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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
Onto-Translate
 
Resource Report
Resource Website
1+ mentions
Onto-Translate (RRID:SCR_005725) Onto-Translate data analysis service, analysis service resource, production service resource, service resource, database, data or information resource In the annotation world, the same piece of information can be stored and viewed differently across different databases. For instance, more than one Affymetrix probe ID can refer to the same GenBank sequence (accession number) and more than one nucleotide sequence from GenBank can be grouped in a single UniGene cluster. The result of Onto-Express depends on whether the input list contains Affymetrix probe IDs, GenBank accession numbers or UniGene cluster IDs. The user has to be aware of relations between the different forms of the data in order to interpret correctly the results. Even if the user is aware of the relationships and knows how to convert them, most existing tools allow conversions of individual genes. Onto-Translate is a tool that allows the user to perform easily such translations. Affymetrix probe IDs, etc., translate GO terms into other identifiers like GenBank accession number, Uniprot IDs. User account required. Platform: Online tool annotation, gene, analysis, database or data warehouse, other analysis, affymetrix probe id, affymetrix, probe id, translate go terms into other identifiers like genbank accession number, genbank accession number, uniprot id, gene ontology, translate is listed by: Gene Ontology Tools
is related to: Gene Ontology
has parent organization: Wayne State University; Michigan; USA
PMID:15215428 Free for academic use nlx_149182 SCR_005725 2026-08-04 09:41:25 3
TAIR Keyword Browser
 
Resource Report
Resource Website
10+ mentions
TAIR Keyword Browser (RRID:SCR_005687) TAIR Keyword Browser data analysis service, analysis service resource, production service resource, service resource, database, data or information resource TAIR Keyword Browser searches and browses for Gene Ontology, TAIR Anatomy, and TAIR Developmental stage terms, and allows you to view term details and relationships among terms. It includes links to genes, publications, microarray experiments and annotations associated with the term or any children terms. Platform: Online tool gene ontology, gene, publication, microarray, annotation, cellular component, biological process, molecular function, plant, growth, development, stage, anatomical entity, anatomy, ontology, browser, ontology or annotation browser is listed by: Gene Ontology Tools
is related to: Gene Ontology
has parent organization: TAIR
Free for academic use nlx_149132 http://www.arabidopsis.org/servlets/Search?action=new_search&type=keyword SCR_005687 TAIR Keyword Search and Browse, The Arabidopsis Information Resource Keyword Browser 2026-08-04 09:41:25 37
GOTaxExplorer
 
Resource Report
Resource Website
GOTaxExplorer (RRID:SCR_005720) GOTaxExplorer data analysis service, analysis service resource, software resource, production service resource, service resource, database, data or information resource GOTaxExplorer presents a new approach to comparative genomics that integrates functional information and families with the taxonomic classification. It integrates UniProt, Gene Ontology, NCBI Taxonomy, Pfam and SMART in one database. GOTaxExplorer provides four different query types: selection of entity sets, comparison of sets of Pfam families, semantic comparison of sets of GO terms, functional comparison of sets of gene products. This permits to select custom sets of GO terms, families or taxonomic groups. For example, it is possible to compare arbitrarily selected organisms or groups of organisms from the taxonomic tree on the basis of the functionality of their genes. Furthermore, it enables to determine the distribution of specific molecular functions or protein families in the taxonomy. The comparison of sets of GO terms allows to assess the semantic similarity of two different GO terms. The functional comparison of gene products makes it possible to identify functionally equivalent and functionally related gene products from two organisms on the basis of GO annotations and a semantic similarity measure for GO. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible gene, molecular function, protein family, taxonomy, visualization, functional similarity, semantic similarity, analysis, comparative genomics analysis, comparative genomics, search engine, ontology or annotation search engine, ontology or annotation visualization, database or data warehouse, function, other analysis is listed by: Gene Ontology Tools
is related to: Gene Ontology
is related to: UniProt
is related to: NCBI Taxonomy
is related to: Pfam
is related to: SMART
is related to: FSST - Functional Similarity Search Tool
has parent organization: Max-Planck-Institute for Informatics; Saarbrucken; Germany
German National Genome Research Network ;
BMBF 016R0453;
DFG KFO 129/1-1;
European Union contract LSHG-CT-2003-503265
PMID:17346342 Free for academic use nlx_149179 SCR_005720 2026-08-04 09:41:26 0
Onto-Miner
 
Resource Report
Resource Website
Onto-Miner (RRID:SCR_005722) OM data analysis service, analysis service resource, production service resource, service resource, database, data or information resource Onto-Miner (OM) provides a single and convenient interface that allows the user to interrogate our databases regarding annotations of known genes. OM will return all known information about a given list of genes. Advantages of OM include the fact it allows queries with multiple genes and allows for scripting. This is unlike GenBank which uses a single gene navigation process. Scripted search of the Onto-Tools database for gene annotations. User account required. Platform: Online tool gene, annotation, search engine, database, analysis, ontology or annotation search engine, database or data warehouse, other analysis, scripted search of the onto-tools database for gene annotations is listed by: Gene Ontology Tools
is related to: Gene Ontology
has parent organization: Wayne State University; Michigan; USA
PMID:15215428
PMID:17584796
Free for academic use nlx_149181 SCR_005722 Onto-Miner (OM) 2026-08-04 09:41:25 0
GOfetcher
 
Resource Report
Resource Website
GOfetcher (RRID:SCR_005681) GOfetcher data analysis service, analysis service resource, production service resource, service resource, database, data or information resource THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 29, 2012. We developed a web application, GOfetcher, with a very comprehensive search facility for the GO project and a variety of output formats for the results. GOfetcher has three different levels for searching the GO: Quick Search, Advanced Search, and Upload Files for searching. The application includes a unique search option which generates gene information given a nucleotide or protein accession number which can then be used in generating gene ontology information. The output data in GOfetcher can be saved into several different formats; including spreadsheet, comma-separated values, and the Extensible Markup Language (XML) format. Platform: Online tool gene, nucleotide, protein, ontology, ontology or annotation browser is listed by: Gene Ontology Tools
is related to: Gene Ontology
has parent organization: University of Southern Mississippi; Mississippi; USA
NSF EPS-0556308;
U.S. Army ;
Environmental Quality Program contract #W912HZ-05-P-0145
PMID:18728045 THIS RESOURCE IS NO LONGER IN SERVICE nlx_149124 http://mcbc.usm.edu/gofetcher/ SCR_005681 GOfetcher: a database with complex searching facility for gene ontology 2026-08-04 09:41:24 0
GoFish
 
Resource Report
Resource Website
1+ mentions
GoFish (RRID:SCR_005682) GoFish data analysis service, source code, analysis service resource, software resource, production service resource, service resource Software program, available as a Java applet online or to download, allows the user to select a subset of Gene Ontology (GO) attributes, and ranks genes according to the probability of having all those attributes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. gene, ontology or annotation browser, java, windows, mac os x, linux, unix, 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: University of Toronto; Ontario; Canada
has parent organization: Harvard Medical School; Massachusetts; USA
Aventis Pharmaceuticals ;
Howard Hughes Medical Institute ;
NHGRI
PMID:12691998 THIS RESOURCE IS NO LONGER IN SERVICE biotools:gofish, nlx_149126, OMICS_02272 http://llama.mshri.on.ca/Software.html, https://bio.tools/gofish SCR_005682 2026-08-04 09:41:25 1
Hepatitis C Virus Database (HCVdb)
 
Resource Report
Resource Website
1+ mentions
Hepatitis C Virus Database (HCVdb) (RRID:SCR_005718) HCVdb, data analysis service, analysis service resource, production service resource, service resource, database, data or information resource The Hepatitis C Virus Database (HCVdb) is a cooperative project of several groups with the mission of providing to the scientific community studying the hepatitis C virus a comprehensive battery of informational and analytical tools. The Viral Bioinformatics Resource Center (VBRC), the Immune Epitope Database and Analysis Resource (IEDB), the Broad Institute Microbial Sequencing Center (MSC), and the Los Alamos HCV Sequence Database (HCV-LANL) are combining forces to acquire and annotate data on Hepatitis C virus, and to develop and utilize new tools to facilitate the study of this group of organisms. hepatitis c, hepatitis c virus, genome, gene, virus, ortholog comparison, ortholog has parent organization: VBRC Hepatitis C virus NIAID contract HHSN266200400036C nlx_149175 SCR_005718 Hepatitis C Viral Database 2026-08-04 09:41:26 4
CLENCH
 
Resource Report
Resource Website
1+ mentions
CLENCH (RRID:SCR_005735) CLENCH data processing software, software application, software resource, source code Cluster Enrichment (CLENCH) allows A. thaliana researchers to perform automated retrieval of GO annotations from TAIR and calculate enrichment of GO terms in gene group with respect to a reference set. Before calculating enrichment, CLENCH allows mapping of the returned annotations to arbitrary coarse levels using GO slim term lists (which can be edited by the user) and a local installation of GO. Platform: Windows compatible, Linux compatible, gene, microarray, function, functional categorization, statistical analysis, slimmer-type tool, gene ontology, annotation is listed by: Gene Ontology Tools
is related to: Gene Ontology
is related to: TAIR
has parent organization: Stanford Center for Biomedical Informatics Research
PMID:14764555 Free for academic use nlx_149216 http://www.personal.psu.edu/nhs109/Clench SCR_005735 CLENCH - Cluster Enrichment, CLENCH: A program for calculating cluster enrichment using the Gene Ontology, Cluster Enrichment, Cluster Enrichment (CLENCH) 2026-08-04 09:41:26 4
AgedBrainSYSBIO
 
Resource Report
Resource Website
1+ mentions
AgedBrainSYSBIO (RRID:SCR_003825) AgedBrainSYSBIO portal, organization portal, data or information resource, consortium Consortium focused on identifying the foundational pathways responsible for the aging of the brain, with a focus on Late Onset Alzheimer's disease. They aim to identify the interactions through which the aging phenotype develops in normal and in disease conditions; modeling novel pathways and their evolutionary properties to design experiments that identify druggable targets. As early steps of neurodegenerative disorders are expected to impact synapse function the project will focus in particular on pre- or postsynaptic protein networks. The concept is to identify subsets of pathways with two unique druggable hallmarks, the validation of interactions occurring locally in subregions of neurons and a human and/or primate accelerated evolutionary signature. The consortium will do this through six approaches: * identification of interacting protein networks from recent Late-Onset Alzheimer Disease-Genome Wide Association Studies (LOAD-GWAS) data, * experimental validation of interconnected networks working in subregion of a neuron (such as dendrites and dendritic spines), * inclusion of these experimentally validated networks in larger networks obtained from available databases to extend possible protein interactions, * identification of human and/or primate positive selection either in coding or in regulatory gene sequences, * manipulation of these human and/or primate accelerated evolutionary interacting proteins in human neurons derived from induced Pluripotent Stem Cells (iPSCs) * modeling predictions in drosophila and novel mouse transgenic models * validation of new druggable targets and markers as a proof-of-concept towards the prevention and cure of aging cognitive defects. The scientists will share results and know-how on Late-Onset Alzheimer Disease-Genome Wide Association Studies (LOAD-GWAS) gene discovery, comparative functional genomics in mouse and drosophila models, in mouse transgenic approaches, research on human induced pluripotent stem cells (hiPSC) and their differentiation in vitro and modeling pathways with emphasis on comparative and evolutionary aspects. The four European small to medium size enterprises (SMEs) involved will bring their complementary expertise and will ensure translation of project results to clinical application. consortium, drug, drug development, brain, phenotype, presynaptic, protein network, postsynaptic, systems biology, synapse, neuron, protein interaction, network, induced pluripotent stem cell, pathway, genome wide association study, cognitive defect, gene, protein is listed by: Consortia-pedia
is related to: Pasteur Institute of Lille; Lille; France
is related to: Mouse Clinical Institute; Alsace; France
is related to: Hybrigenics
is related to: Inserm Transfert
is related to: VIB; Flanders; Belgium
is related to: Quretec
is related to: Gene Bridges
is related to: European Bioinformatics Institute
is related to: Tel Aviv University; Ramat Aviv; Israel
is related to: SIB Swiss Institute of Bioinformatics
is related to: Babraham Institute
has parent organization: National Institute of Health and Medical Research; Rennes; France
has parent organization: Inserm Transfert
European Union FP7 305299 nlx_158132 SCR_003825 2026-08-04 09:41:00 3
BioSHaRE
 
Resource Report
Resource Website
10+ mentions
BioSHaRE (RRID:SCR_003811) BIOSHARE-EU portal, consortium, organization portal, narrative resource, standard specification, data or information resource A consortium of leading biobanks and international researchers from all domains of biobanking science to ensure the development of harmonized measures and standardized computing infrastructures enabling the effective pooling of data and key measures of life-style, social circumstances and environment, as well as critical sub-components of the phenotypes associated with common complex diseases. The overall aim is to build upon tools and methods available to achieve solutions for researchers to use pooled data from different cohort and biobank studies. This, in order to obtain the very large sample sizes needed to investigate current questions in multifactorial diseases, notably on gene-environment interactions. This aim will be achieved through the development of harmonization and standardization tools, implementation of these tools and demonstration of their applicability. BioSHaRE researchers are collaborating with P3G, the Global Alliance for Genomics and Health, IRDiRC (International Rare Diseases Research Consortium), H3Africa and other organizations on the development of an International Code of Conduct for Genomic and Health-Related Data Sharing. A draft version is available for external review. Generic documents have been prepared covering areas of biobanking that are of major importance. SOPs have been finalized for blood withdrawal (SOPWP5001blood withdrawal), manual blood processing (SOPWP5002blood processing), shipping of biosamples (SOPWP5003shipping) and withdrawal, processing and storage of urine samples (SOPWP5004urine). gene-environment interaction, life-style, social circumstance, environment, phenotype, disease, biobank, socio-economic factor, data sharing, gene, clinical is listed by: Consortia-pedia
has parent organization: University of Groningen; Groningen; Netherlands
is parent organization of: BioResource Impact Factor
European Union FP7 nlx_158110 SCR_003811 Biobank Standardisation and Harmonisation for Research Excellence, Biobank Standardisation and Harmonisation for Research Excellence in the European Union 2026-08-04 09:40:59 21
GeneCommittee
 
Resource Report
Resource Website
GeneCommittee (RRID:SCR_004168) geneCommittee data analysis service, analysis service resource, software resource, production service resource, service resource Tool for extensively testing the discriminatory power of biologically relevant gene sets in microarray data classification. While the user can work with different gene set collections and several microarray data files to configure specific classification experiments, the tool is able to run several tests in parallel. It is able to render valuable information for diagnostic analyses and clinical management decisions based on systematically evaluating custom hypothesis over different data sets using complementary classifiers, a key aspect in clinical research. dna, microarray, rna-seq, gene expression, classification, gene set, gene, gene set enrichment, functional annotation is listed by: OMICtools
has parent organization: University of Vigo; Galicia; Spain
PMID:24475928 Acknowledgement requested OMICS_02291 https://github.com/michada/GeneCommittee SCR_004168 2026-08-04 09:41:04 0
MIP-DILI
 
Resource Report
Resource Website
1+ mentions
MIP-DILI (RRID:SCR_003870) MIP-DILI portal, organization portal, data or information resource, consortium Consortium that brings together Europe's top industrial and academic experts to develop new tests that will help researchers detect potential liver toxicity issues much earlier in drug development, saving many patients from the trauma of liver failure. The team aims to deepen the understanding of the science behind drug-induced liver injury, and use that knowledge to overcome the many drawbacks of the tests currently used. A major focus will be on a systematic and evidence-based evaluation of both currently available and new laboratory test systems, including cultures of liver cells in one-dimensional and three dimensional configurations. The project will also develop models that take into account the natural differences between patients. This is important because factors such as certain genes, the liver's immune response, and viral infections have all been associated with an increased risk of DILI. The project will seek to address the current lack of human liver cells available to researchers by using induced pluripotent stem cells (iPSCs) generated from patients who are particularly sensitive to DILI. Another strand of the project will develop computer models to unravel the complex, often inter-related mechanisms behind DILI. Finally, the team will assess how accurate the results of laboratory tests are at predicting actual outcomes in patients. drug, liver, toxicity test, toxicity, drug development, tool development, liver toxicity, preclinical, model, induced pluripotent stem cell, liver cell, gene, immune response, computer model, outcome is listed by: Consortia-pedia
is related to: Abbott Diagnostics
is related to: Janssen Research and Development
is related to: Merck
is related to: Orion
is related to: University of Liverpool; Liverpool; United Kingdom
is related to: University of Freiburg; Baden-Wurttemberg; Germany
is related to: German Cancer Research Center
is related to: Karolinska Institute; Stockholm; Sweden
is related to: University of Rennes 1; Rennes; France
is related to: Leiden University; Leiden; Netherlands
is related to: Utrecht University; Utrecht; Netherlands
is related to: VU University; Amsterdam; Netherlands
is related to: Cellartis
is related to: CXR Biosciences
is related to: Interface Europe
is related to: KaLy-Cell
is related to: Lhasa Limited
is related to: SOLVO Biotechnology
has parent organization: Interface Europe
Innovative Medicines Initiative 115336;
EFPIA
nlx_158195 SCR_003870 Mechanism-Based Integrated Systems for the Prediction of Drug-Induced Liver Injury (MIP-DILI), Mechanism based Integrated systems for the Prediction of Drug Induced Liver Injury, Mechanism-Based Integrated Systems for the Prediction of Drug-Induced Liver Injury 2026-08-04 09:41:00 2
NEWMEDS
 
Resource Report
Resource Website
1+ mentions
NEWMEDS (RRID:SCR_003872) NEWMEDS portal, organization portal, data or information resource, consortium Consortium that will develop new models and methods to enable novel treatments for schizophrenia and depression including three important missing tools that will facilitate the translation of scientific findings into benefits for patients. The project will focus on developing new animal models which use brain recording and behavioral tests to identify innovative and effective drugs for schizophrenia. The project will develop standardized paradigms, acquisition and analysis techniques to apply brain imaging, especially fMRI and PET imaging to drug development. It will examine how new genetic findings (duplication and deletion or changes in genes) influence the response to various drugs and whether this information can be used to choose the right drug for the right patient. And finally, it will try and develop new approaches for shorter and more efficient trials of new medication - trials that may require fewer patients and give faster results. drug, biomarker, neuroimaging, drug development, tool development, animal model, fmri, pet, gene, medicine, clinical trial, genetic variation, molecule, model, dna, protein is listed by: Consortia-pedia
is related to: Abbott Diagnostics
is related to: Janssen Research and Development
is related to: Orion
is related to: Pfizer Animal Genetics
is related to: Roche
is related to: King's College London; London; United Kingdom
is related to: Karolinska Institute; Stockholm; Sweden
is related to: University of Cambridge; Cambridge; United Kingdom
is related to: Central Institute of Mental Health; Mannheim; Germany
is related to: Spanish National Research Council; Madrid; Spain
is related to: University of Manchester; Manchester; United Kingdom
is related to: Bar-Ilan University; Ramat Gan; Isreal
is related to: Psynova Neurotech
is related to: deCODE genetics
is related to: GABO:mi
is related to: AbbVie
has parent organization: King's College London; London; United Kingdom
is parent organization of: DepressionTools.org Clinical Significance Calculator
is parent organization of: Pharmacological Imaging and Pattern Recognition toolbox
is parent organization of: DUPCheck
Innovative Medicines Initiative 115008;
EFPIA
nlx_158196 SCR_003872 Novel Methods leading to New Medications in Depression and Schizophrenia, NEWMEDS - Novel Methods leading to New Medications in Depression and Schizophrenia 2026-08-04 09:41:00 6
Biomarkers of Anti-TNF Treatment Efficacy in Rheumatoid Arthritis - Unresponsive Populations
 
Resource Report
Resource Website
Biomarkers of Anti-TNF Treatment Efficacy in Rheumatoid Arthritis - Unresponsive Populations (RRID:SCR_004019) BATTER-UP topical portal, portal, data or information resource A consortium evaluating a new biomarker screening test that might help identify patients with rheumatoid arthritis (RA) who are unlikely to benefit from anti-tumor necrosis factor-alpha (TNFalpha) medications. BATTER-UP will enroll around 1,000 patients being treated by one of several marketed anti-TNF RA drugs: Enbrel, Remicade, Humira, Simponi, or Cimzia. Through data analyses and predictive response modeling, the consortium aims to better understand which patients with RA will derive the greatest benefit from TNF inhibitors. The investigators in this observational study will attempt to validate an 8-gene biomarker set based on work by Biogen Idec researchers as likely to predict anti-TNF responsiveness in patients with RA. In preliminary results, the 8-gene biomarker set predicted with 89% accuracy individuals who did not reach European League Against Rheumatism (EULAR) Disease Activity Score (DAS)-28 good response after 14 weeks of treatment. The 8 genes included in the screen are CLTB, MXRA7, CXorf52, COL4A3BP, YIPF6, FAM44A, SFRS2, and PGK1. Biological samples and clinical outcome information will be used to confirm and extend the utility of previously published biomarkers that can predict response to anti-TNF agents. These data may also generate new hypotheses for further testing. The BATTER-UP samples and data will be established as a reference set for investigation of personalized medicine in RA. The study will be a resource of DNA and other biological materials that can be investigated for biomarkers in the future as new technologies arise. anti-tumor necrosis factor-alpha, gene, biomarker, drug development, basic research, personalized medicine, enbrel, remicade, humira, simponi, cimzia, cltb, mxra7, cxorf52, col4a3bp, yipf6, fam44a, sfrs2, pgk1, clinical, dna, serum, plasma, rna, whole blood uses: ClinicalTrials.gov
is listed by: Consortia-pedia
is related to: Feinstein Institute for Medical Research
has parent organization: Feinstein Institute for Medical Research
has parent organization: ClinicalTrials.gov
Biogen Idec ;
Bristol-Myers Squibb ;
Centocor ;
Crescendo Bioscience ;
Genentech ;
Medco Health Solutions ;
Regeneron Pharmaceuticals ;
Sanofi-Aventis
nlx_158440 SCR_004019 Biomarkers of Anti-TNF-alpha Therapy Efficacy in Rheumatoid Arthritis to Define Unresponsive Patients, Biomarkers of Anti-TNF- Therapy Efficacy in Rheumatoid Arthritis to Define Unresponsive Patients (BATTER-UP), Biomarkers of Anti-TNF- Therapy Efficacy in Rheumatoid Arthritis to Define Unresponsive Patients 2026-08-04 09:41:02 0
dkCOIN
 
Resource Report
Resource Website
1+ mentions
dkCOIN (RRID:SCR_004438) dkCOIN resource, database, data or information resource THIS RESOURCE IS NO LONGER IN SERVICE, documented October 13, 2014. The resource has moved to the NIDDKInformation Network (dkNET) project. Contact them at info_at_dknet.org with any questions. Database of large pools of data relevant to the mission of NIDDKwith the goal of developing a community-based network for integration across disciplines to include the larger DKuniverse of diseases, investigators, and potential users. The focus is on greater use of this data with the objective of adding value by breaking down barriers between sites to facilitate linking of different datasets. To date (2013/06/10), a total of 1,195 resources have been associated with one or more genes. Of 11,580 total genes associated with resources, the ten most represented are associated with 359 distinct resources. The main method by which they currently interconnect resources between the providers is via EntrezGene identifiers. A total of 780 unique genes provide the connectivity between 3,159 resource pairs across consortia. To further increase interconnectivity, the groups have been further annotating their data with additional gene identifiers, publications, and ontology terms from selected Open Biological and Biomedical Ontologies (OBO). gene, adenovirus construct, antibody, co-immunoprecipitation, embryonic stem cell line, functional genomics, histology, mouse strain, pcr primer, protocol, real time pcr, metadata, diabetes, stem cell, metabolism, tissue development, web service, cloud, embryonic stem cell is used by: NIF Data Federation
is related to: Beta Cell Biology Consortium
is related to: NIDDK Information Network (dkNET)
is related to: National Mouse Metabolic Phenotyping Centers
is related to: Nuclear Receptor Signaling Atlas
is related to: Diabetic Complications Consortium
is related to: T1DBase
is related to: OBO
has parent organization: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases
NIDDK 3U01DK072473-05S3;
NIDDK 5U24DK076169;
NIDDK U19DK062434
PMID:22734043 THIS RESOURCE IS NO LONGER IN SERVICE nlx_44256 SCR_004438 NIDDKConsortium Interconnectivity Network 2026-08-04 09:41:08 1
BrainSpan
 
Resource Report
Resource Website
1+ mentions
BrainSpan (RRID:SCR_004219) expression atlas, atlas, data or information resource Atlas of developing human brain for studying transcriptional mechanisms involved in human brain development. One of the BrainSpan datasets, Exon microarray summarized to genes, is presented. It is a downloadable archive of files containing normalized RNA-Seq expression values for analysis. brain, development, brain development, exon, microarray, gene, rna-seq, expression value, expression is used by: NIF Data Federation
has parent organization: Allen Human Brain Atlas: BrainSpan (Atlas of the Developing Brain)
Free, Freely available nlx_98194, nlx_86215, SCR_004877, SCR_005029, SCR_004344, nlx_37081, nlx_2397 http://brainspan.org/rnaseq/downloads.html?format=html, http://brainspan.org/docs.html http://brainspan.org/docs.html SCR_004219 BrainSpan: RNA-Seq exons, BrainSpan - Exon microarray summarized to genes 2026-08-04 09:41:05 2
TAGS
 
Resource Report
Resource Website
100+ mentions
TAGS (RRID:SCR_004294) TAGS data processing software, data analysis software, time-series analysis software, software resource, software application Software tool for gene set enrichment analysis for expression time series, which can incorporate existing knowledge and analyze the dynamic property of a group of genes that have functional or structural associations. The installation file is for Windows., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. gene, enrichment analysis, time series, function, structure, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: Tsinghua University; Beijing; China
THIS RESOURCE IS NO LONGER IN SERVICE biotools:tags, nlx_31187 https://bio.tools/tags http://166.111.130.26/member/yliu/TAGS/ SCR_004294 2026-08-04 09:41:06 139
NEXTDB
 
Resource Report
Resource Website
10+ mentions
NEXTDB (RRID:SCR_004480) NextDB data analysis service, analysis service resource, expression atlas, production service resource, service resource, atlas, database, data or information resource Expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans through EST analysis and systematic whole mount in situ hybridization. NEXTDB is the database to integrate all information from their expression pattern project and to make the data available to the scientific community. Information available in the current version is as follows: * Map: Visual expression of the relationships among the cosmids, predicted genes and the cDNA clones. * Image: In situ hybridization images that are arranged by their developmental stages. * Sequence: Tag sequences of the cDNA clones are available. * Homology: Results of BLASTX search are available. Users of the data presented on our web pages should not publish the information without our permission and appropriate acknowledgment. Methods are available for: * In situ hybridization on whole mount embryos of C.elegans * Protocols for large scale in situ hybridization on C.elegans larvae rnai phenotype, homology, blast, fasta, chromosome map, cosmid, gene, cdna clone, genome, in situ hybridization, expressed sequence tag, developmental stage, sequence, embryonic caenorhabditis elegans, chromosome, phenotype, blastx, clone, sequence tag, yac, predicted gene, protein, development, larval caenorhabditis elegans, image collection, experimental protocol, FASEB list is related to: Expression Patterns for C. elegans promoter GFP fusions
is related to: Expression Patterns for C. elegans promoter GFP fusions
has parent organization: National Institute of Genetics; Shizuoka; Japan
Core Research for Evolutional Science and Technology ;
Japan Science and Technology Corporation ;
Japanese Ministry of Education Culture Sports Science and Technology MEXT
Permission required, Acknowledgement required nlx_46406 SCR_004480 Nematode Expression Pattern DataBase 2026-08-04 09:41:10 35
Stem Cell Commons
 
Resource Report
Resource Website
1+ mentions
Stem Cell Commons (RRID:SCR_004415) Stem Cell Commons source code, analysis service resource, data set, storage service resource, software resource, data repository, production service resource, service resource, database, data or information resource Open source environment for sharing, processing and analyzing stem cell data bringing together stem cell data sets with tools for curation, dissemination and analysis. Standardization of the analytical approaches will enable researchers to directly compare and integrate their results with experiments and disease models in the Commons. Key features of the Stem Cell Commons * Contains stem cell related experiments * Includes microarray and Next-Generation Sequencing (NGS) data from human, mouse, rat and zebrafish * Data from multiple cell types and disease models * Carefully curated experimental metadata using controlled vocabularies * Export in the Investigation-Study-Assay tabular format (ISA-Tab) that is used by over 30 organizations worldwide * A community oriented resource with public data sets and freely available code in public code repositories such as GitHub Currently in development * Development of Refinery, a novel analysis platform that links Commons data to the Galaxy analytical engine * ChIP-seq analysis pipeline (additional pipelines in development) * Integration of experimental metadata and data files with Galaxy to guide users to choose workflows, parameters, and data sources Stem Cell Commons is based on open source software and is available for download and development. therapeutic target, blood, stem cell, self-renewal, embryonic stem cell, hematopoietic stem cell, leukemia stem cell, gene, protein, phenotype, therapeutic, annotate, share, analyze, data sharing, statistics, visualize, analyze, microarray, next-generation sequencing, statistics, transcription profiling, genome, genome browser, disease model is related to: Galaxy
is related to: ISA Infrastructure for Managing Experimental Metadata
has parent organization: Harvard Stem Cell Institute
Normal, Acute Myelogenous Leukemia, Glioblastoma, Primitive Neuroectodermal Tumor, Etc. PMID:24303302 Open unspecified license nlx_42085 http://bloodprogram.hsci.harvard.edu/ SCR_004415 HSCI Blood Genomics, Harvard Stem Cell Institute Blood Genomics, Harvard Stem Cell Institute Blood Program, HSCI Blood Program 2026-08-04 09:41:09 2
Handbook of Genetic Counseling
 
Resource Report
Resource Website
Handbook of Genetic Counseling (RRID:SCR_004564) Handbook of Genetic Counseling narrative resource, data or information resource, wiki, book The Handbook of Genetic Counseling is a wikibook designed as an introduction to the discipline and practice of genetic counseling. The text provides an introduction to genetic counseling as a clinical practice and includes sample counseling outlines and letters for students of genetic counseling. Additional outline and letter examples are highly encouraged. Wikibooks contains books on many medical topics; however, no warranty whatsoever is made that any of the books are accurate. gene, counseling, genetic, syndrome, disease has parent organization: Wikibooks nlx_79147 SCR_004564 2026-08-04 09:41:10 0

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