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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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GeneNetwork Resource Report Resource Website 100+ mentions |
GeneNetwork (RRID:SCR_002388) | GeneNetwork, WebQTL | service resource, data or information resource, data repository, database, storage service resource | Web platform that provides access to data and tools to study complex networks of genes, molecules, and higher order gene function and phenotypes. Sequence data (SNPs) and transcriptome data sets (expression genetic or eQTL data sets). Quantitative trait locus (QTL) mapping module that is built into GN is optimized for fast on-line analysis of traits that are controlled by combinations of gene variants and environmental factors. Used to study humans, mice (BXD, AXB, LXS, etc.), rats (HXB), Drosophila, and plant species (barley and Arabidopsis). Users are welcome to enter their own private data. | Variation, trait, vertebrate trait ontology, phenotype, systems genetics, quantitative trait, gene mapping, experimental precision medicinenetwork analysis, causal modeling, genomic location, genotype, inbred strain, sex, heterogeneous stock, phenome, phenotype, QTL, expression QTL, genetic reference population, single nucleotide polymorphism, RNA expression, protein expression, metabolite expression, metagenomics, epigenomics, gene-by-environmental interaction, epistasis, FAIR data standards, open source software, FASEB list |
is used by: NIF Data Federation is used by: Hypothesis Center is related to: NIH Data Sharing Repositories has parent organization: University of Tennessee Health Science Center; Tennessee; USA |
NIGMS R01 GM123489; NIAAA U01 AA016662; NIAAA U01 AA13499; NIAAA U24 AA13513; NIAAA U01 AA014425; NIA R01 AG043930; NIDA P20 DA21131; NCI U01 CA105417; NCRR U24 RR021760 |
PMID:8043953 PMID:11737945 PMID:15043217 PMID:15114364 PMID:15043220 PMID:15043219 PMID:15711545 PMID:18368372 PMID:27933521 |
Restricted | nif-0000-00380 | SCR_002388 | GeneNetwork and WebQTL, GeneNetwork / WebQTL, www.genenetwork.org, GeneNetwork WebQTL, The GeneNetwork / WebQTL | 2026-07-28 09:40:24 | 473 | |||||
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PharmGKB Resource Report Resource Website 1000+ mentions |
PharmGKB (RRID:SCR_002689) | PharmGKB | service resource, data set, data or information resource, data repository, database, data access protocol, software resource, web service, storage service resource | Database and central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. PharmGKB welcomes submissions of primary data from all research into genes and genetic variation and their effects on drug and disease phenotypes. PharmGKB collects, encodes, and disseminates knowledge about the impact of human genetic variations on drug response. They curate primary genotype and phenotype data, annotate gene variants and gene-drug-disease relationships via literature review, and summarize important PGx genes and drug pathways. PharmGKB is part of the NIH Pharmacogenomics Research Network (PGRN), a nationwide collaborative research consortium. Its aim is to aid researchers in understanding how genetic variation among individuals contributes to differences in reactions to drugs. A selected subset of data from PharmGKB is accessible via a SOAP interface. Downloaded data is available for individual research purposes only. Drugs with pharmacogenomic information in the context of FDA-approved drug labels are cataloged and drugs with mounting pharmacogenomic evidence are listed. | pharmacogenomics, microarray, pathway, phenotype, snp array, genotype, clinical, genetic variation, drug, gene, genetic variation, disease, cardiovascular, pulmonary, cancer, metabolic, transporter, drug response, small molecule, research, drug response, FASEB list |
is used by: NIF Data Federation is listed by: OMICtools is related to: WikiPathways is related to: ConsensusPathDB is related to: Integrated Molecular Interaction Database is related to: MalaCards is related to: phenomeNET has parent organization: Stanford University; Stanford; California is parent organization of: PharmGKB Ontology |
NIGMS R24 GM61374 | PMID:11908751 | Free, Freely available | nif-0000-00414, OMICS_01586, r3d100012325 | https://doi.org/10.17616/R31H1N | SCR_002689 | Pharmacogenomics Knowledge Base | 2026-07-28 09:40:30 | 1152 | ||||
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University of Nebraska Medical Center Advanced Microscopy Core Facility Resource Report Resource Website 10+ mentions |
University of Nebraska Medical Center Advanced Microscopy Core Facility (RRID:SCR_022467) | access service resource, service resource, core facility | Facility houses imaging technologies ranging from super resolution (~ 0.120 um to 0.020 um) to microscopic (~ 0.300 um) to mesoscopic (~ 1 um) biomedical imaging. Imaging specialists provide training and/or actively assist researchers collecting images across imaging instrumentation. Instrumentation includes Zeiss ELYRA PS.1 is inverted microscope for super resolution (SR) structured illumination microscopy (SIM) and single molecule localization microscopy (SMLM) including, PhotoActivated Localization Microscopy (PALM) using photo switchable/convertible fluorescent proteins, Total Internal Reflection Fluorescence (TIRF) and STochastic Optical Reconstruction Microscopy (STORM);Zeiss 800 CLSM with Airyscan is an inverted microscope dramatically increasing conventional confocal image resolution to ~180 nm using Airyscan technology; Zeiss 710 LSM is inverted microscope supporting most basic imaging applications, multi channel and spectral, co localization, live cell, 3D, and time series imaging; Zeiss Celldiscoverer 7 is widefield imaging system for automated, time lapse imaging of live samples; Zeiss Axioscan 7 is high performance whole slide scanning system for fluorescence, brightfield, and polarization imaging;Miltenyi Biotec Ultramicroscope II Light Sheet fluorescence microscope (LSFM) extends fluorescent imaging into true 3D, large scale volumetric imaging of intact tissues, organs, and small organisms. AMCF also houses several high-end data analysis workstations with premier image analysis software including HALO (Indica Labs) and IMARIS (Oxford Instruments) facilitating data rendering, analyses, and presentation options. | USEDit, ABRF, biomedical imaging, microscopy |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: University of Nebraska; Nebraska; USA |
NIGMS GM103427; NIGMS GM106397; NCI CA036727; NCRR RR027301; NIH Office of the Director OD030486 |
open | ABRF_1375 | https://coremarketplace.org/?FacilityID=1375&citation=1 | SCR_022467 | UNMC Advanced Microscopy Core Facility | 2026-07-28 09:45:34 | 18 | ||||||
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Protofilament Bending Models Resource Report Resource Website 1+ mentions |
Protofilament Bending Models (RRID:SCR_023062) | source code, software resource | Code is written to be run with Matlab version r2020b or higher. Model accepts wave assay pulse amplitude data, and simultaneously solves and fits protofilament deflection models to deduce fundamental biophysical properties of microtubule protofilaments. | Matlab, protofilament, microtubule, strain energy, GTP hydrolysis | uses: MATLAB | NIGMS R35GM134842 | DOI:10.7554/eLife.83225 | Free, Available for download, Freely available | SCR_023062 | 2026-07-28 09:45:46 | 1 | ||||||||
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abSENSE Resource Report Resource Website 1+ mentions |
abSENSE (RRID:SCR_023223) | source code, software resource | Software to interpret undetected homolog.Method that calculates probability that homolog of given gene would fail to be detected by homology search in given species, even if homolog were present and evolving normally. | undetected homolog, gene homolog detection failure, homology search, lineage-specific genes, homology detection failure | Howard Hughes Medical Institute ; NHGRI R01-HG009116; NIGMS RO1-GM43987; NSF 1764269; Simons Center for the Mathematical and Statistical Analysis of Biology 594596; Harvard University |
PMID:33137085 | Free, Available for download, Freely available | http://www.eddylab.org/abSENSE/ | SCR_023223 | 2026-07-28 09:45:53 | 1 | ||||||||
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PTNet Resource Report Resource Website |
PTNet (RRID:SCR_022975) | source code, software resource | Graph based learning model for protein expression estimation by considering miRNA-mRNA interactions. Estimates protein levels by considering miRNA-mRNA interaction network, mRNA expression and miRNA expression. | protein level, protein expression estimation, miRNA-mRNA interactions, mRNA expression, miRNA expression, | NSF III1755761; NIGMS R01GM113952; NIDDK DK097771 |
DOI:10.1093/bib/bbab264 | Free, Available for download, Freely available | SCR_022975 | 2026-07-28 09:45:49 | 0 | |||||||||
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University of Nevada Reno School of Medicine High Spatial and Temporal Resolution Imaging Core Facility Resource Report Resource Website 1+ mentions |
University of Nevada Reno School of Medicine High Spatial and Temporal Resolution Imaging Core Facility (RRID:SCR_024793) | HSTRI Core | access service resource, service resource, core facility | Core provides high spatial and temporal resolution imaging methodologies and instrumentation for studying cellular structure, signaling pathways, and function in health and disease. Offers education, training and expertise in advising investigators in the use of the new technologies. | ABRF, Image acquisition and analysis, high spatial and temporal resolution imaging, |
is listed by: ABRF CoreMarketplace has parent organization: University of Nevada at Reno; Nevada; USA |
NIGMS P20GM130459 | Open | ABRF_2596 | https://coremarketplace.org/?FacilityID=2596&citation=1 | SCR_024793 | , University of Nevada High Spatial and Temporal Resolution Imaging Core | 2026-07-28 09:46:11 | 1 | |||||
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PLAAC Resource Report Resource Website 10+ mentions |
PLAAC (RRID:SCR_024973) | software resource, data access protocol, web service | Web and command-line application to identify proteins with prion-like amino acid composition. Searches protein sequences to identify probable prion subsequences using hidden-Markov model algorithm. | protein sequences search, identify proteins with prion-like amino acid composition, identify proteins, identify probable prion subsequences, | G. Harold and Leila Y. Mathers Foundation ; Howard Hughes Medical Institute ; NIGMS GM025874 |
PMID:24825614 | Free, Freely available | SCR_024973 | Prion Like Amino Acid Composition | 2026-07-28 09:46:13 | 25 | ||||||||
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SomaticSeq Resource Report Resource Website 1+ mentions |
SomaticSeq (RRID:SCR_024891) | software toolkit, software resource | Software accurate somatic mutation detection pipeline implementing stochastic boosting algorithm to produce somatic mutation calls for both single nucleotide variants and small insertions and deletions. NGS variant calling and classification. | NGS variant calling and classification, somatic mutation detection, somatic mutation calls, single nucleotide variants, detect somatic mutations, | NIGMS R01 GM109836; NHGRI R01 HG007834 |
PMID:26381235 | SCR_024891 | 2026-07-28 09:46:14 | 6 | ||||||||||
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PEPhub Resource Report Resource Website 1+ mentions |
PEPhub (RRID:SCR_024892) | data or information resource, database, data access protocol, software resource, web service | Web biological metadata server to view, store, and share your sample metadata in form of Portable Encapsulated Projects. PEPhub takes advantage of PEP biological metadata standard to store, edit, and access your PEPs in one place. Components include database where PEPs are stored; API to programmatically read and write PEPs in database; web based user interface to view and manage these PEPs via front end. | Portable Encapsulated Projects, biological metadata server, sharing, retrieving, validating, sample metadata, | NIGMS R35 GM128636; NHGRI R01 HG012558 |
PMID:37645717 | Free, Available for download, Freely available | https://github.com/pepkit/pephub | SCR_024892 | Portable Encapsulated Projects hub | 2026-07-28 09:46:12 | 2 | |||||||
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Guided Sparse Factor Analysis Resource Report Resource Website 1+ mentions |
Guided Sparse Factor Analysis (RRID:SCR_025023) | GSFA | software toolkit, software resource | Software R package that performs sparse factor analysis and differential gene expression discovery simultaneously on single cell CRISPR screening data. | sparse factor analysis, differential gene expression, discovery simultaneously, single cell CRISPR screening data, | NIMH R01MH110531; NHGRI R01HG010773; NIMH R01MH116281; NIGMS R01 GM126553; NHGRI R01 HG011883; NSF ; Sloan Research Fellowship |
PMID:37770710 | Free, Available for download, Freely available | SCR_025023 | 2026-07-28 09:46:14 | 1 | ||||||||
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PyContact Resource Report Resource Website 1+ mentions |
PyContact (RRID:SCR_025066) | software application, software resource, data analysis software, data processing software | Software tool for analysis of non-covalent interactions in molecular dynamics trajectories. Implemented in Python and is universally applicable to any kind of MD trajectory supported by MDAnalysis package. | non-covalent interactions, molecular dynamics trajectories, | is related to: MDAnalysis | German Research Foundation ; NIGMS P41 GM104601; NSF |
PMID:29414703 | Free, Available for download, Freely available, | https://github.com/maxscheurer/pycontact | SCR_025066 | 2026-07-28 09:46:16 | 3 | |||||||
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Natural Products Atlas Resource Report Resource Website 10+ mentions |
Natural Products Atlas (RRID:SCR_025107) | NP Atlas | knowledge base, data or information resource, atlas | 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 | 2026-07-28 09:46:16 | 19 | ||||||
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Subcellular Location Image Finder Resource Report Resource Website 1+ mentions |
Subcellular Location Image Finder (RRID:SCR_006723) | SLIF | database, data or information resource, image | SLIF finds fluorescence microscope images in on-line journal articles, and indexes them according to cell line, proteins visualized, and resolution. Images can be accessed via the SLIF Web database. SLIF takes on-line papers and scans them for figures that contain fluorescence microscope images (FMIs). Figures typically contain multiple FMIs, to SLIF must segment these images into individual FMIs. When the FMI images are extracted, annotations for the images (for instance, names of proteins and cell-lines) are also extracted from the accompanying caption text. Protein annotation are also used to link to external databases, such as the Gene Ontology DB. The more detailed process includes: segmentation of images into panels; panel classification, to find FMIs; segmentation of the caption, to find which portions of the caption apply to which panels; text-based entity extraction; matching of extracted entities to database entries; extraction of panel labels from text and figures; and alignment of the text segments to the panels. Extracted FMIs are processed to find subcellular location features (SLFs), and the resulting analyzed, annotated figures are stored in a database, which is accessible via SQL queries. | fluorescence, annotation, cell, journal, microscope, protein, subcellular, image, cell line, fluorescence microscope, information retrieval, data mining |
is listed by: Biositemaps has parent organization: Carnegie Mellon University; Pennsylvania; USA |
Commonwealth of Pennsylvania Tobacco Settlement Fund ; National Center for Integrative Biomedical Informatics ; NIGMS R01 GM078622; NIDA U54 DA021519 |
PMID:17990497 | nif-0000-10308 | SCR_006723 | SLIF - Subcellular Location Image Finder | 2026-07-28 09:41:37 | 1 | ||||||
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RNase P Database Resource Report Resource Website 1+ mentions |
RNase P Database (RRID:SCR_006680) | RNase P Database | data or information resource, database | Ribonuclease P is responsible for the 5''-maturation of tRNA precursors. Ribonuclease P is a ribonucleoprotein, and in bacteria (and some Archaea) the RNA subunit alone is catalytically active in vitro, i.e. it is a ribozyme. The Ribonuclease P Database is a compilation of ribonuclease P sequences, sequence alignments, secondary structures, three-dimensional models and accessory information. The database contains information on bacterial, archaeal, and eukaryotic RNase P. The RNase P and protein sequences are available from phylogentically-arranged lists, individual sequences, or aligned in GenBank format. The database also provides secondary structures and 3D models, as well as movies, still images, and other accessory information. | ribonuclease p, ribonucleoprotein, ribozyme, sequence, sequence alignment, secondary structure, 3-d model, rnase p rna | has parent organization: North Carolina State University; North Carolina; USA | Isis Phamaceuticals ; NIGMS GM52894 |
PMID:9847214 | nif-0000-03403 | SCR_006680 | The RNase P Database, Ribonuclease P Database | 2026-07-28 09:41:38 | 8 | ||||||
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AgBase Resource Report Resource Website 100+ mentions |
AgBase (RRID:SCR_007547) | AgBase | data or information resource, database | A curated, open-source, web-accessible resource for functional analysis of agricultural plant and animal gene products. Our long-term goal is to serve the needs of the agricultural research communities by facilitating post-genome biology for agriculture researchers and for those researchers primarily using agricultural species as biomedical models. AgBase provides tools designed to assist with the analysis of proteomics data and tools to evaluate experimental datasets using the GO. Additional tools for sequence analysis are also provided. We use controlled vocabularies developed by the Gene Ontology (GO) Consortium to describe molecular function, biological process, and cellular component for genes and gene products in agricultural species. AgBase will also accept annotations from any interested party in the research communities. AgBase develops freely available tools for functional analysis, including tools for using GO. We appreciate any and all questions, comments, and suggestions. AgBase uses the NCBI Blast program for searches for similar sequences. And the Taxonomy Browser allows users to find the NCBI defined taxon ID for or taxon name for different organisms. | gene ontology, agricultural species, biological process, cellular component for genes, molecular function, protein identification, animals, plants, microbes, parasites, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: IntAct has parent organization: Mississippi State University; Mississippi; USA is parent organization of: GORetriever is parent organization of: GOSlimViewer is parent organization of: GOProfiler is parent organization of: GOanna |
Mississippi State University; Mississippi; USA ; USDA Agriculture and Food Research Initiative Competitive Grant 2011-67015-30332; National Research Initiative of the USDA Cooperative State Research Education and Extension Service 2007-35205-17941; NIGMS project 07111084; NSF EPS 0903787 |
PMID:21075795 | nif-0000-02537, biotools:agbase, r3d100012427 | https://bio.tools/agbase, https://doi.org/10.17616/R3P772 | SCR_007547 | 2026-07-28 09:42:04 | 111 | ||||||
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Klotho: Biochemical Compounds Declarative Database Resource Report Resource Website |
Klotho: Biochemical Compounds Declarative Database (RRID:SCR_007714) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. A database of biochemical compound information. All files are available for download, and all entries are cataloged by accession number. Klotho is part of a larger attempt to model biological processes, beginning with biochemistry. | has parent organization: University of Missouri; Missouri; USA | NIGMS R01-GM56529; NSF DBI-9117005 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03073 | SCR_007714 | Klotho | 2026-07-28 09:41:54 | 0 | ||||||||
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Metalloprotein Site Database Resource Report Resource Website 1+ mentions |
Metalloprotein Site Database (RRID:SCR_007780) | MDB | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 24, 2013. Database and Browser containing quantitative information on all the metal-containing sites available from structures in the PDB distribution. This database contains geometrical and molecular information that allows the classification and search of particular combinations of site characteristics, and answer questions such as: How many mononuclear zinc-containing sites are five coordinate with X-ray resolution better than 1.8 Angstroms?, and then be able to visualize and manipulate the matching sites. The database also includes enough information to answer questions involving type and number of ligands (e.g. "at least 2 His"), and include distance cutoff criteria (e.g. a metal-ligand distance no more than 3.0 Angstroms and no less than 2.2 Angstroms). This database is being developed as part of a project whose ultimate goal is metalloprotein design, allowing the interactive visualization of geometrical and functional information garnered from the MDB. The database is created by automatic recognition and extraction of metal-binding sites from metal-containing proteins. Quantitative information is extracted and organized into a searchable form, by iterating through all the entries in the latest PDB release (at the moment: September 2001). This is a comprehensive quantitative database, which exists in SQL format and contains information on about 5,500 proteins. | software, web service |
is listed by: 3DVC is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) |
NIGMS P01-GM48495 | PMID:11752342 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03116 | SCR_007780 | Metalloprotein Database and Browser | 2026-07-28 09:42:13 | 1 | |||||
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Gemma Resource Report Resource Website 1000+ mentions |
Gemma (RRID:SCR_008007) | Gemma | data or information resource, database | Resource for reuse, sharing and meta-analysis of expression profiling data. Database and set of tools for meta analysis, reuse and sharing of genomics data. Targeted at analysis of gene expression profiles. Users can search, access and visualize coexpression and differential expression results. | chip, microarray, functional genomics, gene expression, coexpression, differential expression, FASEB list |
is used by: NIF Data Federation is used by: Integrated Data Annotation is listed by: Debian is listed by: SoftCite is related to: Gene Ontology is related to: Gene Expression Omnibus is related to: Phenocarta has parent organization: University of British Columbia; British Columbia; Canada is parent organization of: Neurocarta |
NIGMS GM076990; Canadian Foundation for Innovation ; Michael Smith Foundation for Health Research ; Canadian Institutes for Health Research |
PMID:22782548 | Free, Freely available | nif-0000-08127, r3d100012747 | https://sources.debian.org/src/gemma/, https://doi.org/10.17616/R36R54, https://doi.org/10.17616/R36R54 | SCR_008007 | 2026-07-28 09:41:58 | 1112 | |||||
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iTools Resource Report Resource Website 10+ mentions |
iTools (RRID:SCR_009626) | iTools | service resource, data or information resource, data repository, database, data access protocol, software resource, web service, software repository, storage service resource | An infrastructure for managing of diverse computational biology resources - data, software tools and web-services. The iTools design, implementation and meta-data content reflect the broad NCBC needs and expertise (www.NCBCs.org). | computational neuroscience, data, experiment control, hardware, imaging genomics, information specification, java, loni pipeline, model, ontology, os independent, metadata |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: National Centers for Biomedical Computing has parent organization: Laboratory of Neuro Imaging |
NIH Roadmap for Medical Research ; NCRR U54-RR021813; NIDA U54-DA021519; NCI U54-CA121852; NHGRI U54-HG004028; NIGMS U54-GM072970; NIBIB U54-EB005149; NLM U54-LM008748 |
PMID:18509477 | GNU Lesser General Public License | nlx_155852 | http://www.nitrc.org/projects/itools, http://www.loni.usc.edu/research/software | http://itools.loni.ucla.edu/ | SCR_009626 | ITools Resourceome, NCBC iTools | 2026-07-28 09:42:28 | 45 |
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