web API interface for accessing from your Web applications. This document shows how to access the database via our Web API. | mouse, brain, adult, expression profile, affymetrix genechip mouse genome 430 2.0 array, rna, central nervous system, gene expression, gene |
is related to: Allen Mouse Brain Reference Atlas is related to: Allen Institute for Brain Science has parent organization: RIKEN has parent organization: Kindai University School of Medicine; Osaka; Japan |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | PMID:21858037 | BrainStars data, Images and texts (excluding ABA data and images) are licensed under a Creative Commons Attribution 2.1 Japan License. | nlx_149301 | SCR_005810 | BrainStars Database, BrainStars (B*) | 2026-08-04 09:41:27 | 14 | |||||
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GARBAN Resource Report Resource Website |
GARBAN (RRID:SCR_005778) | GARBAN | data analysis service, source code, analysis service resource, software resource, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 12, 2012. GARBAN is a tool for analysis and rapid functional annotation of data arising from cDNA microarrays and proteomics techniques. GARBAN has been implemented with bioinformatic tools to rapidly compare, classify, and graphically represent multiple sets of data (genes/ESTs, or proteins), with the specific aim of facilitating the identification of molecular markers in pathological and pharmacological studies. GARBAN has links to the major genomic and proteomic databases (Ensembl, GeneBank, UniProt Knowledgebase, InterPro, etc.), and follows the criteria of the Gene Ontology Consortium (GO) for ontological classifications. Source may be shared: e-mail garban (at) ceit.es. Platform: Online tool | cdna microarray, proteomics, cdna, microarray, statistical analysis, gene, est, protein, genomic, gene ontology |
is listed by: Gene Ontology Tools is related to: Gene Ontology |
PMID:14594726 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149247 | http://garban.tecnun.es | SCR_005778 | Genomic Analysis and Rapid Biological ANnotation, University of Navarra; Pamplona; Spain | 2026-08-04 09:41:26 | 0 | |||||
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FunCluster Resource Report Resource Website 1+ mentions |
FunCluster (RRID:SCR_005774) | FunCluster | data processing software, software application, software resource, data analysis software | FunCluster is a genomic data analysis algorithm which performs functional analysis of gene expression data obtained from cDNA microarray experiments. Besides automated functional annotation of gene expression data, FunCluster functional analysis aims to detect co-regulated biological processes through a specially designed clustering procedure involving biological annotations and gene expression data. FunCluster''''s functional analysis relies on Gene Ontology and KEGG annotations and is currently available for three organisms: Homo Sapiens, Mus Musculus and Saccharomyces Cerevisiae. FunCluster is provided as a standalone R package, which can be run on any operating system for which an R environment implementation is available (Windows, Mac OS, various flavors of Linux and Unix). Download it from the FunCluster website, or from the worldwide mirrors of CRAN. FunCluster is provided freely under the GNU General Public License 2.0. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | genomic, gene, functional analysis, gene expression, cdna microarray, cdna, microarray, function, cluster, annotation, biological process, statistical analysis, bio.tools |
is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology has parent organization: Cordelier Research Center |
PMID:17007070 PMID:16506959 PMID:16046292 |
Free for academic use, GNU General Public License, v2 | nlx_149242, biotools:funcluster | https://bio.tools/funcluster | SCR_005774 | FunCluster R Package, FunCluster Algorithm | 2026-08-04 09:41:26 | 2 | |||||
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GREAT: Genomic Regions Enrichment of Annotations Tool Resource Report Resource Website 50+ mentions |
GREAT: Genomic Regions Enrichment of Annotations Tool (RRID:SCR_005807) | GREAT | data analysis service, source code, analysis service resource, software resource, production service resource, service resource | Data analysis service that predicts functions of cis-regulatory regions identified by localized measurements of DNA binding events across an entire genome. Whereas previous methods took into account only binding proximal to genes, GREAT is able to properly incorporate distal binding sites and control for false positives using a binomial test over the input genomic regions. GREAT incorporates annotations from 20 ontologies and is available as a web application. The utility of GREAT extends to data generated for transcription-associated factors, open chromatin, localized epigenomic markers and similar functional data sets, and comparative genomics sets. Platform: Online tool | term enrichment, cis-regulatory region, function, gene, genomic, annotation, ontology, chromatin immunoprecipitation, sequencing, chip-seq, comparative genomics, transcription factor binding |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: PRISM (Stanford database) is related to: Gene Ontology has parent organization: Stanford University School of Medicine; California; USA |
Bio-X ; Howard Hughes Medical Institute ; Stanford University; California; USA ; Packard ; Searle Scholar ; Microsoft Research ; Alfred P. Sloan Foundation ; Edward Mallinckrodt Jr. Foundation ; NIH ; Human Frontier Science Program fellowship LT000896/2009-l; NICHD 1R01HD059862; NHGRI R01HG005058; NSF CCF-0939370; DFG Hi 1423/2-1 |
PMID:20436461 PMID:23814184 |
Free for academic use, Acknowledgement requested | nlx_149295, OMICS_00635 | SCR_005807 | Genomic Regions Enrichment of Annotations Tool (GREAT), Genomic Regions Enrichment of Annotations Tool | 2026-08-04 09:41:27 | 82 | |||||
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GOHyperGAll Resource Report Resource Website 1+ mentions |
GOHyperGAll (RRID:SCR_005766) | GOHyperGAll | data processing software, software application, software resource, data analysis software | To test a sample population of genes for overrepresentation of GO terms, the R/BioC function GOHyperGAll computes for all GO nodes a hypergeometric distribution test and returns the corresponding p-values. A subsequent filter function performs a GO Slim analysis using default or custom GO Slim categories. Basic knowledge about R and BioConductor is required for using this tool. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, gene ontology, annotation, statistical analysis, slimmer-type tool |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of California at Riverside; California; USA |
PMID:18354039 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149267 | SCR_005766 | 2026-08-04 09:41:26 | 4 | |||||||
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Expression Atlas of the Marmoset Resource Report Resource Website 1+ mentions |
Expression Atlas of the Marmoset (RRID:SCR_005760) | Marmoset Expression Atlas, RIKEN Marmoset Expression Atlas | expression atlas, data set, atlas, data or information resource | Database of gene expression in the marmoset brain.Comparative anatomy of marmoset and mouse cortex from genomic expression. Atlas comparing brain of neonatal marmoset with mouse using in situ hybridization. | gene, marmoset, gene expression, neonatal, brain, in situ hybridization, gene, cortex, thalamus, dorsal nucleus of lateral geniculate body, dlgn, subplate, hippocampus, primary somatosensory cortex, btbd3, cdh6, cdh8, cplx3, ctgf, epha4, epha5, epha6, epha7, efna5, er81, foxp2, gfralpha1, kitl, lhx9, nr1d1, nr4a2, ntng2, relin, roralpha, satb2, sema6a, tbr1, tcf7l2, zic1, zic4, genomic expression |
is used by: NIF Data Federation has parent organization: RIKEN Brain Science Institute |
RIKEN Brain Science Institute ; Japanese Ministry of Education Culture Sports Science and Technology MEXT ; Funding Program for World-Leading Innovative RD on Science and Technology |
PMID:22496550 | nlx_149225 | http://mmtd.brain.riken.jp/P0marmoset/ | SCR_005760 | Marmoset Gene List, Comparative Anatomy of Marmoset and Mouse Cortex from Genomic Expression, Comparative Anatomy of Marmoset Mouse Cortex from Genomic Expression | 2026-08-04 09:41:26 | 1 | |||||
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TRANSPATH Resource Report Resource Website 1+ mentions |
TRANSPATH (RRID:SCR_005640) | TRANSPATH | data analysis service, analysis service resource, production service resource, service resource, database, data or information resource | Database on eukaryotic transcription factors, their experimentally-proven binding sites, consensus binding sequences (positional weight matrices) and regulated genes. Its broad compilation of binding sites allows the derivation of positional weight matrices. It can either be used as an encyclopedia, for both specific and general information on signal transduction, or can serve as a network analyzer. Cross-references to important sequence and signature databases such as EMBL/GenBank UniProt/Swiss-Prot InterPro or Ensembl EntrezGene RefSeq are provided. The database is equipped with the tools for data visualization and analysis. It has three modules: the first one is the data, which have been manually extracted, mostly from the primary literature; the second is PathwayBuilder, which provides several different types of network visualization and hence facilitates understanding; the third is ArrayAnalyzer, which is particularly suited to gene expression array interpretation, and is able to identify key molecules within signalling networks (potential drug targets). These key molecules could be responsible for the coordinated regulation of downstream events. Manual data extraction focuses on direct reactions between signalling molecules and the experimental evidence for them, including species of genes/proteins used in individual experiments, experimental systems, materials and methods. This combination of materials and methods is used in TRANSPATH to assign a quality value to each experimentally proven reaction, which reflects the probability that this reaction would happen under physiological conditions. Another important feature in TRANSPATH is the inclusion of transcription factor-gene relations, which are transferred from TRANSFAC, a database focused on transcription regulation and transcription factors. Since interactions between molecules are mainly direct, this allows a complete and stepwise pathway reconstruction from ligands to regulated genes. | signal transduction, network analyzer, transcriptional regulator, transcription factor, metabolic pathway, signaling pathway, protein-protein interaction, gene-regulatory pathway, signal transduction pathway, complex, signaling molecule, reaction, molecule, gene, pathway, gene expression |
is related to: TRANSFAC is related to: GeneTrail has parent organization: BIOBASE Corporation |
BMBF 031U210B; BMBF 0313092; European Union FP6 contract LSHG-CT-2004-503568; European Union MRTN-CT-2004-512285 |
PMID:18629064 PMID:16381929 PMID:12519957 PMID:11724734 |
Free for academic use, Free for non-profit use, Account required | nif-0000-03580 | http://transpath.gbf.de, http://www.gene-regulation.com/pub/databases.html, http://www.biobase.de/pages/products/databases.html | SCR_005640 | 2026-08-04 09:41:24 | 2 | |||||
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Roth Laboratory Resource Report Resource Website 1+ mentions |
Roth Laboratory (RRID:SCR_005711) | Roth Lab | portal, laboratory portal, software resource, organization portal, data or information resource | The Roth Laboratory is designing and interpreting large-scale experiments to understand pathway structure and its relationship to phenotype and human disease. Software for research focused on a specific research goal is available. Current experimental interests: * Exploiting parallel sequencing technology to phenotype all pairwise gene deletion combinations in S. cerevisiae, with initial application to genes involved in transcription. * Generation of S. cerevisiae strains carrying dozens of chosen targeted deletions, with initial application to delete all ABC transporters imparting multidrug resistance. * Targeted insertion of gene sets encoding entire human pathways into S. cerevisiae, with initial application to genes involved in drug metabolism. Current computational interests: * Systematic analysis of genetic interaction to reveal redundant systems and order of action in genetic pathways * Integrating large-scale studies - including phenotype, genetic epistasis, protein-protein and transcription-regulatory interactions and sequence patterns - to quantitatively assign function to genes and guide experimentation and disease association studies. * Alternative splicing and its relationship to protein interaction networks. | gene, pathway, phenotype, disease, transcription, drug metabolism, drug, metabolism, protein-protein interaction, transcription-regulatory interaction, protein interaction, protein |
has parent organization: University of Toronto; Ontario; Canada has parent organization: Harvard Medical School; Massachusetts; USA is parent organization of: FuncAssociate: The Gene Set Functionator |
nlx_149163 | http://llama.med.harvard.edu | SCR_005711 | 2026-08-04 09:41:25 | 5 | ||||||||
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GUMC Department of Biostatistics Bioinformatics and Biomathematics - Liu Lab Resource Report Resource Website |
GUMC Department of Biostatistics Bioinformatics and Biomathematics - Liu Lab (RRID:SCR_005708) | GUMC Liu Lab | portal, organization portal, laboratory portal, data or information resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. | microarray, data mining, natural language processing, biomedical, ontology, biomedicine, data analysis, dna microarray, gene | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149157 | SCR_005708 | Georgetown University Medical Center Department of Biostatistics Bioinformatics and Biomathematics - Liu Lab, Georgetown University Medical Center Liu Lab, GUMC Department of Biostatistics Bioinformatics Biomathematics - Liu Lab | 2026-08-04 09:41:25 | 0 | ||||||||
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GeneMANIA Resource Report Resource Website 1000+ mentions |
GeneMANIA (RRID:SCR_005709) | GeneMANIA | data analysis service, analysis service resource, software resource, production service resource, service resource, database, data or information resource | Data analysis service to predict the function of your favorite genes and gene sets. Indexing 1,421 association networks containing 266,984,699 interactions mapped to 155,238 genes from 7 organisms. GeneMANIA interaction networks are available for download in plain text format. GeneMANIA finds other genes that are related to a set of input genes, using a very large set of functional association data. Association data include protein and genetic interactions, pathways, co-expression, co-localization and protein domain similarity. You can use GeneMANIA to find new members of a pathway or complex, find additional genes you may have missed in your screen or find new genes with a specific function, such as protein kinases. Your question is defined by the set of genes you input. If members of your gene list make up a protein complex, GeneMANIA will return more potential members of the protein complex. If you enter a gene list, GeneMANIA will return connections between your genes, within the selected datasets. GeneMANIA suggests annotations for genes based on Gene Ontology term enrichment of highly interacting genes with the gene of interest. GeneMANIA is also a gene recommendation system. GeneMANIA is also accessible via a Cytoscape plugin, designed for power users. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, association data, protein interaction, genetic interaction, pathway, co-expression, co-localization, protein, software library, statistical analysis, term enrichment, analysis, browser, gene ontology, gene predicting, gene prioritization, database or data warehouse, other analysis, interaction browser, protein-protein interaction, interaction, FASEB list |
is listed by: Gene Ontology Tools is related to: Cytoscape is related to: Gene Ontology is related to: PSICQUIC Registry has parent organization: University of Toronto; Ontario; Canada |
Genome Canada ; Ontario Ministry of Research and Innovation 2007-OGI-TD-05 |
PMID:20576703 PMID:18613948 PMID:20926419 |
Open unspecified license, Free for academic use | nlx_149159, r3d100013978 | https://doi.org/10.17616/R31NJNA2 | SCR_005709 | 2026-08-04 09:41:25 | 3358 | |||||
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Whatizit Resource Report Resource Website 1+ mentions |
Whatizit (RRID:SCR_005824) | Whatizit | data analysis service, analysis service resource, web service, software resource, data access protocol, production service resource, service resource | A text processing system that allows you to do textmining tasks on text. It is great at identifying molecular biology terms and linking them to publicly available databases. Whatizit is also a Medline abstracts retrieval/search engine. Instead of providing the text by Copy&Paste, you can launch a Medline search. The abstracts that match your search criteria are retrieved and processed by a pipeline of your choice. Whatizit is also available as 1) a webservice and as 2) a streamed servlet. The webservice allows you to enrich content within your website in a similar way as in the wikipedia. The streamed servlet allows you to process large amounts of text. | textual analysis, protein, gene, gene ontology, text-mining, annotation, literature analysis |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: UniProt is related to: MEDLINE is related to: NCBI Taxonomy has parent organization: European Bioinformatics Institute |
Free for academic use | OMICS_01200, nlx_149329 | http://www.ebi.ac.uk/webservices/whatizit | SCR_005824 | 2026-08-04 09:41:27 | 8 | |||||||
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UM-BBD Resource Report Resource Website 1+ mentions |
UM-BBD (RRID:SCR_005787) | UM-BBD, UM-BBD enzymeID, UM-BBD pathwayID, UM-BBD reactionID, UM-BBD ruleID | data analysis service, analysis service resource, data set, production service resource, service resource, database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 27, 2014. Database containing information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. Its goal is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. The reactions covered are studied for basic understanding of nature, biocatalysis leading to specialty chemical manufacture, and biodegradation of environmental pollutants. Individual reactions and metabolic pathways are presented with information on the starting and intermediate chemical compounds, the organisms that transform the compounds, the enzymes, and the genes. The present database has been successfully used to teach enzymology and use of biochemical Internet information resources to advanced undergraduate and graduate students, and is being expanded primarily with the help of such students. In addition to reactions and pathways, this database also contains Biochemical Periodic Tables and a Pathway Prediction System. * Search the UM-BBD for compound, enzyme, microorganism, pathway, or BT rule name; chemical formula; chemical structure; CAS Registry Number; or EC code. * Go to Pathways and Metapathways in the UM-BBD * Lists of 203 pathways; 1400 reactions; 1296 compounds; 916 enzymes; 510 microorganism entries; 245 biotransformation rules; 50 organic functional groups; 76 reactions of naphthalene 1,2-dioxygenase; 109 reactions of toluene dioxygenase; Graphical UM-BBD Overview; and Other Graphics (Metapathway and Pathway Maps and Reaction Mechanisms). | enzyme, biocatalysis, biodegredation, chemical, pathway, reaction, microorganism, image, chemical compound, gene, enzymology | has parent organization: University of Minnesota Twin Cities; Minnesota; USA | Minnesota Supercomputing Institute ; Lhasa Limited ; University of Minnesota; Minnesota; USA ; European Union FP6 ALARM project ; NIH ; NSF 0543416; DOE DE-FG02-01ER63268; NIGMS R01GM56529; NSF 9630427 |
PMID:19767608 PMID:16381924 PMID:12519997 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03607, r3d100011317 | https://doi.org/10.17616/R33D0V | SCR_005787 | UM-BBD pathwayID, University of Minnesota Biocatalysis and Biodegradation Database, UM-BBD reactionID, Biocatalysis/Biodegradation Database, University of Minnesota Biocatalysis/Biodegradation Database, UM-BBD ruleID, Univeristy of Minnesota Biocatalysis/Biodegradation Database, UM-BBD enzymeID | 2026-08-04 09:41:26 | 9 | ||||
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MolGen Resource Report Resource Website 10+ mentions |
MolGen (RRID:SCR_005700) | MolGen | topical portal, portal, data or information resource | The research of the group concentrates on the molecular biology of Gram-positive bacteria, with Bacillus subtilis and Lactococcus lactis as the main model organisms. A number of important (human) pathogens are also investigated: Bacillus cereus, Streptococcus pneumoniae and Enterococcus faecalis. The nature of the research is both fundamental and application-oriented. Transcript- and protein profiling by high-throughput technologies such as DNA microarrays and proteomics tools are being used. The very large data sets generated are analyzed by employing existing and novel bioinformatics tools. Major lines of research are in the field of functional genomics of these organisms, using systems- and synthetic biology approaches. | molecular biology, gram-positive bacteria, pathogen, transcript, protein, profile, high-throughput, dna microarray, proteomics, dna, microarray, functional genomics, bioinformatics, genetics, gene |
has parent organization: University of Groningen; Groningen; Netherlands is parent organization of: FIVA - Functional Information Viewer and Analyzer |
nlx_149166 | http://molgen.biol.rug.nl/molgen/index.php | SCR_005700 | Molecular Genetics | 2026-08-04 09:41:25 | 27 | |||||||
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DBD - Slim Gene Ontology Resource Report Resource Website |
DBD - Slim Gene Ontology (RRID:SCR_005728) | Slim Gene Ontology | software application, software resource, database, data or information resource | Db for Dummies! is a small database that imports the Generic GO Slim. It allows data to be viewed in a tree. The Gene Ontology describes gene products in terms of their associated biological processes, cellular components and molecular functions. The Generic Slim Gene Ontology is a subset of the whole Gene Ontology. The slim version gives a broad overview and leaves out specific/fine grained terms. This example stores the slim version of the Gene Ontology (goslim_generic_obo) that can be downloaded from www.geneontology.org/GO.slims.shtml. Platform: Windows compatible | gene ontology, gene, hierarchy, visualization, database or data warehouse |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Db for Dummies! |
Free for academic use | nlx_149185 | SCR_005728 | Db for Dummies! - Slim Gene Ontology, Db for Dummies - Slim Gene Ontology | 2026-08-04 09:41:25 | 0 |
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Welcome to the RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on RRID then you can log in from here to get additional features in RRID such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into RRID you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
