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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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NetPath Resource Report Resource Website 50+ mentions |
NetPath (RRID:SCR_003567) | NetPath | data or information resource, database | A manually curated resource of signal transduction pathways in humans. All pathways are freely available for download in BioPAX level 3.0, PSI-MI version 2.5 and SBML version 2.1 formats. The slim pathway models representing only core reactions in each pathway are available at NetSlim. All the NetPath pathway models are also submitted to WikiPathways., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | pathway, signal transduction, molecule, physical interaction, gene, transcriptional regulation, transport, enzyme catalysis, immune, signaling pathway, FASEB list |
is related to: WikiPathways is related to: ConsensusPathDB has parent organization: Johns Hopkins University; Maryland; USA has parent organization: Institute of Bioinformatics; Bangalore; India |
Cancer | PMID:20067622 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_157701, r3d100011009 | https://doi.org/10.17616/R34G98 | SCR_003567 | 2026-09-19 12:56:40 | 91 | |||||
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University of Utah Labs and Facilities Resource Report Resource Website |
University of Utah Labs and Facilities (RRID:SCR_001042) | access service resource, core facility, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2024. Labs and facilities of the University of Utah, which include: Microarray and Genomic Analysis Core Facility, Flow Cytometry Core Facility, Mutation Generation and Detection Facility, and the Transgenic and Gene Targeting Core. | lab, facility, microarray, genomics analysis, flow cytometry, gene, transgenic |
is listed by: ScienceExchange is related to: University of Utah Microarray and Genomic Analysis Core Facility is related to: University of Utah Flow Cytometry Core Facility has parent organization: University of Utah; Utah; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | SciEx_1964 | SCR_001042 | Utah Labs & Facilities, UUtah Labs and Facilities | 2026-09-19 12:58:32 | 0 | ||||||||
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EEG Database Resource Report Resource Website 1+ mentions |
EEG Database (RRID:SCR_001581) | EEG Database | data or information resource, data set | Data set from a large study to examine EEG correlates of genetic predisposition to alcoholism. It contains measurements from 64 electrodes placed on the scalp sampled at 256 Hz (3.9-msec epoch) for 1 second. There were two groups of subjects: alcoholic and control. Each subject was exposed to either a single stimulus (S1) or to two stimuli (S1 and S2) which were pictures of objects chosen from the 1980 Snodgrass and Vanderwart picture set. When two stimuli were shown, they were presented in either a matched condition where S1 was identical to S2 or in a non-matched condition where S1 differed from S2. There were 122 subjects and each subject completed 120 trials where different stimuli were shown. The electrode positions were located at standard sites (Standard Electrode Position Nomenclature, American Electroencephalographic Association 1990). Zhang et al. (1995) describes in detail the data collection process. There are three versions of the EEG data set. * The Small Data Set (smni97_eeg_data.tar.gz) contains data for the 2 subjects, alcoholic a_co2a0000364 and control c_co2c0000337. For each of the 3 matching paradigms, c_1 (one presentation only), c_m (match to previous presentation) and c_n (no-match to previous presentation), 10 runs are shown. * The Large Data Set (SMNI_CMI_TRAIN.tar.gz and SMNI_CMI_TEST.tar.gz) contains data for 10 alcoholic and 10 control subjects, with 10 runs per subject per paradigm. The test data used the same 10 alcoholic and 10 control subjects as with the training data, but with 10 out-of-sample runs per subject per paradigm. * The Full Data Set contains all 120 trials for 122 subjects. The entire set of data is about 700 MBytes. | genetic predisposition, eeg, gene, heredity, picture, stimuli, match, non-match | has parent organization: University of California at Irvine; California; USA | Alcoholism, Alcoholic, Control | PMID:8590074 | Free, Freely available | nlx_153818 | http://kdd.ics.uci.edu/databases/eeg/eeg.html | SCR_001581 | EEG Database Data Set | 2026-09-19 12:58:33 | 4 | ||||
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EBI Genomes Resource Report Resource Website 10+ mentions |
EBI Genomes (RRID:SCR_002426) | data or information resource, data set | The EBI genomes pages give access to a large number of complete genomes including bacteria, archaea, viruses, phages, plasmids, viroids and eukaryotes. Methods using whole genome shotgun data are used to gain a large amount of genome coverage for an organism. WGS data for a growing number of organisms are being submitted to DDBJ/EMBL/GenBank. Genome entries have been listed in their appropriate category which may be browsed using the website navigation tool bar on the left. While organelles are all listed in a separate category, any from Eukaryota with chromosome entries are also listed in the Eukaryota page. Within each page, entries are grouped and sorted at the species level with links to the taxonomy page for that species separating each group. Within each species, entries whose source organism has been categorized further are grouped and numbered accordingly. Links are made to: * taxonomy * complete EMBL flatfile * CON files * lists of CON segments * Project * Proteomes pages * FASTA file of Proteins * list of Proteins | eukaryote genome, gene, gene browser, genome, archaea genome, bacteria genome, phage genome, plasmid genome, viroid genome, viruse genome, sequence, protein, nucleotide, complete genome, gold standard | has parent organization: European Bioinformatics Institute | nif-0000-02778 | SCR_002426 | Genomes Pages - At the EBI, ENA Genomes Server | 2026-09-19 12:58:34 | 26 | |||||||||
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Family Investigation of Nephropathy of Diabetes Resource Report Resource Website |
Family Investigation of Nephropathy of Diabetes (RRID:SCR_001525) | FIND, F.I.N.D. | clinical trial, resource | Multicenter observational study designed to identify genetic determinants of diabetic nephropathy. It is conducted in eleven U.S. clinical centers and a coordinating center, and with four ethnic groups (European Americans, African Americans, Mexican Americans, and American Indians). Two strategies are used to localize susceptibility genes: a family-based linkage study and a case-control study using mapping by admixture linkage disequilibrium (MALD). In the family-based study, probands with diabetic nephropathy are recruited with their parents and selected siblings. Linkage analyses will be conducted to identify chromosomal regions containing genes that influence the development of diabetic nephropathy or related quantitative traits such as serum creatinine concentration, urinary albumin excretion, and plasma glucose concentrations. Regions showing evidence of linkage will be examined further with both genetic linkage and association studies to identify genes that influence diabetic nephropathy or related traits. Two types of MALD studies are being done. One is a case-control study of unrelated individuals of Mexican American heritage in which both cases and controls have diabetes, but only the case has nephropathy. The other is a case-control study of African American patients with nephropathy (cases) and their spouses (controls) unaffected by diabetes and nephropathy; offspring are genotyped when available to provide haplotype data. The specific goals of this program: * Delineate genomic regions associated with the development and progression of renal disease(s) * Evaluate whether there is a genetic link between diabetic nephropathy and diabetic retinopathy * Improve outcomes * Provide protection for people at risk and slow the progression of renal disease * Help establish a resource for genetic studies of kidney disease and diabetic complications by creating a repository of genetic samples and a database * Encourage studies of the genetics of progressive renal disease | genetic susceptibility, genetic pathway, renal, kidney, outcome, gene, genetics, european-american, african-american, mexican-american, american-indian, linkage association study, admixture linkage disequilibrium, mapping by admixture linkage disequilibrium, serum creatinine, urinary protein excretion, plasma glucose level, blood pressure, blood lipid level, trait, linkage, adult human, male, female, clinical |
is listed by: ClinicalTrials.gov is listed by: NIDDK Information Network (dkNET) has parent organization: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
NIDDK 5R01DK053591 | PMID:15642484 | Free, Freely available | nlx_152825 | https://www.niddkrepository.org/studies/find/ | SCR_001525 | Family Investigation of Nephropathy and Diabetes (F.I.N.D.), Family Investigation of Nephropathy & Diabetes | 2026-09-19 12:58:33 | 0 | ||||
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EID: Exon-Intron Database Resource Report Resource Website 10+ mentions |
EID: Exon-Intron Database (RRID:SCR_002469) | EID | data or information resource, data set | Data sets of protein-coding intron-containing genes that contain gene information from humans, mice, rats, and other eukaryotes, as well as genes from species whose genomes have not been completely sequenced. This is a comprehensive and convenient dataset of sequences for computational biologists who study exon-intron gene structures and pre-mRNA splicing. The database is derived from GenBank release 112, and it contains protein-coding genes that harbor introns, along with extensive descriptions of each gene and its DNA and protein sequences, as well as splice motif information. They have created subdatabases of genes whose intron positions have been experimentally determined. The collection also contains data on untranslated regions of gene sequences and intron-less genes. For species with entirely sequenced genomes, species-specific databases have been generated. A novel Mammalian Orthologous Intron Database (MOID) has been introduced which includes the full set of introns that come from orthologous genes that have the same positions relative to the reading frames. | eukaryote genome, exon, exon-intro, gene structure, genome splicing, intron, ortholog, fasta, gene, protein-coding gene, splice, motif, gene prediction, structure, coding region |
is listed by: OMICtools has parent organization: University of Toledo; Ohio; USA |
PMID:16772261 PMID:10592221 |
Free, Available for download, Freely available | OMICS_01886, nif-0000-02793 | http://www.utoledo.edu/med/depts/bioinfo/database.html | http://www.meduohio.edu/bioinfo/eid/, http://mcb.harvard.edu/gilbert/EID | SCR_002469 | The Exon-Intron Database, Exon-Intron Database | 2026-09-19 12:58:34 | 11 | ||||
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HS3D - Homo Sapiens Splice Sites Dataset Resource Report Resource Website 1+ mentions |
HS3D - Homo Sapiens Splice Sites Dataset (RRID:SCR_002939) | HS3D | data or information resource, data set | Data set of Homo Sapiens Exons, Introns and Splice regions extracted from GenBank Rel.123 with an aim of giving standardized material to train and to assess the prediction accuracy of computational approaches for gene identification and characterization. From the complete GenBank (Primate Sequences Division) Rel.123 (162,557 entries), entries of Human Nuclear DNA including Complete CDS and more than one Exon have been selected, and 4523 exons and 3802 introns have been extracted from these entries. Details about extracted exons and introns are reported (Locus, number, Start and End position in the entry, sequence, length, G+C content, presence of not AGCT data (nucleotide scan check)). Statistics are also reported (overall nucleotides, average G+C content, nucleotide scan check results, number of not GT starting / AG ending introns, minimum / maximum / average length, length standard deviation). 3799+3799 donor and acceptor sites, as windows of 140 nucleotides around each splice site have been extracted. After discarding sequences not including canonical GTAG junctions (65+74), including insufficient data (not enough material for a 140 nucleotide window) (686+589), including not AGCT bases (29+30), and redundant (218+226) there are 2796+ 2880 windows. Finally, there are 271,937 + 332,296 windows of false splice sites, selected by searching canonical GTAG pairs in not splicing positions. The false sites in a range of +/- 60 from a true splice site are marked as proximal. | human genome, splice, exon, intron, region, gene, dna, nucleotide, splice region | is related to: GenBank | Free, Available for download, Freely available | nif-0000-02988 | SCR_002939 | Homo Sapiens Splice Sites Dataset, HS3D (Homo Sapiens Splice Sites Dataset) | 2026-09-19 12:58:35 | 7 | |||||||
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MF-GE Resource Report Resource Website |
MF-GE (RRID:SCR_003509) | MF-GE | software resource, source code | A hybrid software system for feature selection and sample classification of high-dimensional datasets. It is designed for microarray but can be applied to any other high-dimensional datasets. It uses multiple filters to produce a normalized score for each feature. The score is an indication of the usefulness of each feature. It is then translated into a frequency map with more useful features receive a higher frequency in the map. | microarray, classification, gene |
is listed by: OMICtools has parent organization: University of Sydney; Sydney; Australia |
PMID:20122224 | OMICS_02295 | SCR_003509 | Multiple Filters enhanced Genetic Ensemble System (MF-GE), Multiple Filters enhanced Genetic Ensemble System | 2026-09-19 12:58:35 | 0 | |||||||
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Speech Language Disorders Database Resource Report Resource Website |
Speech Language Disorders Database (RRID:SCR_003655) | SLDB | data or information resource, data set | Curated lists of genes associated to speech / language phenotypes and structural or functional abnormalities observed in patient populations. Entrez ID gene information, as well as gene expression profiles from the Allen Brain Atlas are available. You can also download expression data for a given gene in JSON or XML format. | gene, speech, language, phenotype, locus, structure, function, gene expression |
is related to: Allen Human Brain Atlas has parent organization: Boston University; Massachusetts; USA |
Speech disorder, Language disorder | nlx_157808 | SCR_003655 | Speech/Language Disorders Database, Speech / Language Disorders Database | 2026-09-19 12:58:36 | 0 | |||||||
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National Gene Vector Biorepository Resource Report Resource Website 10+ mentions |
National Gene Vector Biorepository (RRID:SCR_004760) | NGVB | access service resource, core facility, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Archiving services, insertional site analysis, pharmacology and toxicology resources, and reagent repository for academic investigators and others conducting gene therapy research. Databases and educational resources are open to everyone. Other services are limited to gene therapy investigators working in academic or other non-profit organizations. Stores reserve or back-up clinical grade vector and master cell banks. Maintains samples from any gene therapy related Pharmacology or Toxicology study that has been submitted to FDA by U.S. academic investigator that require storage under Good Laboratory Practices. For certain gene therapy clinical trials, FDA has required post-trial monitoring of patients, evaluating clinical samples for evidence of clonal expansion of cells. To help academic investigators comply with this FDA recommendation, the NGVB offers assistance with clonal analysis using LAM-PCR and LM-PCR technology. | gene therapy, clinical trial, testing, insertion site, gene, clinical, vector, cell line, pharmacology, toxicology, clonal analysis, FASEB list |
is related to: NIDDK Information Network (dkNET) is related to: Phoenix has parent organization: Indiana University School of Medicine; Indiana; USA is parent organization of: NGVB SeqMap Database is parent organization of: NGVB Toxicology Database |
NCRR ; NHLBI |
PMID:31910049 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_76398 | http://www.ngvl.org/, https://www.ngvbcc.org/Home.action | SCR_004760 | 2026-09-19 12:58:37 | 33 | |||||
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Linked Neuron Data Resource Report Resource Website |
Linked Neuron Data (RRID:SCR_003658) | LND | data or information resource, data set | Neuroscience data and knowledge from multiple scales and multiple data sources that has been extracted, linked, and organized to support comprehensive understanding of the brain. The core is the CAS Brain Knowledge base, a very large scale brain knowledge base based on automatic knowledge extraction and integration from various data and knowledge sources. The LND platform provides services for neuron data and knowledge extraction, representation, integration, visualization, semantic search and reasoning over the linked neuron data. Currently, LND extracts and integrates semantic data and knowledge from the following resources: PubMed, INCF-CUMBO, Allen Reference Atlas, NIF, NeuroLex, MeSH, DBPedia/Wikipedia, etc. | neuron, brain, neuroscience, protein, gene, neurotransmitter |
is related to: Common Upper Mammalian Brain Ontology is related to: Neuroscience Information Framework is related to: PubMed is related to: NeuroLex is related to: MeSH is related to: DBpedia is related to: Allen Mouse Brain Reference Atlas is related to: Allen Institute for Brain Science has parent organization: Chinese Academy of Sciences; Beijing; China |
nlx_157812 | SCR_003658 | Linked Neuron Data (LND) | 2026-09-19 12:58:36 | 0 | ||||||||
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Gene Ontology Browsing Utility (GOBU) Resource Report Resource Website |
Gene Ontology Browsing Utility (GOBU) (RRID:SCR_005662) | GOBU | software resource, source code | Gene Ontology Browsing Utility (GOBU) (GOBU) is a Java-based software program for integrating biological annotation catalogs under an extendable software architecture. Users may interact with the Gene Ontology and user-defined hierarchy data of genes, and then use its plugins to (and not limited to) (1) browse the GO hierarchy with user defined data, (2) browse GO-oriented expression levels in the user data, (3) compute GO enrichment, and/or (4) customize data reporting. A set of classes and utility functions has been established so that a customized program can be made as a plugin or a command-line tool that programmically manipulate the Gene Ontology and specified user data. See the source code repository for examples. Reference Lin WD, Chen YC, Ho JM, Hsiao CD. GOBU: Toward an Integration Interface for Biological Objects. Journal of Information Science and Engineering. 2006 22(1):19-29. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | annotation, gene, browser, computation, visualization, software library, statistical analysis, term enrichment, ontology or annotation browser, ontology or annotation visualization |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Academia Sinica; Taipei; Taiwan |
Open unspecified license - Free for academic use | nlx_149098 | SCR_005662 | Gene Ontology Browsing Utility | 2026-09-19 12:58:37 | 0 | |||||||
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Sol Genomics Network - Bulk download Resource Report Resource Website |
Sol Genomics Network - Bulk download (RRID:SCR_007161) | data or information resource, data set | Allows users to download Unigene or BAC information using a list of identifiers or complete datasets with FTP., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | database, dataset, unigene, gene, bac, genomics, clone, array spot, unigene id, bac ends |
is related to: SGN has parent organization: Boyce Thompson Institute for Plant Research |
NSF 0820612; USDA CSREES |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30227 | SCR_007161 | SGN bulk download | 2026-09-19 12:58:39 | 0 | |||||||
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SpliceDB Resource Report Resource Website 1+ mentions |
SpliceDB (RRID:SCR_006262) | SpliceDB | data or information resource, data set | Database of canonical and non-canonical mammalian splice sites. The information about verified splice site sequences for canonical and non-canonical sites is presented with the supporting evidence. Weight matrices were built for the major splice groups, which can be incorporated into gene prediction programs. | gene, expressed sequence tag, splice, canonical, non-canonical, splice site, sequence, data set, splice site sequence |
is listed by: OMICtools is listed by: 3DVC is related to: GenBank has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:11125105 PMID:11058137 |
nlx_151853, OMICS_01892 | http://linux1.softberry.com/berry.phtml?topic=splicedb | http://genomic.sanger.ac.uk/spldb/SpliceDB.htm | SCR_006262 | SpliceDB: canonical and non-canonical splice site sequences in mammalian genes | 2026-09-19 12:58:38 | 2 | |||||
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1000 Genomes Project and AWS Resource Report Resource Website 5000+ mentions |
1000 Genomes Project and AWS (RRID:SCR_008801) | 1000 Genomes Project and AWS | data or information resource, data set | A dataset containing the full genomic sequence of 1,700 individuals, freely available for research use. The 1000 Genomes Project is an international research effort coordinated by a consortium of 75 companies and organizations to establish the most detailed catalogue of human genetic variation. The project has grown to 200 terabytes of genomic data including DNA sequenced from more than 1,700 individuals that researchers can now access on AWS for use in disease research free of charge. The dataset containing the full genomic sequence of 1,700 individuals is now available to all via Amazon S3. The data can be found at: http://s3.amazonaws.com/1000genomes The 1000 Genomes Project aims to include the genomes of more than 2,662 individuals from 26 populations around the world, and the NIH will continue to add the remaining genome samples to the data collection this year. Public Data Sets on AWS provide a centralized repository of public data hosted on Amazon Simple Storage Service (Amazon S3). The data can be seamlessly accessed from AWS services such Amazon Elastic Compute Cloud (Amazon EC2) and Amazon Elastic MapReduce (Amazon EMR), which provide organizations with the highly scalable compute resources needed to take advantage of these large data collections. AWS is storing the public data sets at no charge to the community. Researchers pay only for the additional AWS resources they need for further processing or analysis of the data. All 200 TB of the latest 1000 Genomes Project data is available in a publicly available Amazon S3 bucket. You can access the data via simple HTTP requests, or take advantage of the AWS SDKs in languages such as Ruby, Java, Python, .NET and PHP. Researchers can use the Amazon EC2 utility computing service to dive into this data without the usual capital investment required to work with data at this scale. AWS also provides a number of orchestration and automation services to help teams make their research available to others to remix and reuse. Making the data available via a bucket in Amazon S3 also means that customers can crunch the information using Hadoop via Amazon Elastic MapReduce, and take advantage of the growing collection of tools for running bioinformatics job flows, such as CloudBurst and Crossbow. | genomic data, genome, cloud computing, cloud, human, gene, genetic variation, research, dna |
is used by: HmtVar is related to: Broad Institute Genomics Platform has parent organization: Amazon Web Services |
nlx_144340 | SCR_008801 | 1000 Genomes Project and Amazon Web Services, 000 Genomes Project Amazon Web Services, 1000 Genomes Project AWS | 2026-09-19 12:58:40 | 7076 | ||||||||
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Montana State University Bioinformatics Core Facility Resource Report Resource Website |
Montana State University Bioinformatics Core Facility (RRID:SCR_009937) | access service resource, core facility, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27, 2023. Core for Microarray analysis, Database development, Systems biology analysis, Genome assembly, Pathway data analysis, Expression data analysis, Metagenomics analysis. To maintain equipment and software for bioinformatic research, promote bioinformatics education on the MSU campus, and provide training and support to biologists implementing bioinformatics tools in their research. | nucleic, acid, microarray, assay, database, development, analysis, genome, assembly, pathway, data, gene, expression, metagenomics |
is listed by: Eagle I has parent organization: Montana State University |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156405 | http://cores.montana.edu/bioinformatics/ | SCR_009937 | , Montana State University, core facility, MSU, Bioinformatics Core Laboratory | 2026-09-19 12:58:48 | 0 | |||||||
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WHAIT Resource Report Resource Website |
WHAIT (RRID:SCR_009425) | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software application (entry from Genetic Analysis Software). | gene, genetic, genomic | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154691 | SCR_009425 | Weighted Haplotype test And an Imputation-based Test. | 2026-09-19 12:58:06 | 0 | ||||||||
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ZAPLO Resource Report Resource Website 1+ mentions |
ZAPLO (RRID:SCR_009426) | ZAPLO | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. | gene, genetic, genomic, linux, unix, solaris | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154692 | SCR_009426 | 2026-09-19 12:58:06 | 3 | ||||||||
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UNKNOWN Resource Report Resource Website 10+ mentions |
UNKNOWN (RRID:SCR_009423) | UNKNOWN | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154684 | SCR_009423 | LINKAGE - general pedigrees | 2026-09-19 12:58:06 | 14 | ||||||||
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TFPGA Resource Report Resource Website 50+ mentions |
TFPGA (RRID:SCR_009421) | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software program that calculates descriptive statistics, genetic distances, and F-statistics. It also performs tests for Hardy-Weinberg equilibrium, exact tests for genetic differentiation, Mantel tests, and UPGMA cluster analyses. (entry from Genetic Analysis Software) | gene, genetic, genomic, ms-windows | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154680 | SCR_009421 | Tools For Population Genetic Analyses | 2026-09-19 12:58:06 | 57 |
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