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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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NIGMS - YouTube Resource Report Resource Website |
NIGMS - YouTube (RRID:SCR_005678) | NIGMS - YouTube | data or information resource, video resource | YouTube videos provided by the National Institute of General Medical Sciences (NIGMS). | has parent organization: National Institute of General Medical Sciences | NIGMS | nlx_149378 | SCR_005678 | National Institute of General Medical Sciences - YouTube | 2026-02-14 02:05:53 | 0 | ||||||||
|
WorfDB Resource Report Resource Website 1+ mentions |
WorfDB (RRID:SCR_006028) | data or information resource, database | Database that integrates and disseminates the data from the cloning of complete set of predicted protein-encoding ORFs of Caenorhabditis elegans. It also allows the community to search for availability and quality of cloned ORFs. So far, ORF sequence tags (OSTs) obtained for all individual clones have allowed exon structure corrections for ORFs originally predicted by the C. elegans sequencing consortium. The database contains this OST information along with data pertinent to the cloning process. | open reading frame, c elegans, orf sequence tag |
has parent organization: Dana-Farber Cancer Institute has parent organization: Harvard Medical School; Massachusetts; USA |
NIGMS ; MGRI ; NHGRI 5R01HG01715-02; NCI 7 R33 CA81658-02 |
PMID:12519990 | nif-0000-03644 | SCR_006028 | WorfDB - Worm ORF Database, Worm ORFeome DataBase, Worm ORFeome | 2026-02-14 02:05:54 | 9 | |||||||
|
CRISPRscan Resource Report Resource Website 50+ mentions |
CRISPRscan (RRID:SCR_023777) | data access protocol, software resource, web service | Web tool for predictive sgRNA-scoring that captures sequence features affecting Cas9/sgRNA activity in vivo. Scoring algorithm to help select the best gRNAs for CRISPR. | predictive sgRNA-scoring, sequence features capture, affecting Cas9/sgRNA activity in vivo, select gRNAs for CRISPR, | has parent organization: Yale University; Connecticut; USA | Swiss National Science Foundation ; NICHD R21 HD073768; NIGMS R01 GM103789; NIGMS R01 GM102251; NIGMS R01 GM101108; NIGMS GM081602; NICHD R01 HD081379; Edward Mallinckrodt Jr Foundation |
Free, Freely available | SCR_023777 | 2026-02-14 02:05:14 | 58 | |||||||||
|
PathVisio Resource Report Resource Website 10+ mentions |
PathVisio (RRID:SCR_023789) | data visualization software, data processing software, software toolkit, software application, software resource | Software visualization tool for biological pathways. Pathway analysis and drawing software which allows drawing, editing, and analyzing biological pathways. Developed in Java and can be extended with plugins. | biological pathway editor, pathway editor, visualization and analysis, extendable pathway analysis, | NIGMS R01 GM100039; Netherlands Consortium for Systems Biology ; NIGMS GM080223; NHGRI HG003053; Transnational University Limburg |
PMID:25706687 PMID:18817533 |
Free, Available for download, Freely available | SCR_023789 | PathVisio 3 | 2026-02-14 02:05:01 | 24 | ||||||||
|
PERFect Resource Report Resource Website |
PERFect (RRID:SCR_024682) | software resource, data processing software, software application | Software R package as filtering test for microbiome data. Permutation filtering approach to address two unsolved problems in microbiome data processing: (i) define and quantify loss due to filtering by implementing thresholds and (ii) introduce and evaluate a permutation test for filtering loss to provide a measure of excessive filtering. | filtering test, microbiome data, microbiome data processing, | NSF ; NIGMS 1U54GM104944 |
PMID:29917060 | Free, Available for download, Freely available | SCR_024682 | Permutation Filtering Package in R | 2026-02-14 02:05:10 | 0 | ||||||||
|
WebProtege Resource Report Resource Website 1+ mentions |
WebProtege (RRID:SCR_024627) | software resource, web application | Web based platform for editing biomedical ontologies. Web application for editing OWL 2 ontologies. Open source, lightweight, web based ontology editor implemented in Java and JavaScript using OWL API and Google Web Toolkit. For users who do not wish to host their ontologies on Stanford servers, WebProtégé is available as Web app that can be run locally using Servlet container such as Tomcat. | editing biomedical ontologies, editing OWL 2 ontologies, ontology editor, OBO ontologies, |
has parent organization: Stanford University; Stanford; California has parent organization: Stanford Center for Biomedical Informatics Research |
NIGMS GM103316 | PMID:24771560 | Free, Freely available | https://protegewiki.stanford.edu/wiki/WebProtege | SCR_024627 | WebProtégé | 2026-02-14 02:05:09 | 2 | ||||||
|
MUMmerGPU Resource Report Resource Website 1+ mentions |
MUMmerGPU (RRID:SCR_001200) | MUMmerGPU | software resource, data processing software, software application | 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 |
NLM R01 LM006845; NIGMS R01 GM083873 |
PMID:20161021 | Free, Available for download, Freely available | OMICS_02151 | SCR_001200 | High-throughput sequence alignment using Graphics Processing Units | 2026-02-14 02:05:14 | 5 | |||||
|
Drug Design Data Resource Resource Report Resource Website 1+ mentions |
Drug Design Data Resource (RRID:SCR_000497) | D3R | data or information resource, portal, database | Project portal's database of protein-ligand data sets provided by pharmaceutical partners that provide atomic details of drug mechanisms that will be used to improve computer-aided drug-design methods and thus accelerate drug discovery. The project aims to help companies release the high-quality data they have generated, which has incredible value to researchers working to improve methods of computer-aided drug discovery. Everyone stands to benefit from the ability to develop new medications more quickly and inexpensively. What computational chemists globally are trying to do is to make faster, more accurate, more predictive programs to speed up the process. Part of their mission is to engage the community in these challenges to test newly developed predictive algorithms. | computer-aided drug design, drug design, pharmaceutical, small molecule, ligand-protein interaction, protein, ligand, drug development, drug, binding, data set, affinity, computation, medicine, compound, structure |
uses: Binding MOAD uses: Protein Data Bank Bind Database is used by: NIF Data Federation is listed by: DataCite has parent organization: University of California at San Diego; California; USA has parent organization: University of California; California; USA |
NIGMS 1U01GM111528 | nlx_158375 | https://api.datacite.org/dois?prefix=10.15782 | SCR_000497 | Drug Design Data (D3R) Resource | 2026-02-14 02:05:19 | 3 | ||||||
|
OpenMM Resource Report Resource Website 10+ mentions |
OpenMM (RRID:SCR_000436) | software resource, simulation software, standalone software, software application | Software toolkit to run modern molecular simulations. It can be used either as a standalone application for running simulations, or as a library that enables accelerated calculations for molecular dynamics on high-performance computer architectures. | modeling, molecular dynamics, molecular simulation |
is used by: CHARMM-GUI is listed by: Simtk.org has parent organization: Stanford University; Stanford; California |
NIGMS U54 GM072970; NIGMS R01 GM062868; NCI P30 CA008748 |
PMID:28746339 PMID:23316124 PMID:38154096 DOI:10.1021/acs.jpcb.3c06662 |
Free, Available for download, Freely available | nif-0000-23334 | https://github.com/openmm/openmm https://openmm.org/ https://openmm.org/documentation https://github.com/openmm |
https://simtk.org/home/openmm | SCR_000436 | OpenMM 8, OpenMM, OpenMM 7, OpenMM 4 | 2026-02-14 02:05:23 | 12 | ||||
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NIGMS Human Genetic Cell Repository Resource Report Resource Website 1+ mentions |
NIGMS Human Genetic Cell Repository (RRID:SCR_004517) | NIGMS Repository | biomaterial supply resource, cell repository, material resource | Highly characterized cell lines and high quality DNA for cell and genetic research representing a variety of disease states, chromosomal abnormalities, apparently healthy individuals and many distinct human populations. The NIGMS Repository contains more than 10,600 cell lines, primarily fibroblasts and transformed lymphoblasts, and over 5,500 DNA samples. The NIGMS Repository has a major emphasis on heritable diseases and chromosomally aberrant cell lines. In addition, it contains a large collection dedicated to understanding human variation that includes samples from populations around the world, the CEPH collection, the Polymorphism Discovery Resource, and many apparently healthy controls. Human induced pluripotent stem cell lines, many of which were derived from NIGMS Repository fibroblasts, have recently become available through the NIGMS Repository. Sample donation facilitates all areas of research by making available well-characterized materials to any qualified researcher who might have otherwise been unable to invest the time and resources to collect needed samples independently. Donations to the Repository have created a resource of unparalleled scope. Samples from the collection have been used in more than 5,500 publications and are distributed to scientists in more than 50 countries. This resource is continuously expanding to support new directions in human genetics. | cell, gene, cell line, dna, fibroblast, transformed lymphoblast, lymphoblast, induced pluripotent stem cell line, chromosomal abnormality, healthy, single-gene disorder, complex polygenic disorder, multifactorial birth defect, unaffected first-degree relatives of individuals with genetic disease, heritable disease, genetic disease, human variation, control, clinical data, blood |
is used by: NIF Data Federation is listed by: One Mind Biospecimen Bank Listing is related to: Integrated Cell Lines has parent organization: Coriell Cell Repositories |
Chromosomal abnormality, Healthy, Single-gene disorder, Complex polygenic disorder, Multifactorial birth defect, Unaffected first-degree relatives of individuals with genetic disease, Heritable disease, Genetic disease, Control | NIGMS ; NIH Blueprint for Neuroscience Research |
Public / non-commercial: Cell cultures and DNA samples are distributed only to qualified professional persons who are associated with recognized research, Medical, Educational, Or industrial organizations engaged in biomedical research with Statement of Research Intent and a MTA. Samples obtained from the Repository, And material derived from the samples, May not be used for commercial purposes, Although knowledge gained from their use may be used. | nlx_143798 | SCR_004517 | Human Genetic Cell Repository | 2026-02-14 02:05:04 | 4 | |||||
|
WikiPathways Resource Report Resource Website 1000+ mentions |
WikiPathways (RRID:SCR_002134) | data or information resource, service resource, database | Open and collaborative platform dedicated to curation of biological pathways. Each pathway has dedicated wiki page, displaying current diagram, description, references, download options, version history, and component gene and protein lists. Database of biological pathways maintained by and for scientific community. | database, knowledge environment resource, image, web service, biological pathway, diagram description, reference, pathway, FASEB list |
is used by: NIF Data Federation is used by: Open PHACTS is related to: PharmGKB is related to: Reactome is related to: NetPath is related to: ConsensusPathDB is related to: NCBI BioSystems Database is related to: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit has parent organization: University of California at San Francisco; California; USA has parent organization: Maastricht University; Maastricht; Netherlands |
NIH ; Netherlands Bioinformatics Centre ; Google Summer of Code program ; NWO - Netherlands Organization for Scientific Research ; NIGMS GM080223; NIGMS R01 GM100039 |
PMID:22096230 PMID:18651794 |
Free, Freely available | nif-0000-20925 | SCR_002134 | Wiki Pathways | 2026-02-14 02:05:46 | 1696 | ||||||
|
Aptamer Database - The Ellington Lab Resource Report Resource Website 1+ mentions |
Aptamer Database - The Ellington Lab (RRID:SCR_001781) | data or information resource, database | The Aptamer Database is a comprehensive, annotated repository for information about aptamers and in vitro selection. This resource is provided to collect, organize and distribute all the known information regarding aptamer selection. Aptamers are DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules. Aptamers have been selected which bind nucleic acid, proteins, small organic compounds, and even entire organisms. | aptamer, dna molecule, in vitro selection, ribozyme, rna molecule | has parent organization: University of Texas at Austin; Texas; USA | MURI DAAD19-99-1-0207; NIGMS 1R01 GM61789-01 |
PMID:14681367 | Free, Freely available | nif-0000-02558 | http://aptamer.icmb.utexas.edu | SCR_001781 | Aptamer Database, Ellington Lab Aptamer Database | 2026-02-14 02:06:03 | 3 | |||||
|
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 |
NHGRI U41 HG006104; NHGRI P41 HG02273; NIGMS 5R01GM080646; NIGMS R01 GM080646; NLM G08 LM010720; NCRR P20 RR016472; NSF DBI-0850319; British Heart Foundation ; NEI ; NHLBI ; NIA ; NIAID ; NIDDK ; NIMH ; NCI ; EMBL ; PDUK ; ARUK ; NHGRI U24 HG007722 |
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 | 2026-02-14 02:05:47 | 17565 | |||||
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SuperTarget Resource Report Resource Website 10+ mentions |
SuperTarget (RRID:SCR_002696) | SuperTarget | data or information resource, database | Database for analyzing drug-target interactions, it integrates drug-related information associated with medical indications, adverse drug effects, drug metabolism, pathways and Gene Ontology (GO) terms for target proteins. At present (May 2013), the updated database contains >6000 target proteins, which are annotated with >330 000 relations to 196 000 compounds (including approved drugs); the vast majority of interactions include binding affinities and pointers to the respective literature sources. The user interface provides tools for drug screening and target similarity inclusion. A query interface enables the user to pose complex queries, for example, to find drugs that target a certain pathway, interacting drugs that are metabolized by the same cytochrome P450 or drugs that target proteins within a certain affinity range. | drug metabolism, drug, cytochrome p450, ontology, pathway, target, compound, cytochrome, drug target, protein, side effect, protein-protein interaction |
is listed by: OMICtools has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany |
BMBF MedSys 0315450A; DFG RTG Computational Systems Biology GRK1772; DFG IRTG Systems Biology of Molecular Networks GRK1360; European Union SynSys ; NIGMS GM070064 |
PMID:22067455 PMID:17942422 |
Free, Freely available | r3d100012195, nif-0000-00416, OMICS_01591 | http://bioinf-tomcat.charite.de/supertarget/ http://bioinformatics.charite.de/supertarget https://doi.org/10.17616/R3TM0F |
SCR_002696 | 2026-02-14 02:05:48 | 28 | |||||
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3D Ribosomal Modification Maps Database Resource Report Resource Website 1+ mentions |
3D Ribosomal Modification Maps Database (RRID:SCR_003097) | 3D rRNA modification maps | data or information resource, database | Database of maps showing the sites of modified rRNA nucleotides. Access to the rRNA sequences, secondary structures both with modification sites indicated, 3D modification maps and the supporting tables of equivalent nucleotides for rRNA from model organisms including yeast, arabidopsis, e. coli and human is provided. This database complements the Yeast snoRNA Database at UMass-Amherst and relies on linking to some content from that database, as well as to others by colleagues in related fields. Therefore, please be very cognizant as to the source when citing information obtained herein. Locations of modified rRNA nucleotides within the 3D structure of the ribosome. | human, plant, arabidopsis, ribosome, eukaryote, eubacteria, archaea, eukarya |
is related to: Yeast snoRNA Database has parent organization: University of Massachusetts Amherst; Massachusetts; USA |
U.S. Public Health Service ; NIGMS GM19351 |
PMID:17947322 | Free, Freely available | nif-0000-00552 | SCR_003097 | 2026-02-14 02:05:42 | 2 | ||||||
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MITOMAP - A human mitochondrial genome database Resource Report Resource Website 100+ mentions |
MITOMAP - A human mitochondrial genome database (RRID:SCR_002996) | MITOMAP | data or information resource, database | Database of polymorphisms and mutations of the human mitochondrial DNA. It reports published and unpublished data on human mitochondrial DNA variation. All data is curated by hand. If you would like to submit published articles to be included in mitomap, please send them the citation and a pdf. | gene, genome, diabetes, disease, disease-association, high resolution screening, human, inversion, metabolism, mitochondrial dna, mutation, phenotype, polymorphism, polypeptide assignment, pseudogene, restriction site, rna, sequence, trna, unpublished, variation, mitochondria, dna, insertion, deletion, FASEB list |
is used by: HmtVar is listed by: OMICtools is related to: Hereditary Hearing Loss Homepage has parent organization: Childrens Hospital of Philadelphia - Research Institute; Pennsylvania; USA has parent organization: Emory University School of Medicine; Atlanta; Georgia; USA |
NIH ; Muscular Dystrophy Foundation ; Ellison Foundation ; Diputacion General de Aragon Grupos consolidados B33 ; NIGMS GM46915; NINDS NS21328; NHLBI HL30164; NIA AG10130; NIA AG13154; NINDS NS213L8; NHLBI HL64017; NIH Biomedical Informatics Training Grant T15 LM007443; NSF EIA-0321390; Spanish Fondo de Investigacion Sanitaria PI050647; Ciber Enfermedades raras CB06/07/0043 |
PMID:17178747 PMID:15608272 PMID:9399813 PMID:9016535 PMID:8594574 |
Except where otherwise noted, Creative Commons Attribution License, The community can contribute to this resource | nif-0000-00511, OMICS_01641 | SCR_002996 | 2026-02-14 02:05:42 | 368 | ||||||
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MiST - Microbial Signal Transduction database Resource Report Resource Website 10+ mentions |
MiST - Microbial Signal Transduction database (RRID:SCR_003166) | MiST | data or information resource, database | Database which contains the signal transduction proteins for complete and draft bacterial and archaeal genomes. The MiST2 database identifies and catalogs the repertoire of signal transduction proteins in microbial genomes. | signal transduction proteins, bacterial genome, archaeal genome, microbial genome, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Tennessee Knoxville; Tennessee; USA |
South Carolina Research Association ; DOE Office of Science ; NIH ; NIGMS GM083177 |
PMID:19900966 | Free, Freely available | biotools:mist, nif-0000-03140 | https://bio.tools/mist | SCR_003166 | MiST 2.2, Microbial Signal Transduction Database, Microbial Signal Transduction database (MiST), MiST2 | 2026-02-14 02:06:11 | 31 | ||||
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BALBES Resource Report Resource Website 1+ mentions |
BALBES (RRID:SCR_018763) | software resource, software toolkit, software application, standalone software | Software system for solving protein structures using x-ray crystallographic data. Automatic molecular replacement pipeline for molecular replacement in CCP4. Integrates into one system all components necessary for solving crystal structure by Molecular Replacement. System is automated so that it needs no user intervention when running combination of jobs such as model searching, molecular replacement and refinement. | Molecular replacement pipeline, protein structure, solving protein structure, x-ray crystallographic data, molecular replacement, molecular replacement in CCP4, solving crystal structure, automated system, no user intervention, model searching, refinement |
uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: CCP4 |
Wellcome Trust ; NIGMS R01 GM069758 |
PMID:18094476 | Free, Available for download, Freely available | SCR_018763 | 2026-02-14 02:05:44 | 1 | ||||||||
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arcasHLA Resource Report Resource Website 1+ mentions |
arcasHLA (RRID:SCR_022286) | software resource, data processing software, software application | Software tool for high resolution HLA typing from RNAseq. Fast and accurate in silico inference of HLA genotypes from RNA-seq. | in silico inference of HLA genotypes, RNA-seq data, HLA typing | DARPA ; Phillip A. Sharp award ; NCI U54CA193313; NIGMS R01GM117591 |
PMID:31173059 | Free | SCR_022286 | 2026-02-14 02:05:37 | 8 | |||||||||
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plusTipTracker Resource Report Resource Website 10+ mentions |
plusTipTracker (RRID:SCR_021890) | software resource, image analysis software, data processing software, software application | Software package as quantitative image analysis software for measurement of microtubule dynamics. MATLAB software for tracking full dynamics of microtubules based on plusTIP marker live cell image sequences. | microtubule tracking, microtubule dynamics, microtubule dynamics measurement, plusTIP marker, live cell image sequences | NIGMS U01 GM67230 | PMID:21821130 | Free, Available for download, Freely available | SCR_021890 | 2026-02-14 02:05:48 | 10 |
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