Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Ligand-Gated Ion Channel Database Resource Report Resource Website 1+ mentions |
Ligand-Gated Ion Channel Database (RRID:SCR_002418) | LGICdb | data or information resource, database | Database providing access to information about transmembrane proteins that exist under different conformations, with three primary subfamilies: the cys-loop superfamily, the ATP gated channels superfamily, and the glutamate activated cationic channels superfamily. Due to the lack of evolutionary relationship, these three superfamilies are treated separately. It currently contains 554 entries of ligand-activated ion channel subunits. In this database one may find: the nucleic and proteic sequences of the subunits. Multiple sequence alignments can be generated, and some phylogenetic studies of the superfamilies are provided. Additionally, the atomic coordinates of subunits, or portion of subunits, are provided when available. Redundancy is kept to a minimum, i.e. one entry per gene. Each entry in the database has been manually constructed and checked by a researcher of the field in order to reduce the inaccuracies to a minimum. NOTE: This database is not actively maintained anymore. People should not consider it as an up-to-date trustable resource. For any new work, they should consider using alternative sources, such as UniProt, Ensembl, Protein Databank etc. | equilibrium, extracellular, gabaa, gated, gene, genetics, 3d model, alignment, anionic, atomic, atp, cationic, cellular, molecular, channel, compartment, computation, conformation, coordinate, cys-loop, glutamate, glycine, histamine, homologous, ion, ion channel, ligand, membrane, nicotinic, nucleic acid, phylogenetic, pore, portion, proteic, nucleic acid, protein, phylogeny, receptor, segment, sequence, sequence data, serotonin, subunit, superfamily, transmembrane |
is listed by: re3data.org has parent organization: European Bioinformatics Institute |
College of France; Paris; France ; Centre National de la Recherche Scientifique ; European Union ; Biotech and Biomed contracts ; French Ministry of Higher Education and Research ; Institut Pasteur |
PMID:16381861 PMID:11125117 |
nif-0000-00037, r3d100010796 | https://doi.org/10.17616/R3Q90D | SCR_002418 | LGIC Database | 2026-02-14 02:06:07 | 1 | |||||
|
Genes to Cognition Database Resource Report Resource Website |
Genes to Cognition Database (RRID:SCR_002735) | G2Cdb | data or information resource, database | Database of protein complexes, protocols, mouse lines, and other research products generated from the Genes to Cognition project, a project focused on understanding molecular complexes involved in synaptic transmission in the brain. | allele, gene list, mouse line, human disease, phenotyping, plasticity, behavior, proteonomics, brain, cognition, cognition disorder, learning, memory, neuroscience, experimental protocol, synapse proteomics, synapse | Wellcome Trust ; MRC ; BBSRC ; Gatsby Charitable Foundation ; Human Frontiers Science Programme ; European Union ; Framework Programme ; EPSRC ; NSF |
PMID:18984621 | Free, Freely available | nif-0000-02864 | http://www.genes2cognition.org/cgi-bin/SearchView | SCR_002735 | Genes-to-Cognition Database | 2026-02-14 02:06:11 | 0 | |||||
|
IPD - Immuno Polymorphism Database Resource Report Resource Website 10+ mentions |
IPD - Immuno Polymorphism Database (RRID:SCR_003004) | IPD | data or information resource, database | A set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. IPD currently consists of four databases: * IPD-KIR, contains the allelic sequences of Killer-cell Immunoglobulin-like Receptors, * IPD-MHC, is a database of sequences of the Major Histocompatibility Complex of different species; * IPD-human platelet antigens, alloantigens expressed only on platelets and * IPD-ESTDAB, which provides access to the European Searchable Tumour cell-line database, a cell bank of immunologically characterized melanoma cell lines. | polymorphic gene, immune system, gene, gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: European Bioinformatics Institute |
European Union contract QLRI-CT-200!-01325; NCI P01 111412 |
PMID:19875415 PMID:18449992 PMID:15608253 |
biotools:ipd, nif-0000-03038, r3d100010797 | https://bio.tools/ipd https://doi.org/10.17616/R3KK7K |
SCR_003004 | IPD-The Immuno Polymorphism Database, IPD - The Immuno Polymorphism Database | 2026-02-14 02:05:48 | 24 | |||||
|
Brede Database Resource Report Resource Website |
Brede Database (RRID:SCR_003327) | Brede | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 4th, 2023. A database of human data from functional neuroimaging scientific articles containing Talairach coordinates that provides data for novel information retrieval techniques and automated meta-analyses. Each article in this database is identified by a unique number: A WOBIB. Some of the structure of the Brede database is similar to the structure of the BrainMap database (Research Imaging Center, San Antonio). The database is inspired by the hierarchical structure of BrainMap with scientific articles (bib structures) on the highest level containing one or more experiments (exp structure, corresponding to a contrast in general linear model analyses), these in turn comprising one or more locations (loc structures). The information on the bib level (author, title, ...) is setup automatically from PubMed while the rest of the information is entered manually in a Matlab graphical user interface. On the loc level this includes the 3D stereotactic coordinates in either Talairach or MNI space, the brain area (functional, anatomical or cytoarchitectonic area) and magnitude values such as Z-score and P-value. On the exp level information such as modality, scanner and behavioral domain are recorded with external components (such as face recognition or kinetic boundaries) organized in a directed graph and marked up with Medical Subject Headings (MeSH) where possible. The database is distributed as part of the Brede neuroinformatics toolbox (hendrix.imm.dtu.dk/software/brede/) which also provides the functions to manipulate and analyze the data. The Brede Toolbox is a program package primarily written in Matlab. As of 2006/11, 186 papers with 586 experiments. | neuroinformatics, functional neuroimaging, talairach, mni, brain, fmri, neuroimaging, matlab, pet, positron emission tomography, functional magnetic resonance imaging, multichannel electroencephalography, eeg, magnetoencephalography, near infrared spectroscopic imaging, single photon emission computed tomography, mri, coordinate, brain function, brain region, ontology |
is used by: NIF Data Federation is related to: Brede Wiki is related to: Brede Toolbox is related to: Brede Toolbox is related to: Brede Wiki is related to: brainmap.org is related to: Integrated Manually Extracted Annotation has parent organization: Technical University of Denmark; Lyngby; Denmark |
European Union ; Project MAPAWAMO QLG3-CT-2000-300161 |
PMID:19668704 PMID:23666785 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00064 | SCR_003327 | 2026-02-14 02:05:49 | 0 | ||||||
|
IntEnz- Integrated relational Enzyme database Resource Report Resource Website 10+ mentions |
IntEnz- Integrated relational Enzyme database (RRID:SCR_002992) | IntEnz | data or information resource, database | IntEnz (Integrated relational Enzyme database) is a freely available resource focused on enzyme nomenclature. IntEnz is created in collaboration with the Swiss Institute of Bioinformatics (SIB). This collaboration is responsible for the production of the ENZYME resource. IntEnz contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions. | enzyme categories, enzyme classification, enzyme nomenclature, enzyme reaction categories, enzyme, gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: ENZYME has parent organization: European Bioinformatics Institute has parent organization: SIB Swiss Institute of Bioinformatics |
European Union SLING 226073 | PMID:14681451 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03028, biotools:intenz | https://bio.tools/intenz | SCR_002992 | 2026-02-14 02:06:12 | 13 | |||||
|
Glyco-CD Resource Report Resource Website |
Glyco-CD (RRID:SCR_001574) | GlycoCD, | data or information resource, data set | Manually curated, comprehensive repository of clusters of differentiation (CDs) which are a) defined as distinct oligosaccharide sequences as part of either glycoproteins and/or glycosphingolipids and b) defined as proteins which have carbohydrate recognition sites (CRDs) or as carbohydrate binding lectins. The data base is generated by exhaustive search of literature and other online data banks related to carbohydrates and proteins. This data bank is the beginning of an effort to provide concise, relevant information of carbohydrate-related CDs in a user- friendly manner. For users convenience the data bank under menu browse of GlycoCD is arranged in two section namely carbohydrate recognition CDs (CRD CD) and glycan CD. The carbohydrate recognition CD part is the collection of proteins which recognize glycan structures by means of the CRDs. Glycan CD is the part in which CDs are summarized which characterize specific oligosaccharide structures. The GlycoCD databank has been developed with the aim to assist the immunologist, cell biologist as well as the clinician who wants to keep up with the present knowledge in this field of glycobiology. | carbohydrate, glycobiology, glycan, lectin, antigen, interaction, protein, cell surface molecule, microarray, carbohydrate recognition, cluster of differentiation, oligosaccharide sequence, glycoprotein, glycosphingolipid, carbohydrate recognition site, leukocyte, antibody, endothelial cell, epithelial cell | has parent organization: glycosciences.de | European Union FP7/2007-2013 215536 | PMID:22847935 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152887 | http://www.glycosciences.de//Glyco-CD/ | SCR_001574 | GlycoCD database, Glyco-CD databank, Glyco-CD database | 2026-02-14 02:07:18 | 0 | ||||
|
mirEX Resource Report Resource Website 10+ mentions |
mirEX (RRID:SCR_006060) | mirEX | data analysis service, database, atlas, service resource, production service resource, data or information resource, analysis service resource | mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data. quantitative real-time PCR-based gene expression profiles are stored in a universal and expandable database scheme and wrapped by an intuitive user-friendly interface. A new way of accessing gene expression data in mirEX includes a simple mouse operated querying system and dynamic graphs for data mining analyses. In contrast to other publicly available databases, the mirEX interface allows a simultaneous comparison of expression levels between various microRNA genes in diverse organs and developmental stages. Currently, mirEX integrates information about the expression profile of 190 Arabidopsis thaliana pri-miRNAs in seven different developmental stages: seeds, seedlings and various organs of mature plants. Additionally, by providing RNA structural models, publicly available deep sequencing results, experimental procedure details and careful selection of auxiliary data in the form of web links, mirEX can function as a one-stop solution for Arabidopsis microRNA information. This database aims to be useful to anyone investigating the role of microRNAs in shaping plant development, organ formation and response to different biotic and abiotic stresses. To start exploring the database just press the "Browse Atlas" button or search for a particular microRNA record by typing at least two numbers from its ID in the window. | microrna gene expression, microrna, gene expression, gene, organ, developmental stage, plant, seed, seedling, mature plant, pri-mirna, biotic stress, abiotic stress, organ formation, primer, cdna | has parent organization: Adam Mickiewicz University in Poznan; Poznan; Poland | Foundation for Polish Science ; European Union ; Regional Development Fund MPD 2010/3; Polish Ministry of Science and Higher Education 3011/B/P01/2009/37 |
PMID:22013167 | nlx_151462 | http://bioinfo.amu.edu.pl/mirex | SCR_006060 | 2026-02-15 09:19:18 | 10 | ||||||
|
UMD-BRCA1/ BRCA2 databases Resource Report Resource Website 10+ mentions |
UMD-BRCA1/ BRCA2 databases (RRID:SCR_006128) | UMD-BRCA1/ BRCA2 databases | database, service resource, storage service resource, data repository, data or information resource | The UMD-BRCA1/BRCA2 databases have been set up in a joined national effort through the network of 16 diagnostic laboratories to provide up-to-date information about mutations of the BRCA1 and BRCA2 genes identified in patients with breast and/or ovarian cancer. These databases currently contain published and unpublished information about the BRCA1/BRCA2 mutations reported in French diagnostic laboratories. This database includes 28 references and 5530 mutations (1440 different mutations and 786 protein variants) The databases of BRCA1 and BRCA2 mutations were built using the Universal Mutation Database tool. For each mutation, information is provided at several levels: * at the gene level: exon and codon number, wild type and mutant codon, mutation event, mutation name and, * at the protein level: wild type and mutant amino acid, binding domain, affected domain. If you want to submit a mutation, please contact R. Lidereau., S. Caputo. or E. Rouleau. | cancer, gene, mutation, exon, codon, wild type, mutant, mutation, protein, amino acid, binding domain, affected domain, brca1, brca2, variant, polymorphism, unclassified variant, unknown variant, female, woman, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: National Institute of Health and Medical Research; Rennes; France |
Breast cancer, Ovarian cancer | French National Cancer Institute ; European Union FP7/2007-2013; Association dAide a la Recherche Cancerologique de Saint Cloud |
PMID:22144684 | The UMD- BRCA1 Locus Specific Databases constitute the intellectual property of the curators of the database. Any unauthorized copying, Storage or distribution of this material without written permission from the curators would lead to copyright infringement with possible ensuing litigation. | nlx_151608, biotools:brca_share | https://bio.tools/brca_share | SCR_006128 | UMD-BRCA1 mutations database, UMD-BRCA1 / BRCA2 databases, UMD-BRCA1/BRCA2 databases | 2026-02-15 09:19:19 | 26 | |||
|
European Nucleotide Archive (ENA) Resource Report Resource Website 1000+ mentions |
European Nucleotide Archive (ENA) (RRID:SCR_006515) | ENA | database, service resource, storage service resource, data repository, data or information resource | Public archive providing a comprehensive record of the world''''s nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation. All submitted data, once public, will be exchanged with the NCBI and DDBJ as part of the INSDC data exchange agreement. The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. A typical workflow includes the isolation and preparation of material for sequencing, a run of a sequencing machine in which sequencing data are produced and a subsequent bioinformatic analysis pipeline. ENA records this information in a data model that covers input information (sample, experimental setup, machine configuration), output machine data (sequence traces, reads and quality scores) and interpreted information (assembly, mapping, functional annotation). Data arrive at ENA from a variety of sources including submissions of raw data, assembled sequences and annotation from small-scale sequencing efforts, data provision from the major European sequencing centers and routine and comprehensive exchange with their partners in the International Nucleotide Sequence Database Collaboration (INSDC). Provision of nucleotide sequence data to ENA or its INSDC partners has become a central and mandatory step in the dissemination of research findings to the scientific community. ENA works with publishers of scientific literature and funding bodies to ensure compliance with these principles and to provide optimal submission systems and data access tools that work seamlessly with the published literature. ENA is made up of a number of distinct databases that includes the EMBL Nucleotide Sequence Database (Embl-Bank), the newly established Sequence Read Archive (SRA) and the Trace Archive. The main tool for downloading ENA data is the ENA Browser, which is available through REST URLs for easy programmatic use. All ENA data are available through the ENA Browser. Note: EMBL Nucleotide Sequence Database (EMBL-Bank) is entirely included within this resource. | analysis, bioinformatics, dna, nucleotide, sequencing, web service, rna, molecular biology, nucleotide sequence, protein, gene expression, gene, genome, biochemistry, molecular structure, metabolite, protein binding, chemogenomics, gold standard |
is used by: BioSample Database at EBI 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 related to: NCBI Sequence Read Archive (SRA) is related to: ENA Sequence Version Archive is related to: VBASE2 is related to: DDBJ Sequence Read Archive is related to: ISA Infrastructure for Managing Experimental Metadata is related to: DNA DataBank of Japan (DDBJ) is related to: DNA DataBank of Japan (DDBJ) is related to: NCBI is related to: INSDC is related to: INSDC is related to: NCBI Assembly Archive Viewer has parent organization: European Bioinformatics Institute is parent organization of: ENA Sequence Search works with: Eutherian comparative genomic analysis protocol |
EMBL ; Wellcome Trust ; European Union |
PMID:20972220 | Public, The community can contribute to this resource, Acknowledgement requested | OMICS_01029, r3d100010527, nif-0000-32981 | http://www.ebi.ac.uk/embl/ https://doi.org/10.17616/R3HW3J |
SCR_006515 | ENA, European Nucleotide Archive | 2026-02-15 09:19:18 | 1272 | ||||
|
PROSITE Resource Report Resource Website 1000+ mentions |
PROSITE (RRID:SCR_003457) | PROSITE | data analysis service, database, service resource, production service resource, data or information resource, analysis service resource | Database of protein families and domains that is based on the observation that, while there is a huge number of different proteins, most of them can be grouped, on the basis of similarities in their sequences, into a limited number of families. Proteins or protein domains belonging to a particular family generally share functional attributes and are derived from a common ancestor. It is complemented by ProRule, a collection of rules based on profiles and patterns, which increases the discriminatory power of profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. ScanProsite finds matches of your protein sequences to PROSITE signatures. PROSITE currently contains patterns and profiles specific for more than a thousand protein families or domains. Each of these signatures comes with documentation providing background information on the structure and function of these proteins. The database is available via FTP. | protein domain, protein family, functional site, protein, structure, function, pattern, profile |
is listed by: OMICtools has parent organization: SIB Swiss Institute of Bioinformatics |
Swiss Federal government through the Federal Office of Education and Science ; European Union contract FELICS 021902RII3; European Union contract IMPACT 213037; FNS 315200-116864 |
PMID:23161676 PMID:19858104 PMID:12230035 |
Free, Freely available | nif-0000-03351, OMICS_01699 | http://www.expasy.org/prosite, http://www.expasy.ch/prosite/ | SCR_003457 | PROSITE - Database of protein domains families and functional sites | 2026-02-15 09:18:31 | 2165 | ||||
|
AddNeuroMed Resource Report Resource Website 50+ mentions |
AddNeuroMed (RRID:SCR_003819) | AddNeuroMed | organization portal, portal, database, consortium, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9,2023. Project portal for a cross European study designed to find biomarkers, or tests, for Alzheimer's disease. Its objectives are to produce and improve experimental models of Alzheimer's for biomarker discovery and to identify a biomarker for Alzheimer's disease suitable for diagnosis, prediction, and monitoring disease progression for use in clinical trials and in clinical practice. The baseline dataset database was scheduled to be completed and locked in 2008 and become available to researchers by 2009. Requests to access the data will be reviewed by the scientific projects committee. | biomarker, test, diagnostic, device, clinical, animal model, clinical trial, pre-clinical, consortium, disease progression, mri, proteomics, genomics, lipidomics, neuroimaging, mouse model, rat model, drosophila model, FASEB list |
is listed by: Consortia-pedia is related to: Innovative Medicines Initiative is related to: University of Eastern Finland at Kuopio; Kuopio; Finland is related to: University of Perugia; Perugia; Italy is related to: Aristotle University of Thessaloniki; Thessaloniki; Greece is related to: King's College London; London; United Kingdom is related to: University of Lodz; Lodz; Poland has parent organization: Innovative Medicines Initiative has parent organization: King's College London; London; United Kingdom |
European Union ; EFPIA |
PMID:19906259 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_158122 | SCR_003819 | The AddNeuroMed Study | 2026-02-15 09:18:35 | 77 | |||||
|
PDBe - Protein Data Bank in Europe Resource Report Resource Website 50+ mentions |
PDBe - Protein Data Bank in Europe (RRID:SCR_004312) | PDBe | database, service resource, storage service resource, data repository, data or information resource | The European resource for the collection, organization and dissemination of data on biological macromolecular structures. In collaboration with the other worldwide Protein Data Bank (wwPDB) partners - the Research Collaboratory for Structural Bioinformatics (RCSB) and BioMagResBank (BMRB) in the USA and the Protein Data Bank of Japan (PDBj) - they work to collate, maintain and provide access to the global repository of macromolecular structure data. The main objectives of the work at PDBe are: * to provide an integrated resource of high-quality macromolecular structures and related data and make it available to the biomedical community via intuitive user interfaces. * to maintain in-house expertise in all the major structure-determination techniques (X-ray, NMR and EM) in order to stay abreast of technical and methodological developments in these fields, and to work with the community on issues of mutual interest (such as data representation, harvesting, formats and standards, or validation of structural data). * to provide high-quality deposition and annotation facilities for structural data as one of the wwPDB deposition sites. Several sophisticated tools are also available for the structural analysis of macromolecules. | x-ray, nmr, cryo-em, hybrid method, dna, protein, rna, sugar, ligand, virus, compound, fold, enzyme, 3d spatial image, structure, macromolecule, protein-protein interaction, gold standard, bio.tools |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: DNA DataBank of Japan (DDBJ) is related to: EMDataResource.org is related to: Worldwide Protein Data Bank (wwPDB) is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: DNA DataBank of Japan (DDBJ) is related to: Worldwide Protein Data Bank (wwPDB) is related to: PDBj - Protein Data Bank Japan is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: European Bioinformatics Institute is parent organization of: Electron Microscopy Data Bank at PDBe (MSD-EBI) works with: MOLEonline |
European Molecular Biology Laboratory; Heidelberg; Germany ; Wellcome Trust ; BBSRC ; NIH ; European Union ; MRC ; CCP4 |
PMID:21045060 PMID:21460450 PMID:19858099 |
r3d100012791, biotools:pdbe, nlx_32372 | https://bio.tools/pdbe https://doi.org/10.17616/R3J226 |
SCR_004312 | Protein DataBank Europe, Protein DataBank in Europe, PDBe, Protein Data Bank in Europe, Protein Data Bank Europe, Macromolecular Structure Database | 2026-02-15 09:18:41 | 52 | |||||
|
IntAct Resource Report Resource Website 1000+ mentions |
IntAct (RRID:SCR_006944) | IntAct | database, service resource, storage service resource, data repository, data or information resource | Open source database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions. Direct user submissions of molecular interaction data are encouraged, which may be deposited prior to publication in a peer-reviewed journal. The IntAct Database contains (Jun. 2014): * 447368 Interactions * 33021 experiments * 12698 publications * 82745 Interactors IntAct provides a two-tiered view of the interaction data. The search interface allows the user to iteratively develop complex queries, exploiting the detailed annotation with hierarchical controlled vocabularies. Results are provided at any stage in a simplified, tabular view. Specialized views then allows "zooming in" on the full annotation of interactions, interactors and their properties. IntAct source code and data are freely available. | protein domain, motif, protein interaction, molecular interaction, interaction, protein, binary interaction, complex, data set, protein-protein interaction, pathway, small molecule-protein, nucleic acid-protein, small molecule, nucleic acid, protein binding, chromatin, cancer, apoptosis, molecular biology, virus, source code, isoform, gold standard |
is used by: ChannelPedia is used by: MINT is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is recommended by: NIDDK Information Network (dkNET) 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 related to: 3D-Interologs is related to: IMEx - The International Molecular Exchange Consortium is related to: MPIDB is related to: TissueNet - The Database of Human Tissue Protein-Protein Interactions is related to: InteroPorc is related to: Interaction Reference Index is related to: Pathway Commons is related to: ConsensusPathDB is related to: FlyMine is related to: IMEx - The International Molecular Exchange Consortium is related to: Integrated Molecular Interaction Database is related to: VirHostNet: Virus-Host Network is related to: PSICQUIC Registry is related to: UniProt is related to: SIB Swiss Institute of Bioinformatics is related to: I2D is related to: InnateDB is related to: MatrixDB is related to: MBInfo is related to: AgBase is related to: Cardiovascular Gene Ontology Annotation Initiative is related to: PSI-MI is related to: Agile Protein Interactomes DataServer has parent organization: European Bioinformatics Institute works with: IMEx - The International Molecular Exchange Consortium |
European Union contract FP7-HEALTH-2007-223411; European Union contract FP7-HEALTH-2007-200767 |
PMID:24234451 PMID:22121220 PMID:19850723 PMID:17145710 PMID:14681455 |
Apache License, v2, (software), Creative Commons Attribution License, (data), The community can contribute to this resource | OMICS_01918, r3d100010671, nif-0000-03026 | https://doi.org/10.17616/R3QS4R | SCR_006944 | IntAct | 2026-02-15 09:19:38 | 1892 | ||||
|
Malaria Parasite Metabolic Pathways Resource Report Resource Website 10+ mentions |
Malaria Parasite Metabolic Pathways (RRID:SCR_007072) | Malaria Parasite Metabolic Pathways | image collection, data or information resource, data set | Data set of metabolic pathways for the malaria parasite based on the present knowledge of parasite biochemistry and on pathways known to occur in other unicellular eukaryotes. This site extracted the pertinent information from the universal sites and presented them in an educative and informative format. The site also includes, cell-cell interactions (cytoadherence and rosetting), invasion of the erythrocyte by the parasite and transport functions. It also contains an artistic impression of the ultrastructural morphology of the interaerythrocytic cycle stages and some details about the morphology of mitochondria and the apicoplast. Most pathways are relevant to the erythrocytic phase of the parasite cycle. All maps were checked for the presence of enzyme-coding genes as they are officially annotated in the Plasmodium genome (http://plasmodb.org/). The site is constructed in a hierarchical pattern that permits logical deepening: * Grouped pathways of major chemical components or biological process ** Specific pathways or specific process *** Chemical structures of substrates and products or process **** Names of enzymes and their genes or components of process Each map is linked to other maps thus enabling to verify the origin of a substrate or the fate of a product. Clicking on the EC number that appears next to each enzyme, connects the site to BRENDA, SWISSPROT ExPASy ENZYME, PlasmoDB and to IUBMB reaction scheme. Clicking of the name of a metabolite, connects the site to KEGG thus providing its chemical structure and formula. Next to each enzyme there is a pie that depicts the stage-dependent transcription of the enzyme''s coding gene. The pie is constructed as a clock of the 48 hours of the parasite cycle, where red signifies over-transcription and green, under-transcription. Clicking on the pie links to the DeRisi/UCSF transcriptome database. | enzyme, gene, genome, map, metabolic, mosquito, parasite, pathway, plasmodium falciparum, protein, reaction, sequence, metabolic pathway, chemical structure, cell-cell interaction, transport, morphology, mitochondria, apicoplast | has parent organization: Hebrew University of Jerusalem; Jerusalem; Israel | Malaria | UNDP/World Bank/WHO Special Programme ; NIAID ; European Union ; 6th FP- BioMalPar Network of Excellence on Biology and Pathology of the Malaria Parasite |
nif-0000-21249 | SCR_007072 | 2026-02-15 09:19:41 | 20 | |||||||
|
IMGT/GENE-DB Resource Report Resource Website 50+ mentions |
IMGT/GENE-DB (RRID:SCR_006964) | IMGT/GENE-DB | database, data or information resource, narrative resource, standard specification, international standard specification | IMGT/GENE-DB is the comprehensive IMGT genome database for immunoglobulin (IG) and T cell receptor (TR) genes from human and mouse, and, in development, from other vertebrates. IMGT/GENE-DB is the international reference for the IG and TR gene nomenclature and works in close collaboration with the HUGO Nomenclature Committee, Mouse Genome Database and genome committees for other species. IMGT/GENE-DB allows a search of IG and TR genes by locus, group and subgroup, which are CLASSIFICATION concepts of IMGT-ONTOLOGY. Short cuts allow the retrieval gene information by gene name or clone name. Direct links with configurable URL give access to information usable by humans or programs. An IMGT/GENE-DB entry displays accurate gene data related to genome (gene localization), allelic polymorphisms (number of alleles, IMGT reference sequences, functionality, etc.) gene expression (known cDNAs), proteins and structures (Protein displays, IMGT Colliers de Perles). It provides internal links to the IMGT sequence databases and to the IMGT Repertoire Web resources, and external links to genome and generalist sequence databases. IMGT/GENE-DB manages the IMGT reference directory used by the IMGT tools for IG and TR gene and allele comparison and assignment, and by the IMGT databases for gene data annotation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: IMGT - the international ImMunoGeneTics information system |
Centre National de la Recherche Scientifique ; Ministere de l'Education Nationale de l'Enseignement Superieur et de la Recherche BIOSTIC-LR2004; Ministere de l'Education Nationale de l'Enseignement Superieur et de la Recherche ACI-IMPBIO IMP82-2004; European Union 5th PCRDT programme QLG2-2000-01287 |
PMID:15608191 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03012, biotools:IMGt_GENE-Db, r3d100012536 | https://bio.tools/IMGT_GENE-DB https://doi.org/10.17616/R3Q48Q |
http://imgt.cines.fr, http://imgt.cines.fr/cgi-bin/GENElect.jv | SCR_006964 | 2026-02-15 09:19:25 | 78 | ||||
|
BovMap Database Resource Report Resource Website 1+ mentions |
BovMap Database (RRID:SCR_008145) | BovMap | database, service resource, storage service resource, data repository, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Database containing information on the cattle genome comprising loci list, phenes list, homology query, cattle maps, gene list, and chromosome homology. The objective of BovMap is to develop a set of anchored loci for the cattle genome map. In total, 58 clones were hybridized with chromosomes and identified loci on 22 of the 31 different bovine chromosomes. Three clones contained satellite DNA. Two or more markers were placed on 12 chromosomes. Sequencing of the microsatellites and flanking regions was performed directly from 43 cosmids, as previously reported. Primers were developed for 39 markers and used to describe the polymorphism associated with the corresponding loci. Users are also allowed to summit their own data for Bovmap. An integrated cytogenetic and meiotic map of the bovine genome has also been developed around the Bovmap database. One objective that Bovmap uses as the mapping strategy for the bovine genome uses large insert clones as a tool for physical mapping and as a source of highly polymorphic microsatellites for genetic typing. | genetic, bovine, cattle, chromosome, clone, cosmid, cow, cytogenetic, dna, genome, homology, locus, meiotic, phene, polymorphism, sequence, map, gene | has parent organization: INRA - French National Institute for Agricultural Research; Paris; France | European Union | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20968 | SCR_008145 | 2026-02-15 09:19:28 | 2 | |||||||
|
hFigures Resource Report Resource Website 1+ mentions |
hFigures (RRID:SCR_014201) | software application, data visualization software, data processing software, software resource, network graph visualization software | A Javascript library that aims to deliver a starting point for interactive health data visualization. Examples and demos are available on the site. hFigures was built with d3.js and a copy of the library is included in this repository. All rights and license terms apply to the d3.js library accordingly. | health data, visualization, electronic health record, personal health record, health informatics | has parent organization: University of Tampere; Tampere; Finland | European Union ; TEKES ; BMC Medical Informatics and Decision Making Health Figures Software Article |
PMID:26738061 | Available for download | SCR_014201 | 2026-02-15 09:20:52 | 2 | ||||||||
|
Functional Anatomy of the Cerebro-Cerebellar System (FACCS) Resource Report Resource Website |
Functional Anatomy of the Cerebro-Cerebellar System (FACCS) (RRID:SCR_001661) | FACCS | data analysis service, database, service resource, storage service resource, production service resource, data repository, data or information resource, analysis service resource | Public neuroscience database providing a collection of published data describing structure and structure-function relationships in one of the largest projection systems of the brain: the cerebro-cerebellar system. It also gives access to a suite of tools that allow the user to visualize and analyze any selected combination of data sets. Contact them if you are interested in contributing data. The overall goal is to improve communication of results and permit re-use of previously published data in new contexts. FACCS is a part of the Rat Brain WorkBench, a new research and development project funded by The Research Council of Norway, the Centre for Molecular Biology and Neuroscience, and the European Union. The project is directed by Jan G. Bjaalie, Centre for Molecular Biology and Neuroscience & Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway. | axonal tracer, axon tracing, brain, cerebellum, cerebral cortex, cerebro-cerebellar function, cerebro-cerebellar structure, cerebro-cerebellar system, injection, injection site, labeled cells, labeled fibers, pontine nuclear complex, pontine nuclei, video, cerebellar cortex | has parent organization: University of Oslo; Oslo; Norway | Research Council of Norway ; Centre for Molecular Biology and Neuroscience ; European Union |
PMID:17426352 PMID:16344144 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02317 | SCR_001661 | Functional Anatomy of the Cerebro-Cerebellar System | 2026-02-15 09:18:09 | 0 | |||||
|
MatrixDB Resource Report Resource Website 50+ mentions |
MatrixDB (RRID:SCR_001727) | MatrixDB | data or information resource, database, service resource, production service resource | Freely available database focused on interactions established by extracellular proteins and polysaccharides, taking into account the multimeric nature of the extracellular proteins (e.g. collagens, laminins and thrombospondins are multimers). MatrixDB is an active member of the International Molecular Exchange (IMEx) consortium and has adopted the PSI-MI standards for annotating and exchanging interaction data. It includes interaction data extracted from the literature by manual curation, and offers access to relevant data involving extracellular proteins provided by the IMEx partner databases through the PSICQUIC webservice, as well as data from the Human Protein Reference Database. The database reports mammalian protein-protein and protein-carbohydrate interactions involving extracellular molecules. Interactions with lipids and cations are also reported. MatrixDB is focused on mammalian interactions, but aims to integrate interaction datasets of model organisms when available. MatrixDB provides direct links to databases recapitulating mutations in genes encoding extracellular proteins, to UniGene and to the Human Protein Atlas that shows expression and localization of proteins in a large variety of normal human tissues and cells. MatrixDB allows researchers to perform customized queries and to build tissue- and disease-specific interaction networks that can be visualized and analyzed with Cytoscape or Medusa. Statistics (2013): 2283 extracellular matrix interactions including 2095 protein-protein and 169 protein-glycosaminoglycan interactions. | extracellular, protein fragment, biomolecule, cation, cleavage, collagen, glycosaminoglycan, human, interaction, laminin, lipid, mammalian, matricryptin, matrikin, matrix, molecule, monomer, mulimerization, multimer, polysaccharide, protein, protein-carbohydrate interaction, protein-protein interaction, recognition, thrombospondin, interactome, extracellular protein, protein-polysaccharide interaction, extracellular interaction, molecular interaction, model organism, inorganic, small molecule-protein, small molecule, extracellular matrix protein, protein-glycosaminoglycan interaction, bio.tools, FASEB list |
is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: IMEx - The International Molecular Exchange Consortium is related to: Gene Ontology is related to: PSI-MI is related to: HPRD - Human Protein Reference Database is related to: Interaction Reference Index is related to: ConsensusPathDB is related to: IMEx - The International Molecular Exchange Consortium is related to: PSICQUIC Registry is related to: IntAct has parent organization: Claude Bernard University Lyon 1; Lyon; France |
European Union contract FP7-HEALTH-2007-223411 | PMID:20852260 PMID:19147664 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:matrixdb, r3d100010672, nif-0000-10226 | https://bio.tools/matrixdb https://doi.org/10.17616/R3M03H |
http://matrixdb.ibcp.fr/ | SCR_001727 | MatrixDB: Extracellular Matrix Interactions Database, Extracellular Matrix Interactions Database | 2026-02-15 09:18:10 | 86 | |||
|
Biocatalogue - The Life Science Web Services Registry Resource Report Resource Website 1+ mentions |
Biocatalogue - The Life Science Web Services Registry (RRID:SCR_001679) | BioCatalogue | database, software resource, data access protocol, web service, data or information resource | Crowd-curated catalog of life sciences Web services with over 2400 service entries, thereby enabling users (people and programs) to discover and use these services easily. It provides a platform with several (standardized) interfaces and a suite of tools for registration of services by the community of users as well as empowers the community to extend and enhance the system. BioCatalogue provides a centralized biological web services market place which is accessible to the world as it is searchable and indexable to search engines. Additionally, it provides a quality of service standard for biological web services thereby enabling services to be classified and checked for availability, reliability and other quality measures. Primary goals: * Provide a single registration point for Web Service providers and a single search site for scientists and developers. * Providers, Expert curators and Users will provide oversight, monitor the catalog and provide high quality annotations for services. * BioCatalogue is a place where the community can find contacts and meet the experts and maintainers of these services. | biological, web, life science, programmatic access, bioinformatics, registry, annotation, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: MetaLocGramN is related to: myExperiment is related to: bioDBcore has parent organization: European Bioinformatics Institute has parent organization: University of Manchester; Manchester; United Kingdom |
European Union LHSG-CT-2004-512092; EMBO ASTF 338.00-2009 |
PMID:20484378 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:biocatalogue, nif-0000-10167 | https://bio.tools/biocatalogue | SCR_001679 | Biocatalog | 2026-02-15 09:18:09 | 7 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF 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 NIF then you can log in from here to get additional features in NIF 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 NIF 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.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
