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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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CellML Model Repository Resource Report Resource Website 1+ mentions |
CellML Model Repository (RRID:SCR_008113) | CellML Repository | storage service resource, software resource, software repository, data repository, service resource | Repository of biological models created using CellML, a free, open-source, eXtensible markup language based standard for defining mathematical models of cellular function. Models may be browsed by category, which include: Calcium Dynamics, Cardiovascular Circulation, Cell Cycle, Cell Migration, Circadian Rhythms, Electrophysiology, Endocrine, Excitation-Contraction Coupling, Gene Regulation, Hepatology, Immunology, Ion Transport, Mechanical Constitutive Laws, Metabolism, Myofilament Mechanics, Neurobiology, pH Regulation, PKPD, Signal Transduction, Synthetic Biology. The community can contribute their models to this resource. | cell function, cell model, model, cell, calcium dynamics, cardiovascularc circulation, cell cycle, cell migration, circadian rhythm, electrophysiology, endocrine, excitation-contraction coupling, gene regulation, hepatology, immunology, ion transport, mechanical constitutive law, metabolism, myofilament mechanics, neurobiology, ph regulation, pkpd, signal transduction, synthetic biology, image, exposure |
is used by: NIF Data Federation is listed by: 3DVC is listed by: Integrated Models is related to: Integrated Manually Extracted Annotation has parent organization: CellML |
Wellcome Trust ; Royal Society of New Zealand ; Maurice Wilkins Centre for Molecular Biodiscovery |
PMID:21216774 PMID:18658182 PMID:17947072 PMID:19162720 PMID:19380315 |
The community can contribute to this resource | nif-0000-20828 | SCR_008113 | 2026-08-04 09:42:05 | 6 | ||||||
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CellML Resource Report Resource Website 100+ mentions |
CellML (RRID:SCR_008061) | CellML | markup language, interchange format, narrative resource, standard specification, data or information resource | The CellML language is an open standard based on the XML markup language. The purpose of CellML is to store and exchange computer-based mathematical models. CellML allows scientists to share models even if they are using different model-building software. It also enables them to reuse components from one model in another, thus accelerating model building. Although CellML was originally intended for the description of biological models; CellML includes information about model structure (how the parts of a model are organizationally related to one another), mathematics (equations describing the underlying processes) and metadata (additional information about the model that allows scientists to search for specific models or model components in a database or other repository). The CellML team is committed to providing freely available tools for creating, editing, and using CellML models. We provide information regarding tools we are developing internally and links to external projects developing tools which utilize the CellML format. Please let us know if you have an open source CellML tool looking for a home on the internet, as we are able to offer limited hosting services on cellml.org. | biological model, cell, mathematical model, mathematics, metadata, model structure, model, xml, annotation, mark up language, FASEB list |
is listed by: 3DVC is related to: PathGuide: the pathway resource list is related to: Physiome Model Repository has parent organization: University of Auckland; Auckland; New Zealand is parent organization of: CellML Model Repository |
VPH NoE ; Maurice Wilkins Centre for Molecular Biodiscovery ; International Union of Physiological Sciences: Physiome Project ; aneurIST ; NZIMA ; Foundation for Research Science and Technology ; Wellcome Trust |
PMID:15142756 PMID:18658182 PMID:19564239 PMID:19380315 PMID:18579471 PMID:17947072 PMID:17271569 |
The CellML project is built by an open, Democratic community on an Open unspecified license / free ethic. | nif-0000-10448 | SCR_008061 | CellML project, The CellML Project | 2026-08-04 09:42:01 | 146 | |||||
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ORCID - Open Researcher and Contributor ID Resource Report Resource Website 100+ mentions |
ORCID - Open Researcher and Contributor ID (RRID:SCR_008700) | ORCID | narrative resource, standard specification, service resource, international standard specification, data or information resource | Non-profit organization dedicated to solving the author/contributor name ambiguity problem in scholarly communications by creating a central registry of unique identifiers for individual researchers and an open and transparent linking mechanism between ORCID and other current author ID schemes. These identifiers, and the relationships among them, can be linked to the researcher''s output to enhance the scientific discovery process and to improve the efficiency of research funding and collaboration within the research community. The ideal solution is to establish a registry that is adopted and embraced as the de facto standard by the whole of the community. A resolution to the systemic name ambiguity problem, by means of assigning unique identifiers linkable to an individual''s research output, will enhance the scientific discovery process and improve the efficiency of funding and collaboration. The organization brings together the leaders of the most influential universities, funding organizations, societies, publishers and corporations from around the globe and is managed by a fourteen member Board of Directors. A disambiguated set of authors will allow new services and benefits to be built for the research community by all stakeholders in scholarly communication: from commercial actors to non-profit organizations, from governments to universities. | name ambiguity, scholarly communication, unique identifier, author identification, identifier service, people resource |
is used by: Academic Karma is listed by: FORCE11 is related to: Europe PubMed Central is related to: Academic Karma is parent organization of: ODIN |
American Physical Society ; Nature Publishing Group ; Wiley ; Hindawi ; Oxford University Press ; PLoS ; MIT Libraries ; Springer ; Wellcome Trust ; American Chemical Society ; Microsoft Research ; Elsevier ; American Institute of Physics ; Association for Computing Machinery ; Taylor and Francis Group ; Thompson Reuters |
nif-0000-37710 | SCR_008700 | ORCID: Open Researcher and Contributor ID, Open Reseacher & Contributor ID (ORCID), ORCID - Open Researcher Contributor ID, Open Researcher and Contributor ID, ORCID - Open Researcher and Contributor ID, ORCID - Open Reseacher & Contributor ID | 2026-08-04 09:42:12 | 476 | |||||||
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TriTrypDB Resource Report Resource Website 500+ mentions |
TriTrypDB (RRID:SCR_007043) | TriTrypDB | data analysis service, analysis service resource, web service, software resource, data access protocol, production service resource, service resource, database, data or information resource | An integrated genomic and functional genomic database providing access to genome-scale datasets for kinetoplastid parasites, and supporting a variety of complex queries driven by research and development needs. Currently, TriTrypDB integrates datasets from Leishmania braziliensis, L. infantum, L. major, L. tarentolae, Trypanosoma brucei and T. cruzi. Users may examine individual genes or chromosomal spans in their genomic context, including syntenic alignments with other kinetoplastid organisms. Data within TriTrypDB can be interrogated utilizing a sophisticated search strategy system that enables a user to construct complex queries combining multiple data types. All search strategies are stored, allowing future access and integrated searches. ''''User Comments'''' may be added to any gene page, enhancing available annotation; such comments become immediately searchable via the text search, and are forwarded to curators for incorporation into the reference annotation when appropriate. TriTrypDB provides programmatic access to its searches, via REST Web Services. The result of a web service request is a list of records (genes, ESTs, etc) in either XML or JSON format. REST services can be executed in a browser by typing a specific URL. TriTrypDB and its continued development are possible through the collaborative efforts between EuPathDB, GeneDB and colleagues at the Seattle Biomedical Research Institute (SBRI). | kinetoplastid parasite, pathogen, genome, gene chromosome, annotation, trypanosomatidae, parasite, blast, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: GeneDB is related to: GeneDB Lmajor is related to: GeneDB Tbrucei has parent organization: Eukaryotic Pathogen Database Resources |
Bill and Melinda Gates Foundation 50097; Wellcome Trust WT085822MA; Wellcome Trust WT085775/Z/08/Z |
PMID:19843604 | Public - please cite. Much of the data in TriTrypDB is provided by independent researchers. Please cite them if you use their data. | nlx_152064, biotools:tritrypdb, r3d100011479 | https://bio.tools/tritrypdb, https://doi.org/10.17616/R3J05N | SCR_007043 | 2026-08-04 09:41:45 | 670 | |||||
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IUPHAR/BPS Guide to Pharmacology Resource Report Resource Website 1000+ mentions |
IUPHAR/BPS Guide to Pharmacology (RRID:SCR_013077) | IUPHAR Database, IUPHAR-DB, IUPHAR GPCR, IUPHAR RECEPTOR | portal, narrative resource, standard specification, database, data or information resource | Portal and searchable database of pharmacological information. Information is presented at two levels, the initial view or landing pages for each target family provide expert-curated overviews of the key properties and the available selective ligands and tool compounds. For selected targets, more detailed introductory chapters for each family are available along with curated information on the pharmacological, physiological, structural, genetic and pathophysiogical properties of each target. | pharmacology, drug discovery, portal, guide, physiology, molecular structure, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: NC-IUPHAR |
Wellcome Trust | PMID:21087994 | nif-0000-03056, biotools:iuphar-db, r3d100013308 | https://bio.tools/iuphar-db, https://doi.org/10.17616/R31NJMRG | http://www.iuphar-db.org | SCR_013077 | International Union of Pharmacology Database, International Union of Basic and Clinical Pharmacology Database | 2026-08-04 09:43:08 | 2259 | ||||
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PALM Resource Report Resource Website 10+ mentions |
PALM (RRID:SCR_017029) | PALM | data processing software, software application, software resource, data analysis software | Software tool for inference using permutation methods. Requires Matlab or Octave. Can be executed from inside either environment, or directly from the shell and can be called from scripts. For users who are familiar with statistics and willing to use experimental analysis tools. | statistics, permutation, bootstrap, non parametric, combination, inference |
requires: MATLAB is a plug in for: FSL |
GlaxoSmithKline ; Marie Curie ITN ; Medical Research Council ; Wellcome Trust ; NIBIB R01 EB015611; MRC G0900908; Brazilian National Research Council |
PMID:24530839 PMID:26074200 DOI:10.1002/hbm.23115 PMID:27288322 |
Free, Available for download, Freely available | https://github.com/andersonwinkler/PALM | SCR_017029 | PALM, Permutation Analysis of Linear Models | 2026-08-04 09:44:02 | 47 | |||||
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Physiome Model Repository Resource Report Resource Website 1+ mentions |
Physiome Model Repository (RRID:SCR_017374) | PMR | storage service resource, dynamic model, data repository, service resource, data or information resource, model | Repository of mainly CellML models powered by collection of software tools and libraries with PMR2 software suite as core power. Third party integration suites are RICORDO, Virtuoso, BiVeS/BudHat, OpenCOR, CombineArchive Web, WebCAT, Morre/MaSyMoS. | Physiology, repository, CellML, cell, model, file, metadata, PMR2 |
is used by: SPARC Portal is related to: CellML is related to: International Union of Physiological Sciences: Physiome Project |
British Heart Foundation ; Maurice Wilkins Centre for Molecular Biodiscovery ; Virtual Physiological Human Network of Excellence ; Wellcome Trust ; Auckland Bioengineering Institute |
DOI:10.1093/bioinformatics/btq723 | Free, Available for download, Freely available | http://www.cellml.org/tools/pmr/, http://models.cellml.org/ | SCR_017374 | Physiome Repository, PMR2 | 2026-08-04 09:44:11 | 5 | |||||
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VasoTracker Resource Report Resource Website 1+ mentions |
VasoTracker (RRID:SCR_017233) | data processing software, data analysis software, software resource, software application, data acquisition software | Open source and stand alone software for assessing vascular reactivity. Used in pressure myograph system. | vascular, reactivity, pressure, myograph, system |
is related to: Durham University; Durham; England has parent organization: University of Strathclyde; Glasgow; United Kingdom |
Wellcome Trust ; British Heart Foundation |
PMID:30846942 | Free, Available for download, Freely available | https://github.com/VasoTracker/VasoTracker | SCR_017233 | 2026-08-04 09:44:07 | 5 | |||||||
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Accessible Resource for Integrated Epigenomics Studies Resource Report Resource Website 10+ mentions |
Accessible Resource for Integrated Epigenomics Studies (RRID:SCR_017492) | portal, web service, topical portal, software resource, data access protocol, data or information resource | Portal for epigenomic information on range of human tissues, including DNA methylation data on peripheral blood at multiple time points across lifecourse. Provides web interface to browse methylation variation between groups of individuals and across time. | Epigenomic, human, tissue, DNA, methylation, data, peripheral, blood | BBSRC ; Medical Research Council ; Wellcome Trust ; University of Bristol |
PMID:25991711 | Free, Freely available | http://www.bristol.ac.uk/alspac/ | SCR_017492 | ARIES | 2026-08-04 09:44:10 | 33 | |||||||
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NeuroChaT Resource Report Resource Website 1+ mentions |
NeuroChaT (RRID:SCR_018020) | data processing software, data analysis software, software resource, software application, software toolkit | Software open source python toolbox to analyse neuronal signals recorded in vivo in freely behaving animal, with particular emphasis on spatial coding. Can be used as application programming interface, or as general user interface, and is designed to help simplify adoption of standardised analyses for behavioural neurophysiology and facilitate open data sharing and collaboration between laboratories. | Neuronal signal, analysis, freely behaving animal, spatial coding, behavioural neurophysiology, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
Wellcome Trust | DOI:12688/wellcomeopenres.15533.1 | Free, Available for download, Freely available | biotools:NeuroChat | https://bio.tools/NeuroChaT | SCR_018020 | Neuron Characterisation Toolbox | 2026-08-04 09:44:16 | 2 | |||||
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eVOC Resource Report Resource Website 1+ mentions |
eVOC (RRID:SCR_010704) | eVOC | ontology, data or information resource, controlled vocabulary | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented September 6, 2016. Set of orthogonal controlled vocabularies that unifies gene expression data by facilitating a link between the genome sequence and expression phenotype information. The system associates labelled target cDNAs for microarray experiments, or cDNA libraries and their associated transcripts with controlled terms in a set of hierarchical vocabularies. eVOC consists of four orthogonal controlled vocabularies suitable for describing the domains of human gene expression data including Anatomical System, Cell Type, Pathology and Developmental Stage. The four core eVOC ontologies provide an appropriate set of detailed human terms that describe the sample source of human experimental material such as cDNA and SAGE libraries. These expression terms are linked to libraries and transcripts allowing the assessment of tissue expression profiles, differential gene expression levels and the physical distribution of expression across the genome. Analysis is currently possible using EST and SAGE data, with microarray data being incorporated. The eVOC data is increasingly being accepted as a standard for describing gene expression and eVOC ontologies are integrated with the Ensembl EnsMart database, the Alternate Transcript Diversity Project and the UniProt Knowledgebase. Several groups are currently working to provide shared development of this resource such that it is of maximum use in unifying transcript expression information. | mouse, mapping, cdna, development, microarray, expression, expressed sequence, anatomical system, cell type, developmental stage, experimental technique, microarray platform, pathology, pooling, tissue preparation, treatment, gene expression, genome sequence, expression phenotype, genome, sequence, phenotype, anatomical system, cell type, pathology, anatomy |
is related to: OBO is related to: Bgee: dataBase for Gene Expression Evolution has parent organization: University of the Western Cape; Bellville; South Africa |
South African National Research Foundation ; European Union ; Wellcome Trust ; South African Department of Arts Culture Science and Technology 32146 |
PMID:12799354 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_84448 | SCR_010704 | Expressed Sequence Annotation for Humans, eVOC (Expressed Sequence Annotation for Humans), eVOC Ontologies, eVOContology.org | 2026-08-04 09:42:46 | 4 | |||||
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BioMart MartView Resource Report Resource Website 10+ mentions |
BioMart MartView (RRID:SCR_010714) | data set, web service, software resource, data access protocol, data or information resource | A web server interface of BioMart software and provides a unified view over disparate data sources that enable bioscientists to retrieve data from one or multiple sources in a simple and efficient way. This MartView web server features seamless data federation making cross querying of data sources in a user friendly and unified way. Data sources include major biomolecular sequence, pathway and annotation databases such as Ensembl, Uniprot, Reactome, HGNC, Wormbase, etc. The web server not only provides access through a web interface, it also supports programmatic access through a Perl API as well as RESTful and SOAP oriented web services. | gold standard | is related to: biomaRt | Ontario Institute for Cancer Research ; Wellcome Trust ; EMBL ; European Union FP6 contract LHSG-CT-2004-512092 |
PMID:19420058 PMID:19144180 |
Free, Public | nlx_89178 | SCR_010714 | MartView, BioMart Central Portal | 2026-08-04 09:42:48 | 10 | ||||||
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ISRCTN Registry Resource Report Resource Website 500+ mentions |
ISRCTN Registry (RRID:SCR_006087) | narrative resource, standard specification, international standard specification, database, data or information resource | A primary clinical trial registry which houses proposed, ongoing, and completed clinical research studies. An ISRCTN is a simple numeric system for the unique identification of randomized controlled trials worldwide. The registry provides content validation and curation and the unique identification number necessary for publication. Submitted studies range from cancer to urological diseases. | clinical trial, unique identifier, observational trial, interventional trial, health, registry, clinical, trial, FASEB list |
is used by: Current Controlled Trials is related to: Current Controlled Trials has parent organization: Current Controlled Trials |
Department of Health UK ; Medical Research Council ; Wellcome Trust ; Canadian Institutes of Health Research |
Public | nlx_151501, r3d100013307 | http://www.isrctn.org, https://doi.org/10.17616/R31NJMRF | SCR_006087 | International Standard Randomised Controlled Trial Number Registry, International Standard Randomized Controlled Trial Number Register | 2026-08-04 09:41:30 | 744 | ||||||
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Embryo Imaging Resource Report Resource Website 1+ mentions |
Embryo Imaging (RRID:SCR_006329) | Embryo Imaging | data set, data or information resource, image collection, video resource | Collection of high resolution images and movies of mouse and human embryos produced using high resolution episcopic microscopy (HREM). Each data set is a series of block-face images generated during sectioning through an entire embryo, typically cut at 2-3 micrometers. Datasets are organized by approximate developmental stage and each embryo has been assigned a specimen ID (SID) for identification. This is an ongoing project funded by the Wellcome Trust to provide comprehensive imaging of normal and mutant mouse embryos that will complement the standard anatomical texts and form the basis for systematic phenotyping. * Movies: A 3D reconstruction shows each embryo, and lower resolution movies created through each orthogonal plane enable you to quickly review the data set. * Image Stacks: In the stack viewer, you can step through the images in sequence, zoom in to see fine details and adjust the image contrast. * NEW: Embryo Comparison: Two image stacks can now be compared in the stack viewer. | embryo, embryonic mouse, movie, high resolution image stack, image stack, comparison, high resolution episcopic microscopy, 3d reconstruction, imaging | Normal, Mutant | Wellcome Trust | Creative Commons Attribution-NonCommercial-ShareAlike License | nlx_152031 | SCR_006329 | 2026-08-04 09:41:35 | 4 | |||||||
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PomBase Resource Report Resource Website 100+ mentions |
PomBase (RRID:SCR_006586) | PomBase | database, data or information resource, service resource | Model organism database that provides organization of and access to scientific data for the fission yeast Schizosaccharomyces pombe. PomBase supports genomic sequence and features, genome-wide datasets and manual literature curation. PomBase also provides a community hub for researchers, providing genome statistics, a community curation interface, news, events, documentation, mailing lists, and welcomes data submissions. | fission yeast, gene ontology, genome sequence, schizosaccharomyces pombe (4896), schizosaccharomyces pombe, dna, protein, cosmic assembly, intron, go, chromosome, telomere, centromere, mating region, data mapping, model organism, genome, bio.tools, FASEB list |
is used by: NIF Data Federation is listed by: 3DVC is listed by: Debian is listed by: bio.tools is related to: AmiGO is related to: GeneDB Spombe has parent organization: University of Cambridge; Cambridge; United Kingdom has parent organization: University College London; London; United Kingdom is parent organization of: Fission Yeast Phenotype Ontology is parent organization of: Pompep |
Wellcome Trust WT090548MA | PMID:22039153 | Public, Acknowledgement requested | biotools:pombase, nlx_144356, r3d100011478 | https://bio.tools/pombase, https://doi.org/10.17616/R3NS78 | http://www.sanger.ac.uk/Projects/S_pombe/ | SCR_006586 | Schizosaccharomyces pombeGenome Sequencing Project | 2026-08-04 09:41:39 | 362 | |||
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European Nucleotide Archive (ENA) Resource Report Resource Website 1000+ mentions |
European Nucleotide Archive (ENA) (RRID:SCR_006515) | ENA | storage service resource, data repository, service resource, database, 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 | 2026-08-04 09:41:36 | 1272 | ||||
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PDBsum Resource Report Resource Website 500+ mentions |
PDBsum (RRID:SCR_006511) | PDBsum | data analysis service, analysis service resource, production service resource, service resource, d spatial image, database, data or information resource | Pictorial database of an at-a-glance overview of the contents of each 3D structure deposited in the Protein Data Bank (PDB). It shows the molecule(s) that make up the structure (ie protein chains, DNA, ligands and metal ions) and schematic diagrams of their interactions. Extensive use is made of the freely available RasMol molecular graphics program to view the molecules and their interactions in 3D. Entries are accessed either by their 4-character PDB code, or by one of the two search boxes provided on the PDBsum home page: text search or sequence search. The information given on each PDBsum entry is spread across several pages, as listed below and accessible from the tabs at the top of the page. Only the relevant tabs will be present on any given page. * Top page - summary information including thumbnail image of structure, molecules in structure, enzyme reaction diagram (where relevant), GO functional assignments, and selected figures from key reference * Protein - wiring diagram, topology diagram(s) by CATH domain, and residue conservation (where available) * DNA/RNA - DNA/RNA sequence and NUCPLOT showing interactions made with protein * Ligands - description of bound molecule and LIGPLOT showing interactions made with protein * Prot-prot - schematic diagrams of any protein-protein interfaces and the residue-residue interactions made across them * Clefts - listing of top ten clefts in the surface of the protein, listed by volume with any bound ligands shown * Links - links to external databases Additionally, it accepts users'''' own PDB format files and generates a private set of analyses for each uploaded structure. | 3d structure, protein, molecule, structure, protein chain, dna, ligand, metal ion, interaction, gold standard |
is related to: ProFunc is related to: SAS - Sequence Annotated by Structure is related to: ArchSchema is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: DrugPort is related to: Enzyme Structures Database has parent organization: European Bioinformatics Institute |
Wellcome Trust | PMID:18996896 PMID:15608193 PMID:11125097 PMID:9433130 |
nlx_40623 | SCR_006511 | 2026-08-04 09:41:36 | 546 | |||||||
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HumanNet Resource Report Resource Website 100+ mentions |
HumanNet (RRID:SCR_016146) | data processing software, data analysis software, software resource, software application, web application, database, data or information resource | Database of human protein-encoding genes that is constructed by a modified Bayesian integration of 'omics' data from multiple organisms. Each data type is weighted according to how well it links genes that are known to function together in humans, and each interaction has an associated log-likelihood score (LLS) that measures the probability of an interaction representing a true functional linkage between two genes. | probability, gene, protein, encode, statistic, likelihood, network, bayesian, omic, pathway, guilt by association, FASEB list |
has parent organization: University of Texas at Austin; Texas; USA has parent organization: Yonsei University; Seoul; South Korea |
National Research Foundation of Korea (NRF) ; Korean government (MEST) 2010-0017649; POSCO TJ ; U.S. Army Research 58343-MA; Welch F1515; Packard Foundations ; Wellcome Trust 076113; Wellcome Trust 085475 |
Freely available | SCR_016146 | 2026-08-04 09:43:49 | 132 | |||||||||
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Research Data Management Platform Resource Report Resource Website 1+ mentions |
Research Data Management Platform (RRID:SCR_016268) | RDMP | data management software, storage service resource, software resource, software application, data repository, service resource, software toolkit, data or information resource | Software toolkit which automates the loading, storage, linkage and provision of data sets. It also cleans, transforms and documents provenance meta-data and domain knowledge to make data sets “research ready”. | metadata, reproducibility, anonymization, security, audit, clinical, dataset, translational, research, data, management, catalogue, health, informatics, linkage | has parent organization: University of Dundee; Scotland; United Kingdom | Medical Research Council (MRC) MR/M501633/1; Wellcome Trust WT086113; EU Horizon 2020 633983 |
Free, Available for download | https://hic.dundee.ac.uk/Installers/RDMP/Stable/ | SCR_016268 | 2026-08-04 09:43:52 | 2 | |||||||
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Gaussian-Copula Mutual Information (GCMI) Resource Report Resource Website 1+ mentions |
Gaussian-Copula Mutual Information (GCMI) (RRID:SCR_016450) | GCMI | data processing software, software application, software resource, data analysis software | Software package of functions for calculating mutual information and other information theoretic quantities using a parametric Gaussian copula. | gaussian, copula, parametric, equation, calculation, python, matlab, repository, statistic | Wellcome Trust 098433; Wellcome Trust 107802; UK Biotechnology and Biological Sciences Research Council (BBSRC) BB/J018929/1; UK Biotechnology and Biological Sciences Research Council (BBSRC) BB/D01400X1; UK Biotechnology and Biological Sciences Research Council (BBSRC) BB/M009742/1; UK Biotechnology and Biological Sciences Research Council (BBSRC) BB/L027534/1; European Research Council 646657 |
Free, Available for download | SCR_016450 | gcmi : Gaussian-Copula Mutual Information, Gaussian-Copula Mutual Information | 2026-08-04 09:43:55 | 9 |
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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 RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on RRID then you can log in from here to get additional features in RRID such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into RRID you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
