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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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BioMart Project Resource Report Resource Website 100+ mentions |
BioMart Project (RRID:SCR_002987) | web service, software resource, data access protocol, project portal, data or information resource, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.Platform provides free software and data services to international scientific community in order to foster scientific collaboration and facilitate scientific discovery process. Project adheres to open source philosophy that promotes collaboration and code reuse. | biology, data, management, data mining, search, descriptive, graphical, application, perl, java, gold standard |
is used by: Blueprint Epigenome is related to: Mouse Genome Informatics (MGI) is related to: biomaRt has parent organization: Ontario Institute for Cancer Research has parent organization: European Bioinformatics Institute |
Wellcome Trust ; Spanish Government ; Sandra Ibarra Foundation for Cancer ; Breast Cancer Campaign Tissue Bank ; U.S. Department of Energy ; NSF NRF 2013M3A6A4043695; Center for Genome Regulation ; Center for Mathematical Modelling ; European Molecular Biology Laboratory |
PMID:21930506 PMID:19144180 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30184 | SCR_002987 | BioMart software | 2026-08-02 09:03:31 | 284 | ||||||
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European Bioinformatics Institute Resource Report Resource Website 1000+ mentions |
European Bioinformatics Institute (RRID:SCR_004727) | EMBL-EBI | institution | Non-profit academic organization for research and services in bioinformatics. Provides freely available data from life science experiments, performs basic research in computational biology, and offers user training programme, manages databases of biological data including nucleic acid, protein sequences, and macromolecular structures. Part of EMBL. | organization, academic, bioinformatics, research, service, data, computational, biology, training, database, DNA, protein |
is used by: Blueprint Epigenome is listed by: re3data.org is related to: AgedBrainSYSBIO is related to: ProteomeXchange is related to: Open PHACTS is related to: RHEA is related to: TraCeR is related to: 3D-Beacons is related to: RNAcentral has parent organization: European Molecular Biology Laboratory is parent organization of: CoGenT++ is parent organization of: ENA Sequence Version Archive is parent organization of: Reaper - Demultiplexing trimming and filtering sequencing data is parent organization of: PeakAnalyzer is parent organization of: Tally is parent organization of: Clustal Omega is parent organization of: Biocatalogue - The Life Science Web Services Registry is parent organization of: Experimental Network for Functional Integration: A European Network of Excellence for Data Integration and Systems Biology is parent organization of: The Alternatve Splicing Database is parent organization of: BioModels is parent organization of: CHEBI is parent organization of: MAGE is parent organization of: Ensembl is parent organization of: MIAME is parent organization of: UniProt is parent organization of: Ligand-Gated Ion Channel Database is parent organization of: EBI Genomes is parent organization of: IMEx - The International Molecular Exchange Consortium is parent organization of: Toolbox at the European Bioinformatics Institute is parent organization of: Clustal W2 is parent organization of: ArrayExpress is parent organization of: IMGT/HLA is parent organization of: IntEnz- Integrated relational Enzyme database is parent organization of: IPD - Immuno Polymorphism Database is parent organization of: IPI is parent organization of: MicroArray and Gene Expression Markup Language is parent organization of: DaliLite Pairwise comparison of protein structures is parent organization of: Chemical Information Ontology is parent organization of: PANDIT : Protein and Associated Nucleotide Domains with Inferred Trees is parent organization of: Proteomics Identifications (PRIDE) is parent organization of: Software Ontology is parent organization of: FSSP - Families of Structurally Similar Proteins is parent organization of: Experimental Factor Ontology is parent organization of: Identifiers.org is parent organization of: HipSci is parent organization of: ProteomeXchange is parent organization of: Taxonomy is parent organization of: PDBe - Protein Data Bank in Europe is parent organization of: EBI Dbfetch is parent organization of: ProFunc is parent organization of: WSDbfetch (SOAP) is parent organization of: QuickGO is parent organization of: SAS - Sequence Annotated by Structure is parent organization of: UniProt DAS is parent organization of: UniParc at the EBI is parent organization of: Patent Abstracts is parent organization of: BioSample Database at EBI is parent organization of: Database of Genomic Variants Archive (DGVa) is parent organization of: European Genome phenome Archive is parent organization of: UniSave is parent organization of: ArchSchema is parent organization of: UniRef at the EBI is parent organization of: EBIMed is parent organization of: Kraken is parent organization of: SIMBioMS is parent organization of: Expression Profiler is parent organization of: Whatizit is parent organization of: InterProScan is parent organization of: VectorBase is parent organization of: DRCAT Resource Catalogue is parent organization of: FunTree is parent organization of: CREATE is parent organization of: BioMedBridges is parent organization of: PSICQUIC Registry is parent organization of: PDBsum is parent organization of: European Nucleotide Archive (ENA) is parent organization of: DrugPort is parent organization of: Ontology Lookup Service is parent organization of: EDAM Ontology is parent organization of: InterPro is parent organization of: MIRIAM Resources is parent organization of: EB-eye Search is parent organization of: SBO is parent organization of: Ensembl Genomes is parent organization of: NeuronVisio is parent organization of: IntAct is parent organization of: WSsas - Web Service for the SAS tool is parent organization of: Enzyme Structures Database is parent organization of: EMBOSS CpGPlot/CpGReport/Isochore is parent organization of: PaperMaker is parent organization of: CluSTr is parent organization of: Genome Reviews is parent organization of: GOA is parent organization of: Integr8 : Access to complete genomes and proteomes is parent organization of: IPD-ESTDAB- The European Searchable Tumour Line Database is parent organization of: IPD-HPA - Human Platelet Antigens is parent organization of: IPD-KIR - Killer-cell Immunoglobulin-like Receptors is parent organization of: IPD-MHC- Major Histocompatibility Complex is parent organization of: HilbertVis is parent organization of: Gene Expression Atlas is parent organization of: Parasite genome databases and genome research resources is parent organization of: Alternative Exon Database is parent organization of: AltExtron Database is parent organization of: Patent Data Resources is parent organization of: Pompep is parent organization of: Mouse finder is parent organization of: Gene Regulation Ontology is parent organization of: CiteXplore literature searching is parent organization of: MaxSprout is parent organization of: SRS is parent organization of: MicroCosm Targets is parent organization of: Kalign is parent organization of: MUSCLE is parent organization of: FASTA is parent organization of: WU-BLAST is parent organization of: Oases is parent organization of: HTS Mappers is parent organization of: CRAM is parent organization of: CSA - Catalytic Site Atlas is parent organization of: ArrayExpress (R) is parent organization of: WiggleTools is parent organization of: vsn is parent organization of: rlsim is parent organization of: ISA Infrastructure for Managing Experimental Metadata is parent organization of: BioMart Project is parent organization of: BioPerl is parent organization of: BioJS is parent organization of: EMDataResource.org is parent organization of: HTqPCR is parent organization of: Reactome is parent organization of: Europe PubMed Central is parent organization of: h5vc is parent organization of: LexGrid is parent organization of: Consensus CDS is parent organization of: 1000 Genomes: A Deep Catalog of Human Genetic Variation is parent organization of: OrChem is parent organization of: Orphanet Rare Disease Ontology is parent organization of: Reflect is parent organization of: BioLayout Express 3D is parent organization of: Virtual Fly Brain is parent organization of: GeneWise is parent organization of: PhenoMeNal is parent organization of: Ensembl Metazoa is parent organization of: Velvet |
EMBL member states ; European Union ; NIH ; Wellcome Trust ; UK Research Councils ; Industry Programme partners ; BBSRC |
grid.225360.0, Wikidata: Q1341845, ISNI: 0000 0000 9709 7726, nlx_72386 | https://ror.org/02catss52 | SCR_004727 | EBI, European Molecular Biology Laboratory - European Bioinformatics Institute | 2026-08-01 12:02:44 | 3696 | ||||||
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Mouse Genome Informatics (MGI) Resource Report Resource Website 1000+ mentions |
Mouse Genome Informatics (MGI) (RRID:SCR_006460) | MGI | database, data or information resource | International database for laboratory mouse. Data offered by The Jackson Laboratory includes information on integrated genetic, genomic, and biological data. MGI creates and maintains integrated representation of mouse genetic, genomic, expression, and phenotype data and develops reference data set and consensus data views, synthesizes comparative genomic data between mouse and other mammals, maintains set of links and collaborations with other bioinformatics resources, develops and supports analysis and data submission tools, and provides technical support for database users. Projects contributing to this resource are: Mouse Genome Database (MGD) Project, Gene Expression Database (GXD) Project, Mouse Tumor Biology (MTB) Database Project, Gene Ontology (GO) Project at MGI, and MouseCyc Project at MGI. | RIN, Resource Information Network, molecular neuroanatomy resource, human health, human disease, animal model, gene expression, phenotype, genotype, gene, pathway, orthology, tumor, strain, single nucleotide polymorphism, recombinase, function, blast, image, pathology, model, data analysis service, genome, genetics, gold standard, RRID Community Authority |
uses: InterMOD is used by: NIF Data Federation is used by: Resource Identification Portal is used by: PhenoGO is used by: Integrated Animals is used by: Cytokine Registry is used by: NIH Heal Project is recommended by: Resource Identification Portal is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: 3DVC is listed by: re3data.org is listed by: OMICtools is listed by: NIH Data Sharing Repositories is listed by: InterMOD is listed by: Resource Information Network is affiliated with: InterMOD is related to: MONARCH Initiative is related to: MouseCyc is related to: AmiGO is related to: Gene Expression Database is related to: Bgee: dataBase for Gene Expression Evolution is related to: HomoloGene is related to: Rat Gene Symbol Tracker is related to: Enhancer Trap Line Browser is related to: Integrated Brain Gene Expression is related to: MalaCards is related to: Gene Ontology is related to: BioMart Project is related to: NIH Data Sharing Repositories is related to: RIKEN integrated database of mammals is related to: JAX Neuroscience Mutagenesis Facility is related to: PhenoGO is related to: International Mouse Strain Resource is related to: Mouse Genome Database is related to: Mouse Tumor Biology Database has parent organization: Jackson Laboratory is parent organization of: Anatomy of the Laboratory Mouse is parent organization of: Mouse Genome Informatics Transgenes is parent organization of: Federation of International Mouse Resources is parent organization of: MGI GO Browser is parent organization of: Recombinase (cre) Activity is parent organization of: Mouse Genome Informatics: The Mouse Gene Expression Information Resource Project is parent organization of: Deltagen and Lexicon Knockout Mice and Phenotypic Data Resource is parent organization of: MGI strains is parent organization of: MPO is parent organization of: Phenotypes and Mutant Alleles is parent organization of: Human Mouse Disease Connection is parent organization of: Functional Annotation is parent organization of: Strains, SNPs and Polymorphisms is parent organization of: Vertebrate Homology is parent organization of: Batch Data and Analysis Tool is parent organization of: Nomenclature |
NHGRI HG000330; NHGRI HG002273; NICHD HD033745; NCI CA089713 |
PMID:19274630 PMID:18428715 |
Free, Freely available | nif-0000-00096, OMICS_01656, r3d100010266 | http://www.informatics.jax.org/batch, http://www.informatics.jax.org/submit.shtml, http://www.informatics.jax.org/expression.shtml, https://doi.org/10.17616/R35P54 | SCR_006460 | , MGI, Mouse Genome Informatics | 2026-08-02 09:04:55 | 1119 | ||||
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Ontario Institute for Cancer Research Resource Report Resource Website 1+ mentions |
Ontario Institute for Cancer Research (RRID:SCR_010609) | OICR | funding resource, data or information resource, topical portal, portal | The Ontario Institute for Cancer Research (OICR) is a centre of excellence in cancer research with a focus on prevention, early detection, diagnosis and treatment of cancer. The Institute is an independent, not-for-profit corporation bringing together multi-disciplinary, multi-institutional collaborations, which will allow complex questions to be pursued. It is translating research findings into programs, technologies and therapies. Established in December, 2005, the Institute will support more than 50 internationally recognized principal investigators; there will be a strong core of scientists at the MaRS Centre with the remainder in nodes of excellence around the province. The Institute is leveraging the current research excellence at universities, research hospitals and health research institutes across Ontario, leading to greater integration of cancer research efforts across institutions. The Ontario Cancer Research Network, established in 2002, has been incorporated into the Institute. Its initiatives will continue under the umbrella of the Institute and will include: Cancer Research Fund, Clinical Trials Infrastructure Fund, Clinical Trials Network, OntarioCancerTrials.ca, Ontario Cancer Research Ethics Board, and Ontario Tumour Bank. |
is parent organization of: Bioinformatics Jobs Board is parent organization of: Bioinformatics Experts is parent organization of: BioMart Project is parent organization of: NanoStringNorm is parent organization of: Reactome is parent organization of: Ontario Tumour Bank is parent organization of: Canadian Bioinformatics Workshops is parent organization of: Bioinformatics Links Directory |
Government of Ontario Ministry of Research and Innovation | nlx_51701 | SCR_010609 | 2026-08-02 09:05:57 | 3 | |||||||||
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biomaRt Resource Report Resource Website 1000+ mentions |
biomaRt (RRID:SCR_019214) | data analysis software, software resource, data processing software, software application | Software package that integrates BioMart data resources with data analysis software in Bioconductor. Can annotate range of gene or gene product identifiers including Entrez Gene and Affymetrix probe identifiers with information such as gene symbol, chromosomal coordinates, Gene Ontology and OMIM annotation. Enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis. | BioMart databases, Bioconductor, data analysis, BioMart data integration, gene annotation, gene product identifiers annotation, gene symbol retrival, chromosomal coordinates retrival, genomic sequence retrival, nucleotide polimorphism information, , bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: BioMart Project is related to: BioMart MartView is related to: Entrez Gene is related to: Affymetrix is related to: Gene Ontology is related to: OMIM is related to: Affymetrix |
PMID:16082012 | Free, Available for download, Freely available | biotools:biomart | https://bio.tools/biomart | SCR_019214 | biomaRt v 2.42.1 | 2026-08-02 09:07:58 | 2638 | ||||||
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Blueprint Epigenome Resource Report Resource Website 100+ mentions |
Blueprint Epigenome (RRID:SCR_003844) | BLUEPRINT | organization portal, protocol, data or information resource, portal, consortium | Consortium to further the understanding of how genes are activated or repressed in both healthy and diseased human cells with a focus on distinct types of haematopoietic cells from healthy individuals and on their malignant leukemic counterparts. They will generate at least 100 reference epigenomes and study them to advance and exploit knowledge of the underlying biological processes and mechanisms in health and disease. Reference epigenomes will be generated by state-of-the-art technologies from highly purified cells for a comprehensive set of epigenetic marks in accordance with quality standards set by International Human Epigenome Consortium (IHEC). Access to the data is provided as well as the protocols used to collect the different blood cell types, to perform the different types of epigenomic analyses, etc.). This resource-generating activity will be complemented by hypothesis-driven research into blood-based diseases, including common leukemias and autoimmune disease (Type 1 Diabetes), by discovery and validation of epigenetic markers for diagnostic use and by epigenetic target identification. Since epigenetic changes are reversible, they can be targets for the development of novel and more individualized medical treatments. The involvement of companies will energize epigenomic research in the private sector by the development of smart technologies for better diagnostic tests and by identifying new targets for compounds. Thus the results of the project may lead to targeted diagnostics, new treatments and preventive measures for specific diseases in individual patients, an approach known as "personalized medicine". The Blueprint Data Access Committee will consider applications for access to data sets stored in the European Genome-phenome Archive (EGA) when authorized to do so by the Blueprint consortium and the holders of the original consent documents. Access is conditional upon availability of samples and/or data and signed agreement by the researcher(s) and the responsible employing Institution to abide by policies related to publication, data disposal, ethical approval and confidentiality. At EBI, the ftp site with the data can be found. You can either opt to link to the track hubs yourself or you can add the track hub to a genome browser - UCSC or ENSEMBL. Also Meta Data files and README are available. The data can also be accessed via the BIOMART system. | epigenome, hematopoiesis, gene, data set, biomaterial supply resource, antibody, blood cell, blood, cord blood precursor cell, cell, cord blood, bone marrow, rna-seq, dname-seq, dnasei-seq, chip-seq, monocyte, granulocyte neutrophil, eosinophil, macrophage, m0, m1, m2, naive cd4+, naive cd8+, pathway |
uses: European Genome phenome Archive uses: European Bioinformatics Institute uses: BioMart Project uses: UCSC Genome Browser uses: Ensembl is used by: Deep Blue Epigenomic Data Server is listed by: Consortia-pedia is listed by: One Mind Biospecimen Bank Listing has parent organization: Radboud University; Nijmegen; The Netherlands |
Leukemia, Blood disease, Autoimmune disease, Type 1 diabetes, Diabetes | European Union FP7 282510 | Authorization required, Application required, Data Access Agreement, Acknowledgement required | nlx_158155 | SCR_003844 | BLUEPRINT - A BLUEPRINT of Haematopoietic Epigenomes | 2026-08-02 09:03:48 | 110 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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