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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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GenBank Resource Report Resource Website 10000+ mentions |
GenBank (RRID:SCR_002760) | GB | data or information resource, data repository, database, service resource, storage service resource | NIH genetic sequence database that provides annotated collection of all publicly available DNA sequences for almost 280 000 formally described species (Jan 2014) .These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using web-based BankIt or standalone Sequin programs, and GenBank staff assigns accession numbers upon data receipt. It is part of International Nucleotide Sequence Database Collaboration and daily data exchange with European Nucleotide Archive (ENA) and DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through NCBI Entrez retrieval system, which integrates data from major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of GenBank database are available by FTP. | genetic sequence, dna sequence, human genetics, human genome, nucleotide sequence, nucleotide, dna, dna data bank, gene mapping, genetics, gold standard |
is used by: Structural Genomics Consortium is used by: xFITOM is used by: Transcriptional Regulatory Element Database is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: OMICtools is listed by: re3data.org is listed by: CINERGI is related to: High Throughput Genomic Sequences Division is related to: DNA DataBank of Japan (DDBJ) is related to: HS3D - Homo Sapiens Splice Sites Dataset is related to: Influenza Virus Resource is related to: TPA is related to: Anopheles gambiae (African malaria mosquito) genome view is related to: Nucleotide database is related to: NCBI BioSample is related to: NCBI Nucleotide is related to: SpliceDB is related to: MaizeGDB is related to: NCBI Assembly Archive Viewer is related to: DNA DataBank of Japan (DDBJ) is related to: European Molecular Biology Laboratory is related to: INSDC is related to: NCBI Protein Database is related to: TrED is related to: Xenopus Gene Collection is related to: Mammalian Gene Collection is related to: Zebrafish Gene Collection is related to: INSDC is related to: NCBI Virus is related to: Codon and Codon-Pair Usage Tables has parent organization: NCBI is parent organization of: NCBI Genome Survey Sequences Database is parent organization of: NCBI Genome Survey Sequences Database works with: OGDraw works with: A plasmid Editor works with: Webcutter works with: merge-gbk-records works with: PremierBiosoft Proteo IQ Software works with: SARS-CoV-2-Sequences works with: rentrez works with: MiMeDB |
NLM | PMID:24217914 PMID:23193287 PMID:21071399 |
Free, Freely available | nif-0000-02873, r3d100010528, OMICS_01650 | https://doi.org/10.17616/R3D31X | SCR_002760 | , Gen Bank, GenBank | 2026-09-05 06:24:53 | 64417 | ||||
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SumsDB Resource Report Resource Website 10+ mentions |
SumsDB (RRID:SCR_002759) | SumsDB, WebCaret | analysis service resource, atlas, data analysis service, data or information resource, data repository, database, image repository, production service resource, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 11, 2016. Repository of brain-mapping data (surfaces and volumes; structural and functional data) derived from studies including fMRI and MRI from many laboratories, providing convenient access to a growing body of neuroimaging and related data. WebCaret is an online visualization tool for viewing SumsDB datasets. SumsDB includes: * data on cerebral cortex and cerebellar cortex * individual subject data and population data mapped to atlases * data from FreeSurfer and other brainmapping software besides Caret SumsDB provides multiple levels of data access and security: * Free (public) access (e.g., for data associated with published studies) * Data access restricted to collaborators in different laboratories * Owner-only access for work in progress Data can be downloaded from SumsDB as individual files or as bundles archived for offline visualization and analysis in Caret WebCaret provides online Caret-style visualization while circumventing software and data downloads. It is a server-side application running on a linux cluster at Washington University. WebCaret "scenes" facilitate rapid visualization of complex combinations of data Bi-directional links between online publications and WebCaret/SumsDB provide: * Links from figures in online journal article to corresponding scenes in WebCaret * Links from metadata in WebCaret directly to relevant online publications and figures | segmentation, volume, neuroimaging, brain, fmri, stereotaxic foci, stereotaxic coordinate, brain-mapping, foci, structural mri, mri, cerebral cortex, cerebellar cortex, afni brik, analyze, atlas, nifti, registration, rendering, spatial transformation, surface analysis, surface rendering, visualization, volume rendering, brain mapping, neuroanatomy |
is used by: NIF Data Federation is listed by: Biositemaps is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: re3data.org is related to: Computerized Anatomical Reconstruction and Editing Toolkit is related to: Integrated Manually Extracted Annotation has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
Mental disease, Neurological disorder, Normal | Human Brain Project ; NSF ; NCI ; NLM ; NASA ; National Partnership for Advanced Computational Infrastructure ; NIMH R01 MH60974-06 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00016, r3d100010169 | http://brainvis.wustl.edu/wiki/index.php/Sums:About http://www.nitrc.org/projects/sumsdb, https://doi.org/10.17616/R3JC76 | SCR_002759 | SumsDB WebCaret, SumsDB Database, Web Caret, WebCaret Online Visualization, Surface Management System Database and WebCaret Online Visualization, SumsDB and WebCaret, Sums database, SumsDB (Surface Management System Database) and WebCaret Online Visualization, Sums DB, SumsDB (Surface Management System Database) WebCaret Online Visualization, Surface Management System Database | 2026-09-05 06:24:53 | 14 | ||||
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Predictive Networks Resource Report Resource Website |
Predictive Networks (RRID:SCR_006110) | PN | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource, software resource, source code | A flexible, open-source, web-based application and data services framework that enables the integration, navigation, visualization and analysis of gene interaction networks. The primary goal of PN is to allow biomedical researchers to evaluate experimentally derived gene lists in the context of large-scale gene interaction networks. The PN analytical pipeline involves two key steps. The first is the collection of a comprehensive set of known gene interactions derived from a variety of publicly available sources. The second is to use these ''known'' interactions together with gene expression data to infer robust gene networks. The regression-based network inference algorithm creates a graph of gene interactions in which cycles may be present (but no self-loops). Based on information-theoretic techniques, a causal gene interaction network is inferred from both prior knowledge (interactions extracted from biomedical literature and structured biological databases) and gene expression data. A prediction model is fitted for each gene, given its parents, enabling assessment of the predictive ability of the network model. | gene interaction network, gene, interaction, gene expression, graph, visualization, gene interaction, gene network, predictive network analysis, model, bio.tools |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools has parent organization: Dana-Farber Cancer Institute has parent organization: SourceForge |
NLM 1R01LM010129 | PMID:22096235 | Apache License, v2 | nlx_151582, biotools:predictivenetworks | https://bio.tools/predictivenetworks | SCR_006110 | 2026-09-05 06:25:47 | 0 | |||||
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BrainInfo Resource Report Resource Website 10+ mentions |
BrainInfo (RRID:SCR_003142) | atlas, data or information resource, database, narrative resource, portal, standard specification, topical portal | Portal to neuroanatomical information on the Web that helps you identify structures in the brain and provides a variety of information about each structure by porting you to the best of 1500 web pages at 100 other neuroscience sites. BrainInfo consists of three basic components: NeuroNames, a developing database of definitions of neuroanatomic structures in four species, their most common acronyms and their names in eight languages; NeuroMaps, a digital atlas system based on 3-D canonical stereotaxic atlases of rhesus macaque and mouse brains and programs that enable one to map data to standard surface and cross-sectional views of the brains for presentation and publication; and the NeuroMaps precursor: Template Atlas of the Primate Brain, a 2-D stereotaxic atlas of the longtailed (fascicularis) macaque brain that shows the locations of some 250 architectonic areas of macaque cortex. The NeuroMaps atlases will soon include a number of overlays showing the locations of cortical areas and other neuroscientific data in the standard frameworks of the macaque and mouse atlases. Viewers are encouraged to use NeuroNames as a stable source of unique standard terms and acronyms for brain structures in publications, illustrations and indexing systems; to use templates extracted from the NeuroMaps macaque and mouse brain atlases for presenting neuroscientific information in image format; and to use the Template Atlas for warping to MRIs or PET scans of the macaque brain to estimate the stereotaxic locations of structures. | brain, neuroanatomy |
is used by: NIF Data Federation is listed by: Biositemaps is related to: INIA19 Primate Brain Atlas has parent organization: University of Washington; Seattle; USA has parent organization: University of California at San Diego; California; USA |
The Human Brain Project ; NIBIB ; NLM LM/OD-06243; NIH Office of the Director LM/OD-06243; NIMH MHO69259; NCRR RR-00166 |
PMID:21789500 PMID:21163300 PMID:18368361 PMID:15055392 |
Free, Freely available | nif-0000-00019 | SCR_003142 | Brain Info | 2026-09-05 06:24:58 | 16 | ||||||
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FMA Resource Report Resource Website 1+ mentions |
FMA (RRID:SCR_003379) | FMA | controlled vocabulary, data analysis software, data or information resource, data processing software, database, ontology, software application, software resource | A domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body in a form that is understandable to humans and is also navigable, parseable and interpretable by machine-based systems. Its ontological framework can be applied and extended to all other species. The description of how the OWL version was generated is in Pushing the Envelope: Challenges in a Frame-Based Representation of Human Anatomy by N. F. Noy, J. L. Mejino, C. Rosse, M. A. Musen: http://bmir.stanford.edu/publications/view.php/pushing_the_envelope_challenges_in_a_frame_based_representation_of_human_anatomy The Foundational Model of Anatomy ontology has four interrelated components: # Anatomy taxonomy (At), # Anatomical Structural Abstraction (ASA), # Anatomical Transformation Abstraction (ATA), # Metaknowledge (Mk), The ontology contains approximately 75,000 classes and over 120,000 terms; over 2.1 million relationship instances from over 168 relationship types link the FMA's classes into a coherent symbolic model. | anatomy, informatics, model, neuroanatomy, protg, reference, standard, structural, taxonomy, owl, phenotype |
is listed by: BioPortal is related to: T3DB is related to: HIV Brain Sequence Database is related to: CELDA Ontology has parent organization: University of Washington; Seattle; USA |
RSNA-NIBIB ; University of Washington; Washington; USA ; Murdock Charitable Trust ; Microsoft ; Intel Corporation ; NLM LM006822; NLM LM06316; NLM contract LM03528; NHLBI HL08770 |
PMID:18688289 PMID:18360535 PMID:16779026 |
Free, Freely available | nif-0000-00066 | http://bioportal.bioontology.org/ontologies/FMA | SCR_003379 | Foundational Model of Anatomy Ontology, Foundational Model of Anatomy | 2026-09-05 06:25:02 | 8 | ||||
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Protege Resource Report Resource Website 100+ mentions |
Protege (RRID:SCR_003299) | Protege | authoring tool, software application, software resource | Protege is a free, open-source platform that provides a growing user community with a suite of tools to construct domain models and knowledge-based applications with ontologies. At its core, Protege implements a rich set of knowledge-modeling structures and actions that support the creation, visualization, and manipulation of ontologies in various representation formats. Protege can be customized to provide domain-friendly support for creating knowledge models and entering data. Further, Protege can be extended by way of a plug-in architecture and a Java-based Application Programming Interface (API) for building knowledge-based tools and applications. An ontology describes the concepts and relationships that are important in a particular domain, providing a vocabulary for that domain as well as a computerized specification of the meaning of terms used in the vocabulary. Ontologies range from taxonomies and classifications, database schemas, to fully axiomatized theories. In recent years, ontologies have been adopted in many business and scientific communities as a way to share, reuse and process domain knowledge. Ontologies are now central to many applications such as scientific knowledge portals, information management and integration systems, electronic commerce, and semantic web services. The Protege platform supports two main ways of modeling ontologies: * The Protege-Frames editor enables users to build and populate ontologies that are frame-based, in accordance with the Open Knowledge Base Connectivity protocol (OKBC). In this model, an ontology consists of a set of classes organized in a subsumption hierarchy to represent a domain's salient concepts, a set of slots associated to classes to describe their properties and relationships, and a set of instances of those classes - individual exemplars of the concepts that hold specific values for their properties. * The Protege-OWL editor enables users to build ontologies for the Semantic Web, in particular in the W3C's Web Ontology Language (OWL). An OWL ontology may include descriptions of classes, properties and their instances. Given such an ontology, the OWL formal semantics specifies how to derive its logical consequences, i.e. facts not literally present in the ontology, but entailed by the semantics. These entailments may be based on a single document or multiple distributed documents that have been combined using defined OWL mechanisms (see the OWL Web Ontology Language Guide). Protege is based on Java, is extensible, and provides a plug-and-play environment that makes it a flexible base for rapid prototyping and application development. | ontology, java, develop, manage, edit, plug-in, FASEB list |
is listed by: Biositemaps is related to: National Center for Biomedical Ontology is related to: Jambalaya has parent organization: Stanford University School of Medicine; California; USA has parent organization: Stanford Center for Biomedical Informatics Research |
Defense Advanced Research Projects Agency ; eBay ; NCI ; NIST - National Institute of Standards and Technology ; National Centers for Biomedical Computing ; NSF ; Neural ElectroMagnetic Ontologies NEMO ; Pfizer ; NLM LM007885 |
PMID:17687607 | Free, download Freely available | nif-0000-31708 | SCR_003299 | Protégé, Protege Project | 2026-09-05 06:25:01 | 165 | |||||
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Michigan Molecular Interactions Resource Report Resource Website 1+ mentions |
Michigan Molecular Interactions (RRID:SCR_003521) | MiMI | analysis service resource, data access protocol, data analysis service, data or information resource, database, production service resource, service resource, software resource, web service | MiMi Web gives you an easy to use interface to a rich NCIBI data repository for conducting your systems biology analyses. This repository includes the MiMI database, PubMed resources updated nightly, and text mined from biomedical research literature. The MiMI database comprehensively includes protein interaction information that has been integrated and merged from diverse protein interaction databases and other biological sources. With MiMI, you get one point of entry for querying, exploring, and analyzing all these data. MiMI provides access to the knowledge and data merged and integrated from numerous protein interactions databases and augments this information from many other biological sources. MiMI merges data from these sources with deep integration into its single database with one point of entry for querying, exploring, and analyzing all these data. MiMI allows you to query all data, whether corroborative or contradictory, and specify which sources to utilize. MiMI displays results of your queries in easy-to-browse interfaces and provides you with workspaces to explore and analyze the results. Among these workspaces is an interactive network of protein-protein interactions displayed in Cytoscape and accessed through MiMI via a MiMI Cytoscape plug-in. MiMI gives you access to more information than you can get from any one protein interaction source such as: * Vetted data on genes, attributes, interactions, literature citations, compounds, and annotated text extracts through natural language processing (NLP) * Linkouts to integrated NCIBI tools to: analyze overrepresented MeSH terms for genes of interest, read additional NLP-mined text passages, and explore interactive graphics of networks of interactions * Linkouts to PubMed and NCIBI's MiSearch interface to PubMed for better relevance rankings * Querying by keywords, genes, lists or interactions * Provenance tracking * Quick views of missing information across databases. Data Sources include: BIND, BioGRID, CCSB at Harvard, cPath, DIP, GO (Gene Ontology), HPRD, IntAct, InterPro, IPI, KEGG, Max Delbreuck Center, MiBLAST, NCBI Gene, Organelle DB, OrthoMCL DB, PFam, ProtoNet, PubMed, PubMed NLP Mining, Reactome, MINT, and Finley Lab. The data integration service is supplied under the conditions of the original data sources and the specific terms of use for MiMI. Access to this website is provided free of charge. The MiMI data is queryable through a web services api. The MiMI data is available in PSI-MITAB Format. These files represent a subset of the data available in MiMI. Only UniProt and RefSeq identifiers are included for each interactor, pathways and metabolomics data is not included, and provenance is not included for each interaction. If you need access to the full MiMI dataset please send an email to mimi-help (at) umich.edu. | gene, interaction, molecule, protein, protein interaction, protein-protein interaction |
is related to: MiMI Plugin for Cytoscape has parent organization: National Center for Integrative Biomedical Informatics |
Michigan Center for Biological Information ; National Center for Integrative Biomedical Informatics ; Pfizer ; Medical and Academic Partnerships ; Howard Hughes Medical Institute ; Microsoft Corporation ; NLM R01 LM008106; NIDA U54 DA021519; NSF IIS 0219513 |
PMID:18978014 PMID:17130145 |
nif-0000-00214 | SCR_003521 | 2026-09-05 06:25:05 | 5 | |||||||
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MiMI Plugin for Cytoscape Resource Report Resource Website 1+ mentions |
MiMI Plugin for Cytoscape (RRID:SCR_003424) | MiMI Plugin | data processing software, data visualization software, software application, software resource | The Cytoscape MiMI Plugin is an open source interactive visualization tool that you can use for analyzing protein interactions and their biological effects. The Cytoscape MiMI Plugin couples Cytoscape, a widely used software tool for analyzing bimolecular networks, with the MiMI database, a database that uses an intelligent deep-merging approach to integrate data from multiple well-known protein interaction databases. The MiMI database has data on 119,880 molecules, 330,153 interactions, and 579 complexes. By querying the MiMI database through Cytoscape you can access the integrated molecular data assembled in MiMI and retrieve interactive graphics that display protein interactions and details on related attributes and biological concepts. You can interact with the visualization by expanding networks to the next nearest neighbors and zooming and panning to relationships of interest. You also can perceptually encode nodes and links to show additional attributes through color, size and the visual cues. You can edit networks, link out to other resources and tools, and access information associated with interactions that has been mined and summarized from the research literature information through a biology natural language processing database (BioNLP) and a multi-document summarization system, MEAD. Additionally, you can choose sub-networks of interest and use SAGA, a graph matching tool, to match these sub-networks to biological pathways. | protein interaction, network visualization, xquery, interactive database, information refining, molecular interaction, bioinformatics tool, java, protein-protein interaction, interaction network, biological effect, bimolecular, interaction, molecular, network, pathway, protein, visualization, plugin |
is listed by: Biositemaps is related to: Cytoscape is related to: Michigan Molecular Interactions has parent organization: University of Michigan; Ann Arbor; USA has parent organization: National Center for Integrative Biomedical Informatics |
NIH ; NIDA U54 DA021519; NLM R01 LM008106; NCRR P41 RR018627 |
PMID:18812364 | nif-0000-33090 | http://mimiplugin.ncibi.org/index.html | SCR_003424 | Cytoscape Plugin for MiMI, MiMI Plugin - Cytoscape Plugin for MiMI | 2026-09-05 06:25:03 | 1 | |||||
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Protein Data Bank Markup Language Resource Report Resource Website 1+ mentions |
Protein Data Bank Markup Language (RRID:SCR_005085) | PDBML | data or information resource, interchange format, markup language, narrative resource, standard specification | Markup Language that provides a representation of PDB data in XML format. The description of this format is provided in XML schema of the PDB Exchange Data Dictionary. This schema is produced by direct translation of the mmCIF format PDB Exchange Data Dictionary Other data dictionaries used by the PDB have been electronically translated into XML/XSD schemas and these are also presented in the list below. * PDBML data files are provided in three forms: ** fully marked-up files, ** files without atom records ** files with a more space efficient encoding of atom records * Data files in PDBML format can be downloaded from the RCSB PDB website or by ftp. * Software tools for manipulating PDB data in XML format are available. | xml |
is related to: RCSB PDB Software Tools has parent organization: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) |
NSF ; NIGMS ; DOE ; NLM ; NCI ; NCRR ; NIBIB ; NINDS |
PMID:15509603 | nlx_144096 | SCR_005085 | PDBML: Protein Data Bank Markup Language | 2026-09-05 06:25:29 | 2 | ||||||
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SNPs3D Resource Report Resource Website 100+ mentions |
SNPs3D (RRID:SCR_010787) | SNPs3D | data or information resource, database | A website which assigns molecular functional effects of non-synonymous SNPs based on structure and sequence analysis. | single nucleotide polymorphism, single nucleotide variation, gene, FASEB list |
is listed by: OMICtools has parent organization: University of Maryland; Maryland; USA |
NLM | The community can contribute to this resource | OMICS_00163 | SCR_010787 | 2026-09-05 06:32:00 | 117 | |||||||
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NRG-CING Resource Report Resource Website 1+ mentions |
NRG-CING (RRID:SCR_006079) | NRG-CING | data or information resource, database | NRG-CING presents a complete validation report for all 9,000+ wwPDB NMR entries including remediated experimental data such as chemical shifts from BMRB and restraints from NRG . These CING reports are compiled from internal analyses and those by CCPN, DSSP, PROCHECK-NMR/Aqua, ShiftX, Talos+, Vasco, Wattos, and WHAT_CHECK. The NRG-CING website is a collection of CING reports that has been pre-calculated for all PDB files solved by NMR. (See website for more information on CING.) In case the underlying experimental data is available, these have been cleaned up and made syntactically and semantically correct and homogeneous. For many macromolecular NMR ensembles from the Protein Data Bank (PDB) the experiment-based restraint lists used in the structure calculation are accessible, while other experimental data, mainly chemical shift values, are often available from the BioMagResBank. Assessment of the quality of the structural result is paramount to their usage and a combined, integrated repository of both input data and structural results greatly facilitates such an analysis. In addition, the accuracy and precision of the coordinates in these macromolecular NMR ensembles can be improved by recalculations using the available experimental data and present-day software with improved protocols and force fields. Such efforts, however, generally fail on over half of all deposited structures due to the syntactic and semantic heterogeneity of the data and the wide variety of formats used for their deposition. We have combined the cleaned-up restraints information from the NMR Restraints Grid (NRG) database with available chemical shifts from the BioMagResBank in the weekly updated NRG-CING database. Eleven programs, in addition to CING itself, have been included in the NRG-CING production pipeline to arrive at validation reports that list for each entry the potential inconsistencies between the coordinates and the available restraint and chemical shift data. The longitudinal validation of this data yielded a set of indicators that can be used to judge the quality of every macromolecular structure solved with NMR. The cleaned up NMR experimental datasets and the validation reports are freely available. | macromolecular structure, nmr, macromolecule, restraint, chemical shift, validation report, validation, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Worldwide Protein Data Bank (wwPDB) is related to: NMR Restraints Grid is related to: Biological Magnetic Resonance Data Bank (BMRB) has parent organization: Radboud University; Nijmegen; The Netherlands |
Netherlands Organization for Scientific Research (NWO) 700.55.443; Netherlands Bioinformatics Centre (NBIC) ; EU FP6 LSHG-CT-2005-018988; EU FP6 LHSG-CT-2004-512092; EU FP7 261572; Brussels Institute for Research and Innovation BB2B 2010-1-12; NLM LM05799 |
PMID:22139937 | Free | nlx_151486, biotools:nrg-cing | https://bio.tools/nrg-cing | SCR_006079 | 2026-09-05 06:31:33 | 1 | |||||
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GO-Module Resource Report Resource Website 1+ mentions |
GO-Module (RRID:SCR_005813) | GO-Module | analysis service resource, data analysis service, production service resource, service resource | GO-Module provides an interface to reduce the dimensionality of GO enrichment results and produce interpretable biomodules of significant GO terms organized by hierarchical knowledge that contain only true positive results. Users can download a text file of GO terms annotated with their significance and identified biomodules, a network visualization of resultant GO IDs or terms in PDF format, and view results in an online table. Platform: Online tool | functional similarity, visualization, other analysis, reduce the dimensionality of go enrichment results, produce interpretable biomodules of significant go terms, gene ontology, ontology or annotation visualization, annotation |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: AmiGO has parent organization: University of Illinois at Chicago; Illinois; USA |
NIH ; Cancer Research Foundation ; NLM K22 LM008308; NCI 1U54CA121852; NCRR UL1 RR024999 |
PMID:21421553 | Free for academic use | nlx_149322 | SCR_005813 | Hierarchical optimization of enriched GO terms | 2026-09-05 06:31:32 | 3 | |||||
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Worldwide Protein Data Bank (wwPDB) Resource Report Resource Website 1000+ mentions |
Worldwide Protein Data Bank (wwPDB) (RRID:SCR_006555) | wwPDB | data or information resource, database | Public global Protein Data Bank archive of macromolecular structural data overseen by organizations that act as deposition, data processing and distribution centers for PDB data. Members are: RCSB PDB (USA), PDBe (Europe) and PDBj (Japan), and BMRB (USA). This site provides information about services provided by individual member organizations and about projects undertaken by wwPDB. Data available via websites of its member organizations. | 3-dimentional, bioinformatics, protein, research, structure, macromolecule, structural data, 3d spatial image, gold standard |
is used by: Ligand Expo is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: Proteopedia - Life in 3D is related to: NRG-CING is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: DNA DataBank of Japan (DDBJ) is related to: PDBe - Protein Data Bank in Europe is related to: PDBe - Protein Data Bank in Europe is related to: PDBj - Protein Data Bank Japan is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: PDB Validation Server is related to: Structural Antibody Database is parent organization of: PDB-Dev works with: PDB-REDO |
BBSRC ; DOE ; European Molecular Biology Laboratory ; European Union ; Heidelberg; Germany ; Japan Science and Technology Agency ; NBDC - National Bioscience Database Center ; NCI ; NIDDK ; NIGMS ; NIH ; NINDS ; NLM ; NSF ; Wellcome Trust |
PMID:14634627 | Free, Freely available | nif-0000-23903, r3d100011104 | https://doi.org/10.17616/R3462V | SCR_006555 | World Wide Protein DataBank, wwPDB, Worldwide Protein Data Bank (wwPDB), World Wide Protein Data Bank, Worldwide Protein DataBank | 2026-09-05 06:31:35 | 1340 | ||||
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MUMmerGPU Resource Report Resource Website 1+ mentions |
MUMmerGPU (RRID:SCR_001200) | MUMmerGPU | data processing software, software application, software resource | Software tool as high throughput DNA sequence alignment program that runs on nVidia G80-class GPUs. Aligns sequences in parallel on video card to accelerate widely used serial CPU program MUMmer. | parallel computation 4, high-throughput sequencing, sequence alignment, dna, graphics processing unit |
is listed by: OMICtools is related to: MUMmer has parent organization: SourceForge has parent organization: University of Maryland; Maryland; USA |
NIGMS R01 GM083873; NLM R01 LM006845 |
PMID:20161021 | Free, Available for download, Freely available | OMICS_02151 | SCR_001200 | High-throughput sequence alignment using Graphics Processing Units | 2026-09-05 06:30:36 | 5 | |||||
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NCBI Resource List Resource Report Resource Website |
NCBI Resource List (RRID:SCR_005628) | NCBI Resources | data or information resource, organization portal, portal | The National Center for Biotechnology Information''s listing of resources. Sort by alphabetical character, Databases, Downloads, Submissions, Tools and How-To; or by Topic: Chemicals & Bioassays; Data & Software; DNA & RNA; Domains & Structures; Genes & Expression; Genetics & Medicine; Genomes & Maps; Homology; Literature; Proteins; Sequence Analysis; Taxonomy; Training & Tutorials; Variation. | database, download, submission, tool, chemical, bioassay, data, software, dna, rna, domain, structure, gene, expression, genetics, medicine, genomes, map, homology, literature, protein, sequence analysis, taxonomy, training, tutorial, variation, gold standard | has parent organization: NCBI | NLM | nlx_146242 | SCR_005628 | NCBI Resource Guide, NCBI Resource List (A-Z) | 2026-09-05 06:30:41 | 0 | |||||||
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pRESTO Resource Report Resource Website 50+ mentions |
pRESTO (RRID:SCR_001782) | pRESTO | software resource, software toolkit | Software toolkit for processing raw reads from high-throughput sequencing of lymphocyte repertoires. | lymphocyte, high throughput sequencing, processing, raw reads, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Yale School of Medicine; Connecticut; USA |
EMD/Merck/Serono ; United States-Israel Binational Science Foundation 2009046; NCRR RR19895; NLM T15 LM07056; NIAAA U19AI089992; NIAAA U19AI050864 |
PMID:24618469 | Free, Freely available | SCR_001782 | REpertoire Sequencing TOolkit | 2026-09-05 06:32:25 | 72 | ||||||
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UniProt Resource Report Resource Website 10000+ mentions |
UniProt (RRID:SCR_002380) | UniProt | data or information resource, database | Collection of data of protein sequence and functional information. Resource for protein sequence and annotation data. Consortium for preservation of the UniProt databases: UniProt Knowledgebase (UniProtKB), UniProt Reference Clusters (UniRef), and UniProt Archive (UniParc), UniProt Proteomes. Collaboration between European Bioinformatics Institute (EMBL-EBI), SIB Swiss Institute of Bioinformatics and Protein Information Resource. Swiss-Prot is a curated subset of UniProtKB. | collection, protein, sequence, annotation, data, functional, information |
is used by: LIPID MAPS Proteome Database is used by: ChannelPedia is used by: Open PHACTS is used by: DisGeNET is used by: Smart Dictionary Lookup is used by: MitoMiner is used by: Cytokine Registry is used by: MobiDB is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is used by: Phospho.ELM is used by: GEROprotectors is used by: SwissLipids 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: re3data.org is listed by: LabWorm is related to: Clustal W2 is related to: UniProt DAS is related to: UniParc at the EBI is related to: ProDom is related to: LegumeIP is related to: Pathway Commons is related to: NIH Data Sharing Repositories is related to: FlyMine is related to: IMEx - The International Molecular Exchange Consortium is related to: 3D-Interologs is related to: Biomine is related to: EBIMed is related to: STOP is related to: Coremine Medical is related to: BioExtract is related to: STRAP is related to: GOTaxExplorer is related to: GoAnnotator is related to: IT-GOM: Integrated Tool for IC-based GO Semantic Similarity Measures is related to: Whatizit is related to: MOPED - Model Organism Protein Expression Database is related to: Polbase is related to: PredictSNP is related to: PSICQUIC Registry is related to: IntAct is related to: p300db is related to: UniProt Proteomes is related to: SARS-CoV-2 mutation effects and 3D structure prediction from sequence covariation has parent organization: European Bioinformatics Institute has parent organization: SIB Swiss Institute of Bioinformatics has parent organization: Protein Information Resource is parent organization of: UniProtKB is parent organization of: NEWT is parent organization of: UniParc is parent organization of: UniProt Chordata protein annotation program is parent organization of: UniRef works with: Genotate works with: CellPhoneDB works with: MOLEonline works with: MiMeDB |
ARUK ; British Heart Foundation ; EMBL ; NCI ; NCRR P20 RR016472; NEI ; NHGRI P41 HG02273; NHGRI U24 HG007722; NHGRI U41 HG006104; NHLBI ; NIAID ; NIA ; NIDDK ; NIGMS 5R01GM080646; NIGMS R01 GM080646; NIMH ; NLM G08 LM010720; NSF DBI-0850319; PDUK |
PMID:19843607 PMID:18836194 PMID:18045787 PMID:17142230 PMID:16381842 PMID:15608167 PMID:14681372 |
nif-0000-00377, SCR_018750, r3d100010357 | http://www.ebi.uniprot.org, http://www.uniprot.org/uniprot/, http://www.pir.uniprot.org, ftp://ftp.uniprot.org, https://doi.org/10.17616/R3BW2M | SCR_002380 | , The Universal Protein Resource, Universal Protein Resource, UNIPROT Universal Protein Resource | 2026-09-05 06:31:17 | 19823 | |||||
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Directory of Health Organizations Online Resource Report Resource Website 1+ mentions |
Directory of Health Organizations Online (RRID:SCR_002331) | DIRLINE | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented July 15, 2016. Database containing location and descriptive information about a wide variety of information resources including organizations, research resources, projects, and databases concerned with health and biomedicine. This information may not be readily available in bibliographic databases. Each record may contain information on the publications, holdings, and services provided. These information resources fall into many categories including federal, state, and local government agencies; information and referral centers; professional societies; self-help groups and voluntary associations; academic and research institutions and their programs; information systems and research facilities. Topics include HIV/AIDS, maternal and child health, most diseases and conditions including genetic and other rare diseases, health services research and technology assessment. DIRLINE can be searched using subject words (such as disease or condition) including Medical Subject Headings (MeSH) or for the name or location of a resource. It now offers an A to Z list of over 8,500 organizations. | genetic, aids, biomedicine, child, condition, disease, health, hiv, maternal, medicine, public health | has parent organization: National Library of Medicine | NLM N01LM023524 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21122 | SCR_002331 | Directory of Information Resources Online | 2026-09-05 06:31:17 | 1 | ||||||
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DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins Resource Report Resource Website 10+ mentions |
DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins (RRID:SCR_003039) | DP-Bind | analysis service resource, data analysis service, production service resource, service resource | This web-server takes a user-supplied sequence of a DNA-binding protein and predicts residue positions involved in interactions with DNA. Prediction can be performed using a profile of evolutionary conservation of the input sequence automatically generated by the web-server or the input sequence alone. Three prediction methods are run for each input sequence and consensus prediction is generated. | dna binding | has parent organization: University at Albany; New York; USA | NLM 1R03LM009034-01 | PMID:17237068 PMID:16568445 |
Free, Freely available | nif-0000-30426 | SCR_003039 | 2026-09-05 06:31:19 | 20 | ||||||
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Distant Regulatory Elements Resource Report Resource Website 10+ mentions |
Distant Regulatory Elements (RRID:SCR_003058) | DiRE | analysis service resource, data analysis service, production service resource, service resource | Web server based on the Enhancer Identification (EI) method, to determine the chromosomal location and functional characteristics of distant regulatory elements (REs) in higher eukaryotic genomes. The server uses gene co-expression data, comparative genomics, and combinatorics of transcription factor binding sites (TFBSs) to find TFBS-association signatures that can be used for discriminating specific regulatory functions. DiRE's unique feature is the detection of REs outside of proximal promoter regions, as it takes advantage of the full gene locus to conduct the search. DiRE can predict common REs for any set of input genes for which the user has prior knowledge of co-expression, co-function, or other biologically meaningful grouping. The server predicts function-specific REs consisting of clusters of specifically-associated TFBSs, and it also scores the association of individual TFs with the biological function shared by the group of input genes. Its integration with the Array2BIO server allows users to start their analysis with raw microarray expression data. | regulatory element, enhancer identification, genome, prediction, transcription factor binding site, gene, co-expression, co-function, function, transcription factor, comparative genomics, regulatory function, gene locus, chromosome, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: NCBI |
NLM ; Intramural Research Program |
PMID:18487623 | Free, Freely available | nif-0000-30448, biotools:dire | https://bio.tools/dire | SCR_003058 | Distant Regulatory Elements of co-regulated genes | 2026-09-05 06:31:19 | 25 |
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