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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PatchDock Resource Report Resource Website 50+ mentions |
PatchDock (RRID:SCR_017589) | software resource, data access protocol, web service, simulation software, software application | Web server for molecular docking. Performs structure prediction of protein–protein and protein–small molecule complexes. Molecular docking algorithm based on shape complementarity principles. | Molecular, docking, structure, prediction, protein, molecule, shape, complex, bio.tools |
is listed by: Debian is listed by: bio.tools |
Israel Science Foundation ; Hermann Minkowski-Minerva Center for Geometry at Tel Aviv University ; Israeli Ministry of Science ; National Cancer Institute ; NIH |
PMID:15980490 | Free, Freely available | biotools:patchdock | https://bio.tools/patchdock | SCR_017589 | 2026-02-12 09:47:11 | 85 | ||||||
|
immuneXpresso Resource Report Resource Website |
immuneXpresso (RRID:SCR_017578) | text-mining software, software resource, service resource, software application, data or information resource | Software tool as text-mining engine that structures and standardizes knowledge of immune intercellular communication. Knowledgebase contains interactions and separate mentions of cells or cytokines in context of thousands of diseases. Intercellular interactions were text-mined from all available PubMed abstracts across disease conditions. | Structure, standardize, immune, cellular, interaction, cytokine, disease, cell, PubMed, abstract |
is listed by: NIDDK Information Network (dkNET) is listed by: OMICtools |
NIH ; NIAID ; Rappaport Family Institute for Research in the Medical Sciences |
PMID:29912209 | Free, Freely available | SCR_017578 | 2026-02-12 09:46:54 | 0 | ||||||||
|
DISCO Resource Report Resource Website 100+ mentions |
DISCO (RRID:SCR_004586) | DISCO | service resource, software resource | DISCO is an information integration approach designed to facilitate interoperation among Internet resources. It consists of a set of tools and services that allows resource providers who maintain information to share it with automated systems such as NIF. NIF is then able to harvest the information and keep those sets of information up-to-date. How is this accomplished? By using a series of files and/or scripts which are then placed in the root directory of the resource developer''s resource. (NIF can also host the files on its servers and crawl for changes there.) Once the files of the resource providers are in place, and DISCO is notified, the DISCO server can then recognize and consume the information shared, providing machine understandable information to NIF Integrator Servers (also known as Aggregators) about your resource. What can DISCO do for my resource? * Inform search engines about your resource and keep your NIF Registry resource description up-to-date. * Expose your data (semi-structured datasets or fields within your structured database) through NIF''s Data Federation you choose what data will be shared. * Create links from an NCBI database (e.g., PubMed, Protein, Nucleotide, etc.) to your data records in NIF using Entrez LinkOut. * Advertise your terminology or ontological information. * Share your resource''s news with the NIF community., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | interoperation, sitemap, linkout, news, harvest, aggregate, FASEB list |
is used by: NIF Data Federation has parent organization: Neuroscience Information Framework has parent organization: Yale School of Medicine; Connecticut; USA |
NIH | PMID:20387131 PMID:18975149 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_143827 | SCR_004586 | registration and interoperation framework, DISCO: Extensible Web resource DISCOvery | 2026-02-12 09:43:55 | 332 | |||||
|
Xenopus Gene Collection Resource Report Resource Website 1+ mentions |
Xenopus Gene Collection (RRID:SCR_007023) | XGC | material resource, biomaterial supply resource | NIH initiative to support production of cDNA libraries, clones and 5'/3' sequences and to provide set of full-length (open reading frame) sequences and cDNA clones of expressed genes for Xenopus laevis and Xenopus tropicalis. Clones distribution is outsourced to for profit companies. Project concluded in September 2008. Resources generated by XGC are publicly accessible to biomedical research community. All sequences are deposited into GenBank.Corresponding clones are available through IMAGE clone distribution network. With conclusion of XGC project, GenBank records of XGC sequences will be frozen, without further updates. Since knowledge of what constitutes full-length coding region for some of genes and transcripts for which we have XGC clones will likely change in future, users planning to order XGC clones will need to monitor for these changes. Users can make use of genome browsers and gene-specific databases, such as UCSC Genome browser, NCBI's Map Viewer, and Entrez Gene, to view relevant regions of genome (browsers) or gene-related information (Entrez Gene). | est sequencing, expressed gene, frog, gene, adult, cdna, genomic, open reading frame, sequencing, stage, tag, xenopus laevis, xenopus tropicalis, sequence, expressed sequence tag, cdna, vector, cdna library, clone, 5'/3' sequence, frozen |
is listed by: One Mind Biospecimen Bank Listing is related to: One Mind Biospecimen Bank Listing is related to: ATCC is related to: GenBank is related to: Invitrogen Clones has parent organization: National Cancer Institute |
NIH Blueprint for Neuroscience Research ; NIH |
Free, Freely available | nif-0000-00224 | https://genecollections.nci.nih.gov/XGC/ | SCR_007023 | Xenopus Gene Collection | 2026-02-12 09:44:27 | 4 | |||||
|
ZMP Resource Report Resource Website 10+ mentions |
ZMP (RRID:SCR_006161) | ZMP | material resource, biomaterial supply resource | Create knockout alleles in protein coding genes in the zebrafish genome, using a combination of whole exome enrichment and Illumina next generation sequencing, with the aim to cover them all. Each allele created is analyzed for morphological differences and published on the ZMP site. Transcript counting is performed on alleles with a morphological phenotype. Alleles generated are archived and can be requested from this site through the Zebrafish International Resource Center (ZIRC). You may register to receive updates on genes of interest, or browse a complete list, or search by Ensembl ID, gene name or human and mouse orthologue. | phenotype, genome, gene, disease model, allele, orthologue, mutant, chromosome, human orthologue, mouse orthologue, mutation, knockout, human, mouse, transcript |
is listed by: One Mind Biospecimen Bank Listing is related to: Zebrafish International Resource Center has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust Sanger Institute; Hinxton; United Kingdom ; NIH ; ZF-HEALTH |
Free and open | nlx_151662 | SCR_006161 | Zebrafish Mutation Project (ZMP), Zebrafish Mutation Project, ZMP - Zebrafish Mutation Project | 2026-02-12 09:44:11 | 25 | ||||||
|
XTRACT Resource Report Resource Website 1+ mentions |
XTRACT (RRID:SCR_024933) | software application, software resource | Software command line tool for automated tractography. Standardised protocols for automated tractography in human and macaque brain. | automated tractography, tractography, human, macaque, brain | is a plug in for: FSL | Medical Research Council PhD Studentship UK ; Marie Skłodowska-Curie Individual Fellowship Grant ; Biotechnology and Biological Sciences Research Council ; Netherlands Organization for Scientific Research NWO Netherlands ; Sir Henry Dale Wellcome Trust Fellowship UK ; MRC Career Development Fellowship UK ; Wellcome Trust Collaborative Award UK ; UK Engineering and Physical Sciences Research Council ; Wellcome Trust grant UK ; Human Connectome Project ; NIMH 1U54MH091657; McDonnell Center for Systems Neuroscience at Washington University ; NIH ; UK Biobank Resource ; Wellcome Trust |
PMID:32407993 | Free, Freely available | SCR_024933 | 2026-02-12 09:48:08 | 2 | ||||||||
|
Natural Products Atlas Resource Report Resource Website 10+ mentions |
Natural Products Atlas (RRID:SCR_025107) | NP Atlas | data or information resource, atlas, knowledge base | Open access knowledge base for microbial natural products discovery. Database of microbially derived natural product structures. Provides coverage of bacterial and fungal natural products to visualize chemical diversity. Includes compounds and contains referenced data for structure, compound names, source organisms, isolation references, total syntheses, and instances of structural reassignment. Interactive web portal permits searching by structure, substructure, and physical properties. Provides mechanisms for visualizing natural products chemical space and dashboards for displaying author and discovery timeline data. Atlas has been developed under FAIR principles. | FAIR principles, microbial natural products discovery, natural product structures, bacterial and fungal natural products, visualize chemical diversity, | has parent organization: Simon Fraser University; British Columbia; Canada | NSERC Discovery ; NCCIH U41 AT008718; NIGMS R01 GM125943; NCCIH F31 AT010098; NCI F31 CA236237; NCCIH T32 AT007533; NIH D43 TW010530; NSF ; BBSRC ; Carnegie Trust for the Universities of Scotland ; Netherlands eScience Center ; Sao Paulo Research Foundation ; NCCIH AT008718; NIGMS GM124461; Natural Sciences and Engineering Research Council of Canada ; Ministry of Science ; Technology and Telecommunications of Costa Rica |
PMID:31807684 DOI:10.1093/nar/gkab941 |
Free, Freely available, | SCR_025107 | , The Natural Products Atlas, The Natural Products Atlas 2.0 | 2026-02-12 09:48:12 | 19 | ||||||
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baseline Resource Report Resource Website |
baseline (RRID:SCR_025128) | software resource, web service, data access protocol | Web tool to detect under- or over-dispersion in a baseline table from baseline table. | detect under dispersion, detect over dispersion, baseline table, | NIH | PMID:37360941 | Free, Freely available | SCR_025128 | 2026-02-12 09:48:23 | 0 | |||||||||
|
CellChat Resource Report Resource Website 500+ mentions |
CellChat (RRID:SCR_021946) | software toolkit, software resource | Software R toolkit for inference, visualization and analysis of cell-cell communication from single cell data.Quantitatively infers and analyzes intercellular communication networks from single-cell RNA-sequencing data. Predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Classifies signaling pathways and delineates conserved and context specific pathways across different datasets. | inference, visualization, analysis, cell-cell communication, single cell data, intercellular communication networks, single-cell RNA-sequencing data | NSF DMS1763272; Simons Foundation ; NIH U01 AR073159; NIGMS R01 GM123731; NIH P30 AR07504; Pew Charitable Trust ; LEO Foundation ; UC Irvine ; Howard Hughes Medical Institute |
PMID:33597522 | Free, Available for download, Freely available | http://www.cellchat.org/ | SCR_021946 | 2026-02-12 09:47:26 | 536 | ||||||||
|
University of Nebraska Medical Center Bioassay Core Facility Resource Report Resource Website |
University of Nebraska Medical Center Bioassay Core Facility (RRID:SCR_026270) | service resource, access service resource, core facility | Core provides equipment, personnel, and protocols for routine and advanced cellular and molecular assays for research. | ABRF, protocols for routine and advanced cellular and molecular assays, bioassay, service |
is listed by: ABRF CoreMarketplace has parent organization: University of Nebraska; Nebraska; USA |
NIH P20GM152326 | ABRF_3017 | https://coremarketplace.org/?FacilityID=3017&citation=1 | SCR_026270 | University of Nebraska Medical Center Bioassay Core | 2026-02-12 09:48:36 | 0 | |||||||
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National High Magnetic Field Laboratory High B/T Core Facility Resource Report Resource Website |
National High Magnetic Field Laboratory High B/T Core Facility (RRID:SCR_017360) | B/T | service resource, access service resource, core facility | Facility to conduct experiments in high magnetic fields up to 15 tesla and at very low temperatures down to 0.4 mK simultaneously. Located at University of Florida in Gainesville, it is operated as part of Physics Department Microkelvin Laboratory. | Magnetic, field, temperature | is related to: University of Florida; Florida; USA | NSF DMR-1644779; Florida State ; NIH ; Department of Energy ; Department of Defense |
Restricted | SCR_017360 | NHMF Laboratory High B/T Facility, High B/T (magnetic field / temperature) Facility, High B/T Facility | 2026-02-12 09:47:07 | 0 | |||||||
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Cincinnati Children's Hospital Office for Clinical and Translational Research Core Facility Resource Report Resource Website |
Cincinnati Children's Hospital Office for Clinical and Translational Research Core Facility (RRID:SCR_022633) | OCTR | service resource, access service resource, core facility | Clinical research support center for investigators and industry sponsors.Provides support services, research tools, experienced research personnel, and facilities to conduct or facilitate pediatric and adult clinical research from identification and development of research opportunities to phase I through phase IV clinical research trials. | USEDit, ABRF, pediatric and adult clinical research, phase I through phase IV clinical research trials, industry sponsors |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: Cincinnati Children's Hospital Medical Center; Cincinnati; Ohio |
NIH | ABRF_1487 | https://coremarketplace.org/?FacilityID=1487&citation=1 | SCR_022633 | Cincinnati Children's Hospital Office for Clinical and Translational Resarch, Office for Clinical and Translational Reearch | 2026-02-12 09:48:06 | 0 | ||||||
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Genetics of Kidneys in Diabetes Resource Report Resource Website |
Genetics of Kidneys in Diabetes (RRID:SCR_000133) | GoKinD, Go KinD | material resource, biomaterial supply resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Collect, store, and distribute genetic samples from cases and controls of type 1 diabetes and diabetic nephropathy for investigator-driven research into the genetic basis of diabetic nephropathy. As the risk of kidney complications in type 1 diabetes appears to have a considerable genetic component, this study assembled a large data resource for researchers attempting to identify causative genetic variants. The types of data collected allowed traditional case-control testing, a rapid and often powerful approach, and family-based analysis, a robust approach that is not influenced by population substructure. | clinical, genetics, genetic variant, gene, data set |
is listed by: One Mind Biospecimen Bank Listing is listed by: NIDDK Information Network (dkNET) has parent organization: George Washington University; Washington D.C.; USA |
Type 1 diabetes, Diabetes, Diabetic nephropathy, Kidney disease | JDRF ; NIH |
PMID:16775037 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152764 | http://www.gokind.org/access | SCR_000133 | Genetics of Kidneys in Diabetes (GoKinD) Study, Genetics of Kidneys in Diabetes Study | 2026-02-12 09:42:55 | 0 | |||
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Donald Danforth Plant Science Center Advanced Bioimaging Laboratory Core Facility Resource Report Resource Website 10+ mentions |
Donald Danforth Plant Science Center Advanced Bioimaging Laboratory Core Facility (RRID:SCR_018951) | service resource, access service resource, core facility | Core provides instruments for live cell imaging including Leica SP8-X confocal microscope and other fluorescence microscopes. Facility provides workstation for confocal image processing, ancillary equipment required for transmission electron microscopy. Services are provided as self services after user training by IMF staff or as full services done by core facility staff. | Live cell imaging, Leica SP8-X, confocal microscope, flulorescent microscope, confocal image processing, transmission electron microscopy, ABRF, ABRF |
is listed by: ABRF CoreMarketplace has parent organization: Donald Danforth Plant Science Center |
NSF ; NIH |
ABRF_1026 | https://www.scienceexchange.com/labs/advanced-bioimaging-laboratory https://coremarketplace.org/?FacilityID=1026 |
SCR_018951 | Advanced Bioimaging Laboratory, Donald Danforth Plant Science Center Integrated Microscopy Facility | 2026-02-12 09:47:07 | 20 | |||||||
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Scripps Research Institute Resource Report Resource Website 1+ mentions |
Scripps Research Institute (RRID:SCR_001907) | TSRI | institution | Nonprofit American medical research facility that focuses on research and education in the biomedical sciences. Headquartered in San Diego, California with a sister facility in Jupiter, Florida, the institute has laboratories employing scientists, technicians, graduate students, and administrative and other staff, making it the largest private, non-profit biomedical research organization in the United States and among the largest in the world. | institution, American, medical, research, education, biomedical, private, organization |
uses: DIRECT2experts is related to: Clinical and Translational Science Awards Consortium is related to: The Pancreatic Beta-Cell Consortium is parent organization of: piCALL is parent organization of: GeneChip Operating Software is parent organization of: TSRI-Yates Lab is parent organization of: BioGPS: The Gene Portal Hub is parent organization of: METLIN is parent organization of: AutoDock Vina is parent organization of: ViReMa is parent organization of: Autopack is parent organization of: Integrative Neuroscience Initiative on Alcoholism is parent organization of: Joint Center for Structural Genomics is parent organization of: Functional Glycomics Research is parent organization of: VIPERdb is parent organization of: GOEx - Gene Ontology Explorer is parent organization of: VIPERdb is parent organization of: Zinc Finger Tools is parent organization of: XCMS is parent organization of: Chemoproteomic identification and therapeutic validation of proteins of metabolic significance is parent organization of: Leginon is parent organization of: outbreak.info is parent organization of: Scripps Research Institute Florida Cell Based High Throughput Screening Core Facility |
NIH | THIS RESOURCE IS NO LONGER IN SERVICE | grid.214007.0, ISNI: 122199231, Wikidata: Q793867, nif-0000-10475 | https://ror.org/02dxx6824 | SCR_001907 | The Scripps Research Institute, Scripps Research | 2026-02-07 02:05:46 | 1 | |||||
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Feinstein Institute for Medical Research Resource Report Resource Website |
Feinstein Institute for Medical Research (RRID:SCR_004470) | Feinstein Institute | institution | The Feinstein Institute for Medical Research is the research branch of the North Shore-Long Island Jewish Health System. Biomedical research has been a vital aspect of its two academic medical centers North Shore University Hospital and Long Island Jewish Medical Center since their establishment in the early 1950''s. Through its connection to the hospital system, the Institute bridges the gap between biomedical research and patient care, accessing hundreds of thousands of patients in the health system''s 15 hospitals, four long-term care facilities, three trauma centers, six home health agencies and dozens of outpatient facilities. Institute scientists collaborate with clinicians throughout the system to shed light on basic biological processes underlying disease. This knowledge is used to develop new therapies and diagnostics. Currently, more than 800 scientists and investigators are conducting research in oncology, immunology and inflammation, genetics, psychiatry, neurology, pediatrics, surgery, urology, obstetrics/gynecology and many other specialties. In 2008, the Feinstein received funding from the National Institutes of Health in excess of $28 million, and an additional $10 million from other federal sources. Total annual research funding from all sources exceeded $44 million in 2008. We stand at the threshold of an extraordinary time in medicine. Over the last 100 years, biomedical science has progressed very rapidly. Advances coming from the integration of genomics, proteomics and bioinformatics into the biomedical toolkit hold the promise that this transformation will continue well into the 21st century. The Feinstein Institute for Medical Research is a growing force in research innovation, education and progress. | biomedical research, research |
is related to: Biomarkers of Anti-TNF Treatment Efficacy in Rheumatoid Arthritis - Unresponsive Populations is parent organization of: Feinstein Biorepository is parent organization of: Biomarkers of Anti-TNF Treatment Efficacy in Rheumatoid Arthritis - Unresponsive Populations is parent organization of: Genetic Analysis Software |
NIH | ISNI: 0000 0000 9566 0634, Wikidata: Q7733638, grid.250903.d, nlx_143748 | https://ror.org/05dnene97 | SCR_004470 | Feinstein Institute | 2026-02-07 02:06:47 | 0 | ||||||
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ConceptMapper Resource Report Resource Website 10+ mentions |
ConceptMapper (RRID:SCR_006548) | Concept Mapper | software resource | Software tool that stores definitions of views of data, along with the ontology concepts they represent. This is a part of the Neuroscience Information Framework (NIF) code stack. | resource:google refine | has parent organization: Neuroscience Information Framework | NIH | nlx_157720 | SCR_006548 | 2026-02-07 02:07:31 | 11 | ||||||||
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Pennington Biomedical Research Center Resource Report Resource Website |
Pennington Biomedical Research Center (RRID:SCR_002946) | PBRC | institution | Research institute which investigates chronic disease and its triggers. | chronic disease, chronic disease research, chronic disease institute |
is parent organization of: Pennington Biomedical Research Center Nutrition and Obesity Research Center Animal Models and Phenotyping Core is parent organization of: Pennington Biomedical Research Center Nutrition and Obesity Research Center Molecular Mechanisms Core is parent organization of: Pennington Biomedical Research Center Nutrition and Obesity Research Center Human Phenotyping Core is parent organization of: Pennington Biomedical Research Center Nutrition and Obesity Research Center is parent organization of: Louisiana State University Pennington Biomedical Nutrition Obesity Research Center Core Facility |
State of Louisiana ; U.S. Department of Agriculture ; U.S. Department of Defense ; private sector organizations and companies ; NIH |
ISNI: 0000 0001 2159 6024, grid.250514.7, Wikidata: Q7163465, nif-0000-30066 | https://ror.org/040cnym54 | SCR_002946 | Pennington Center | 2026-02-07 02:05:53 | 0 | ||||||
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PHAST Resource Report Resource Website 50+ mentions |
PHAST (RRID:SCR_003204) | PHAST | software resource | A freely available software package for comparative and evolutionary genomics that consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations. For the most part, PHAST focuses on two kinds of applications: the identification of novel functional elements, including protein-coding exons and evolutionarily conserved sequences; and statistical phylogenetic modeling, including estimation of model parameters, detection of signatures of selection, and reconstruction of ancestral sequences. It consists of over 60,000 lines of C code. | evolutionary genomic, evolution, genomics, sequence alignment, phylogenetic tree, genomic annotation, functional element, protein-coding exon, conserved sequence, phylogenetic modeling, ancestral sequence, c |
is listed by: OMICtools is listed by: Debian has parent organization: Cornell University; New York; USA |
NIH ; David and Lucile Packard Foundation ; NHGRI ; University of California Biotechnology Research and Education Program ; NSF DBI-0644111; NIGMS R01-GM082901-01 |
PMID:21278375 DOI:10.1093/bib/bbq072 |
Free, Available for download, Freely available | OMICS_01557 | https://sources.debian.org/src/phast/ | SCR_003204 | Phylogenetic Analysis with Space/Time Models | 2026-02-07 02:06:12 | 55 | ||||
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Consed Resource Report Resource Website 500+ mentions |
Consed (RRID:SCR_005650) | Consed | software resource | A graphical tool for sequence finishing (BAM File Viewer, Assembly Editor, Autofinish, Autoreport, Autoedit, and Align Reads To Reference Sequence) | next-generation sequencing, graphical editor, linux, macosx, solaris, c++ |
is listed by: OMICtools has parent organization: University of Washington; Seattle; USA |
NIH ; NHGRI R01HG005710 |
PMID:23995391 PMID:9521923 |
Free for academic use, Free for non-profit use, Commercial license | OMICS_00879 | SCR_005650 | 2026-02-07 02:06:48 | 594 |
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