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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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NCBI Resource List Resource Report Resource Website |
NCBI Resource List (RRID:SCR_005628) | NCBI Resources | data or information resource, organization portal, portal | The National Center for Biotechnology Information''s listing of resources. Sort by alphabetical character, Databases, Downloads, Submissions, Tools and How-To; or by Topic: Chemicals & Bioassays; Data & Software; DNA & RNA; Domains & Structures; Genes & Expression; Genetics & Medicine; Genomes & Maps; Homology; Literature; Proteins; Sequence Analysis; Taxonomy; Training & Tutorials; Variation. | database, download, submission, tool, chemical, bioassay, data, software, dna, rna, domain, structure, gene, expression, genetics, medicine, genomes, map, homology, literature, protein, sequence analysis, taxonomy, training, tutorial, variation, gold standard | has parent organization: NCBI | NLM | nlx_146242 | SCR_005628 | NCBI Resource Guide, NCBI Resource List (A-Z) | 2026-09-12 01:00:56 | 0 | |||||||
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LAPSTRUCT Resource Report Resource Website 1+ mentions |
LAPSTRUCT (RRID:SCR_007550) | software application, software resource | Software application to describe population structure using biomarker data ( typically SNPs, CNVs etc.) available in a population sample. The main features different from PCA are: (1) geometrically motivated and graphic model based; (2)robustness of outliers. (entry from Genetic Analysis Software) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | Free | nlx_154589, SCR_009367, nlx_154209 | SCR_007550 | R/LAPSTRUCT, LAPlacian eigenfunctions learn population STRUCTure | 2026-09-12 01:00:57 | 3 | ||||||||
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A Comprehensive Resource Base for C. elegans K+ Channels Resource Report Resource Website |
A Comprehensive Resource Base for C. elegans K+ Channels (RRID:SCR_008360) | material resource, reagent supplier | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 18, 2016. Supplies potassium channel cDNA clones in vectors suitable for functional expression and stocks of gene knockout strains. Supporting this resource base are studies showing the basic biophysical properties of the channels, studies showing the phenotypes of mutants, and information on the cell-type expression patterns of potassium channels. Studies of potassium channel cell-type expression patterns and functional properties; studies of behavioral phenotypes; generation of knockout mutants. Full-length cDNAs encoding C. elegans potassium channels in a vector suitable for functional expression in Xenopus oocytes and mammalian cell lines are available on request. Information is also provided describing the cell-type expression patterns and basic biophysical properties of potassium channels. And data on behavioral phenotypes are also available. C. elegans strains carrying knockouts of potassium channels are also generated and deposited at the C. elegans stock center at the University of Minnesota. | expression, gene, behavioral, biophysical, cdna, c. elegans, cell, clone, ion channel, knockout, mammalian, mutant, oocyte, phenotype, potassium, vector, xenopus | has parent organization: Washington State University; Washington; USA | NCRR R24 RR017342 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-25471 | SCR_008360 | Resource Base for C. elegans K+ Channels | 2026-09-12 01:00:58 | 0 | |||||||
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Pedigree-Draw Resource Report Resource Website 1+ mentions |
Pedigree-Draw (RRID:SCR_008302) | commercial organization, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2024. Software application for pedigree drawing (entry from Genetic Analysis Software) | gene, genetic, genomic, macos, bio.tools |
is listed by: Genetic Analysis Software is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: OMICtools |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154520, OMICS_00213, SCR_010795 | SCR_008302 | PEDIGREE/DRAW | 2026-09-12 01:00:58 | 1 | ||||||||
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German Gene Trap Consortium Resource Report Resource Website |
German Gene Trap Consortium (RRID:SCR_008532) | GGTC | biomaterial supply resource, cell repository, material resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on October 23, 2014. Consortium that generated a reference library of gene trap sequence tags (GTST) from insertional mutations generated in mouse embryonic stem (ES) cells. The gene trap database represents a repository of sequences produced in a large scale gene trap screen in mouse ES cells using various gene trapping vectors which are delivered either by electroporation or retroviral infections. A type of retroviral gene trap vector has been developed that can induce conditional mutations in most genes expressed in mouse embryonic stem (ES) cells. The vectors rely on directional site-specific recombination systems that can repair and re-induce gene trap mutations when activated in succession. After the gene traps are inserted into the mouse genome, genetic mutations can be produced at a particular time and place in somatic cells. In addition to their conditional features, the vectors create multipurpose alleles amenable to a wide range of post-insertional modifications. Here they have used these directional recombination vectors to assemble the largest library of ES cell lines with conditional mutations in single genes yet assembled, presently totaling 1,000 unique genes. The trapped ES cell lines, which can be ordered from the German Gene Trap Consortium, are freely available to the scientific community. | phenotyping, molecular neuroanatomy, gene trap sequence tag, embryonic stem cell line, mutation, gene | is listed by: One Mind Biospecimen Bank Listing | German Federal Ministry of Research and Education ; National Genome Research Network |
PMID:15870191 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30613 | http://genetrap.helmholtz-muenchen.de/ | SCR_008532 | German Gene Trap Consortium | 2026-09-12 01:00:58 | 0 | ||||
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GenePaint Interactive Anatomy Atlas Resource Report Resource Website |
GenePaint Interactive Anatomy Atlas (RRID:SCR_007680) | GenePaint.org Interactive Anatomy Atlas | atlas, data or information resource, reference atlas | A digital atlas of gene expression patterns in the mouse. Expression patterns are determined by non-radioactive in situ hybridization on serial tissue sections. An accompanying atlas based on maps of sagittal sections at embryonic day 14.5. E14.5 NMRI embryo was prepared, sectioned and imaged identically to the embryos used for in situ hybridization. Maps are accessed from the set viewer page using the appropriate button above the image directory. Both, the in situ hybridization section and the appropriate atlas section can be viewed side-by-side. Section thickness is 20 m and inter-section distance is 100 m. Tissue was stained with cresyl violet (Nissl-method). All sections were digitally scanned using a 5x objective. Structures annotated for gene expression are indicated in the maps with red pointers. Boundaries between brain regions are indicated with dashed yellow lines. | gene, gene expression, gene expression pattern, cellular resolution, in-situ hybridization, mouse, nissl stain, molecular neuroanatomy resource, development, developing |
is related to: GUDMAP Ontology is related to: NIDDK Information Network (dkNET) has parent organization: Max-Planck-Gesellschaft has parent organization: GenePaint |
nif-0000-02886 | SCR_007680 | GenePaint Embryo Atlas, GenePaint Atlas of Embryo Maps, GenePaint.org Atlas of Embryo Maps | 2026-09-12 01:00:57 | 0 | ||||||||
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IBDREG Resource Report Resource Website |
IBDREG (RRID:SCR_013127) | software application, software resource | Software package in S-PLUS and R to test genetic linkage with covariates by regression methods with response IBD sharing for relative pairs. Account for correlations of IBD statistics and covariates for relative pairs within the same pedigree. (entry from Genetic Analysis Software) | gene, genetic, genomic, r/s-plus | is listed by: Genetic Analysis Software | nlx_154588, SCR_009366, nlx_154407 | http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm | SCR_013127 | R/IBDREG | 2026-09-12 01:01:01 | 0 | ||||||||
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Human Genetics Laboratory: WFS1 Gene Mutation and Polymorphism Database Resource Report Resource Website 1+ mentions |
Human Genetics Laboratory: WFS1 Gene Mutation and Polymorphism Database (RRID:SCR_001113) | data or information resource, data repository, database, service resource, storage service resource | This web site lists the disease causing mutations and polymorphisms found in the Wolfram syndrome (WFS1) gene. Sponsors: This resource is supported by the University of Michigan at Ann Arbor. | frequency, gene, auditory, disease, hearing, neuropathy, polymorphism, research, wolfram syndrome | has parent organization: University of Michigan; Ann Arbor; USA | nif-0000-10276 | SCR_001113 | WFS1 | 2026-09-12 01:00:07 | 3 | |||||||||
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ToppCluster Resource Report Resource Website 100+ mentions |
ToppCluster (RRID:SCR_001503) | ToppCluster | analysis service resource, data analysis service, production service resource, resource, service resource | A tool for performing multi-cluster gene functional enrichment analyses on large scale data (microarray experiments with many time-points, cell-types, tissue-types, etc.). It facilitates co-analysis of multiple gene lists and yields as output a rich functional map showing the shared and list-specific functional features. The output can be visualized in tabular, heatmap or network formats using built-in options as well as third-party software. It uses the hypergeometric test to obtain functional enrichment achieved via the gene list enrichment analysis option available in ToppGene. | term enrichment, gene, analysis, gene enrichment analysis, connectivity, heatmap, ortholog, microarray, function, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: GenitoUrinary Development Molecular Anatomy Project is related to: ToppGene Suite |
NIDDK 1U01DK70219; NIDDK P30DK078392; NCRR U54 RR025216; NIDCR U01DE020049 |
PMID:20484371 | Free | OMICS_02225, nlx_152801, biotools:toppcluster | https://bio.tools/toppcluster | SCR_001503 | ToppCluster: A multiple gene list feature analyzer for the dissection of biological systems | 2026-09-12 01:00:07 | 152 | ||||
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FACTA+. Resource Report Resource Website 1+ mentions |
FACTA+. (RRID:SCR_001767) | FACTA+ | data access protocol, service resource, software resource, web service | Text mining tool to discover associations between biomedical concepts from MEDLINE articles. Use the service from your browser or via a Web Service. The whole MEDLINE corpus containing more than 20 million articles is indexed with an efficient text search engine, and it allows you to navigate such associations and their textual evidence in a highly interactive manner - the system accepts arbitrary query terms and displays relevant concepts immediately. A broad range of important biomedical concepts are covered by the combination of a machine learning-based term recognizer and large-scale dictionaries for genes, proteins, diseases, and chemical compounds. There is also a FACTA+ visualization service that can be found here: http://www.nactem.ac.uk/facta-visualizer/ | text mining, gene, protein, disease, symptom, drug, enzyme, compound, biomedical, association, machine learning, chemical, text-mining software, bio.tools |
is listed by: OMICtools is listed by: FORCE11 is listed by: bio.tools is listed by: Debian is related to: MEDLINE has parent organization: National Centre for Text Mining |
JISC | PMID:18772154 | Free, Freely available | biotools:facta_plus, nif-0000-10272, OMICS_01181 | http://refine1-nactem.mc.man.ac.uk/facta/, https://bio.tools/facta_plus | SCR_001767 | Finding Associated Concepts with Text Analysis | 2026-09-12 01:00:07 | 2 | ||||
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Gene Weaver Resource Report Resource Website 10+ mentions |
Gene Weaver (RRID:SCR_003009) | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | Freely accessible phenotype-centered database with integrated analysis and visualization tools. It combines diverse data sets from multiple species and experiment types, and allows data sharing across collaborative groups or to public users. It was conceived of as a tool for the integration of biological functions based on the molecular processes that subserved them. From these data, an empirically derived ontology may one day be inferred. Users have found the system valuable for a wide range of applications in the arena of functional genomic data integration. | phenotype, microarray, gene, genome, functional genomics, process, pathway, function, gene set, genomic data integration, analysis, visualization |
is used by: NIF Data Federation is used by: Integrated Datasets is listed by: OMICtools is related to: Integrated Manually Extracted Annotation has parent organization: Jackson Laboratory |
Integrative Neuroscience Initiative on Alcoholism ; NIAAA R01 AA18776; NIAAA U01 AA13499; NIAAA U24 AA13513 |
PMID:22080549 PMID:19733230 |
Free, Freely available | r3d100012464, OMICS_02232, nif-0000-00517 | http://ontologicaldiscovery.org/, https://doi.org/10.17616/R3248T | SCR_003009 | GeneWeaver, GeneWeaver - A system for the integration of functional genomics experiments, Ontological Discovery Environment, GeneWeaver.org | 2026-09-12 01:00:09 | 39 | |||||
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LINCS Data Portal Resource Report Resource Website 10+ mentions |
LINCS Data Portal (RRID:SCR_014939) | data or information resource, portal | Portal which provides a unified interface for searching LINCS dataset packages and reagents. Users can use the portal to access datasets, small molecules, cells, genes, proteins and peptides, and antibodies. | portal, assay, lincs, kinome, dataset, small molecule, cell, gene, protein, peptide, and antibodies. |
is related to: LINCS Data Portal 2.0 has parent organization: University of Miami; Florida; USA is parent organization of: CycIF.org |
NIH Common Fund ; NHLBI 1U01HL111561; NHLBI 3U01HL111561-01S1; NHLBI 3U01HL111561-02S1; NHGRI U54HG006097; NHGRI U54 HG006093 |
Freely available | SCR_014939 | 2026-09-12 01:01:03 | 14 | |||||||||
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Digital Differential Display (DDD) Resource Report Resource Website |
Digital Differential Display (DDD) (RRID:SCR_016638) | DDD | data processing software, software application, software resource | Software tool for comparing EST profiles in order to identify genes with significantly different expression levels. | comparing, EST, profile, identify, gene, different, expression, level |
has parent organization: NCBI works with: UniGene |
Public, Free, Freely available | SCR_016638 | Digital Differential Display | 2026-09-12 01:01:04 | 0 | ||||||||
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KOMP2 Resource Report Resource Website 1+ mentions |
KOMP2 (RRID:SCR_017528) | data or information resource, portal, project portal | Knockout Mouse Phenotyping Project, JAX information about their contributions to KOMP2 project. Project to generate and phenotype single gene KO mouse strains from KOMP ES cell lines. Strains are phenotyped using protocols in pipeline designed by International Mouse Phenotyping Consortium. There are three NIH-funded phenotyping centers in United States: JAX, BaSH Consortium (Baylor College of Medicine, the Wellcome Trust Sanger Institute and MRC Harwell), and the DTCC Consortium (University of California at Davis, the Toronto Center for Phenogenomics, Children’s Hospital Oakland Research Institute (CHORI) and Charles River ). | Generate, phenotype, single, gene, KO mouse, strain, KOMP ES cell line, IMPC, JAX |
is related to: International Mouse Phenotyping Consortium (IMPC) is related to: Knockout Mouse Project is related to: Knockout Mouse Project |
NIH | Free, Freely available | SCR_017528 | Knockout Mouse Phenotyping Project | 2026-09-12 01:01:06 | 2 | ||||||||
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refine.bio Resource Report Resource Website 1+ mentions |
refine.bio (RRID:SCR_017471) | data processing software, software application, software resource | Software tool to uniformly process and normalize large amounts of data. Harmonizes petabytes of publicly available biological data into ready-to-use datasets for cancer researchers and AI/ML scientists. | Process, normalize, large, amount, data, cancer, dataset, standardized, pipeline, gene, expression | Free, Available for download, Freely available | https://www.refine.bio/ | SCR_017471 | 2026-09-12 01:01:06 | 1 | ||||||||||
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ExonerateTransferAnnotation Resource Report Resource Website |
ExonerateTransferAnnotation (RRID:SCR_017557) | data processing software, software application, software resource | Software tool as pipeline to make anntotations using cDNA and CDS sequences. | Exonerate, transfer, annotation, cDNA, CDS, sequence, pipeline, gene | uses: Exonerate | Free, Available for download, Freely available | SCR_017557 | Resource | 2026-09-12 01:01:06 | 0 | |||||||||
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Honey Bee Brain EST Project Resource Report Resource Website 1+ mentions |
Honey Bee Brain EST Project (RRID:SCR_002389) | Bee-ESTdb | biomaterial supply resource, material resource | A database integrating data from the bee brain EST sequencing project with data from sequencing and gene research projects from other organisms, primarily the fruit fly Drosophila melanogaster. The goal of Bee-ESTdb is to provide updated information on the genes of the honey bee, currently using annotation primarily from flies to suggest cellular roles, biological functions, and evolutionary relationships. The site allows searches by sequence ID, EST annotations, Gene Ontology terms, Contig ID and using BLAST. Very nice resource for those interested in comparative genomics of brain. A normalized unidirectional cDNA library was made in the laboratory of Prof. Bento Soares, University of Iowa. The library was subsequently subtracted. Over 20,000 cDNA clones were partially sequenced from the normalized and subtracted libraries at the Keck Center, resulting in 15,311 vector-trimmed, high-quality, sequences with an average read length of 494 bp. and average base-quality of 41. These sequences were assembled into 8966 putatively unique sequences, which were tested for similarity to sequences in the public databases with a variety of BLAST searches. The Clemson University Genomics Institute is the distributor of these public domain cDNA clones. For information on how to purchase an individual clone or the entire collection, please contact www.genome.clemson.edu/orders/ or generobi (at) life.uiuc.edu. | expressed sequence tag, brain, behavior, cdna, blast, gene, annotation, microarray, gene expression, comparative genomics, cdna clone, resource:genbank |
is listed by: One Mind Biospecimen Bank Listing is related to: One Mind Biospecimen Bank Listing is related to: Gene Ontology has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA |
NSF ; University of Illinois Critical Research Initiatives Program ; Burroughs Wellcome Fund |
PMID:11932240 | Free | nif-0000-00118 | SCR_002389 | Honeybee EST Project | 2026-09-12 01:02:27 | 5 | |||||
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GERMLINE Resource Report Resource Website 100+ mentions |
GERMLINE (RRID:SCR_001720) | GERMLINE | software application, software resource | Software application for discovering long shared segments of Identity by Descent (IBD) between pairs of individuals in a large population. It takes as input genotype or haplotype marker data for individuals (as well as an optional known pedigree) and generates a list of all pairwise segmental sharing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, c++, linux, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Columbia University; New York; USA |
PMID:18971310 | Free, Available for download, Freely available | biotools:germline, OMICS_00202, nlx_154080 | https://bio.tools/germline | http://www1.cs.columbia.edu/~gusev/germline/ | SCR_001720 | 2026-09-12 01:02:26 | 451 | |||||
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OLORIN Resource Report Resource Website |
OLORIN (RRID:SCR_002015) | OLORIN | software application, software resource | An interactive filtering tool for next generation sequencing data coming from the study of large complex disease pedigrees. It integrates gene flow output from Merlin and next generation sequencing data. Users can interactively filter and prioritize variants based on haplotype sharing across different sets of selected individuals and allele frequency in reference datasets. (entry from Genetic Analysis Software) | gene, genetic, genomic, java, any platform with java 1.6 or later, next generation sequencing, variant, haplotype, allele frequency, java swing |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom has parent organization: SourceForge |
PMID:23052039 | Free, Available for download, Freely available | nlx_154503, OMICS_01556 | http://sourceforge.net/p/olorin/ | SCR_002015 | 2026-09-12 01:02:27 | 0 | ||||||
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SIMIBD Resource Report Resource Website |
SIMIBD (RRID:SCR_002094) | SIMIBD | 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, c, unix, (sunos/solaris/hp/dec-unix) | is listed by: Genetic Analysis Software | PMID:9002040 | Free, Available for download, Freely available | nlx_154622 | http://watson.hgen.pitt.edu/register/soft_doc.html, http://watson.hgen.pitt.edu/~davis/ | SCR_002094 | 2026-09-12 01:02:27 | 0 |
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
