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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Phevor Resource Report Resource Website 1+ mentions |
Phevor (RRID:SCR_002273) | Phevor | analysis service resource, data analysis service, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. Tool that integrates phenotype, gene function, and disease information with personal genomic data for improved power to identify disease-causing alleles. It works by combining knowledge resident in multiple biomedical ontologies with the outputs of variant prioritization tools. It does so using an algorithm that propagates information across and between ontologies. This process enables Phevor to accurately reprioritize potentially damaging alleles identified by variant prioritization tools in light of gene function, disease, and phenotype knowledge. Phevor is especially useful for single exome and family trio-based diagnostic analyses, the most commonly occurring clinical scenarios, and ones for which existing personal-genomes diagnostic tools are most inaccurate and underpowered. Phevor not only improves diagnostic accuracy for individuals presenting with established disease phenotypes, but also for those with previously undescribed and atypical disease presentations. Importantly, Phevor is not limited to known diseases, or known disease-causing alleles. | genome interpretation, variant prioritization, disease gene prioritization, phenotype, gene function, disease, genomic, disease-causing allele, gene, function, allele | has parent organization: University of Utah School of Medicine; Utah; USA | PMID:24702956 | THIS RESOURCE IS NO LONGER IN SERVICE | SciRes_000139 | SCR_002273 | Phenotype Driven Variant Ontological Re-Ranking Tool | 2026-09-05 06:31:17 | 9 | ||||||
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Greengenes Resource Report Resource Website 1000+ mentions |
Greengenes (RRID:SCR_002830) | data or information resource, database | Database that provides access to the current and comprehensive 16S rRNA gene sequence alignment for browsing, blasting, probing, and downloading. The data and tools can assist the researcher in choosing phylogenetically specific probes, interpreting microarray results, and aligning/annotating novel sequences. The 16S rRNA gene database provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. ARB users can use Greengenes to update local databases., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | microbiome, rrna, 16s rrna, gene, dna, rna, chimera, alignment, taxonomic classification, taxonomy, FASEB list |
is listed by: OMICtools is listed by: re3data.org is listed by: Human Microbiome Project has parent organization: Lawrence Berkeley National Laboratory |
Department of Energy contract DE-AC02-05CH11231 | PMID:16820507 | Free, Freely available | OMICS_01512, r3d100010549, nif-0000-02927 | http://greengenes.lbl.gov, https://doi.org/10.17616/R36C8G | SCR_002830 | 2026-09-05 06:31:18 | 3162 | ||||||
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AceView Resource Report Resource Website 100+ mentions |
AceView (RRID:SCR_002277) | AceView/WormGenes | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented August 29, 2016. AceView offers an integrated view of the human, nematode and Arabidopsis genes reconstructed by co-alignment of all publicly available mRNAs and ESTs on the genome sequence. Our goals are to offer a reliable up-to-date resource on the genes and their functions and to stimulate further validating experiments at the bench. AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-aligned on the genome then clustered into a minimal number of alternative transcript variants and grouped into genes. Using exhaustively and with high quality standards the available cDNA sequences evidences the beauty and complexity of mammals' transcriptome, and the relative simplicity of the nematode and plant transcriptomes. Genes are classified according to their inferred coding potential; many presumably non-coding genes are discovered. Genes are named by Entrez Gene names when available, else by AceView gene names, stable from release to release. Alternative features (promoters, introns and exons, polyadenylation signals) and coding potential, including motifs, domains, and homologies are annotated in depth; tissues where expression has been observed are listed in order of representation; diseases, phenotypes, pathways, functions, localization or interactions are annotated by mining selected sources, in particular PubMed, GAD and Entrez Gene, and also by performing manual annotation, especially in the worm. In this way, both the anatomy and physiology of the experimentally cDNA supported human, mouse and nematode genes are thoroughly annotated. Our goals are to offer an up-to-date resource on the genes, in the hope to stimulate further experiments at the bench, or to help medical research. AceView can be queried by meaningful words or groups of words as well as by most standard identifiers, such as gene names, Entrez Gene ID, UniGene ID, GenBank accessions. | est, exon, expression, function, gene, alignment, arabidopsis, cdna, co-alignment, coding, disease, genome, genomic, human, intron, localization, mammal, mouse, mrna, nematode, pathway, phenotype, plant, polyadenylation, promoter, rat, sequence, signal, tissue, transcript, transcriptome, worm, blast, gold standard | has parent organization: NCBI | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21007, r3d100010651 | https://doi.org/10.17616/R3260G | http://www.ncbi.nih.gov/IEB/Research/Acembly/ | SCR_002277 | AceView genes, AceView/WormGenes, The AceView Genes | 2026-09-05 06:31:17 | 186 | |||||
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Phenoscape Knowledgebase Resource Report Resource Website 10+ mentions |
Phenoscape Knowledgebase (RRID:SCR_002821) | Phenoscape Knowledgebase | data or information resource, database | Knowledgebase that uses ontologies to integrate phenotypic data from genetic studies of zebrafish with evolutionary variable phenotypes from the systematic literature of ostariophysan fishes. Users can explore the data by searching for anatomical terms, taxa, or gene names. The expert system enables the broad scale analysis of phenotypic variation across taxa and the co-analysis of these evolutionarily variable features with the phenotypic mutants of model organisms. The Knowledgebase currently contains 565,158 phenotype statements about 2,527 taxa, sourced from 57 publications, as well as 38,189 phenotype statements about 4,727 genes, retrieved from ZFIN. 2013-01-26. | fish, gene, anatomy, model organism, ostariophysan, phenotype, taxis, ontology, anatomy, variation, taxon, genetic, evolution, development, web service, source code |
uses: Teleost Anatomy Ontology is related to: Zebrafish Information Network (ZFIN) is related to: Catalog of Fishes is related to: FishBase is related to: AmphibiaWeb is related to: NCBI Taxonomy is related to: Catalogue of Life has parent organization: NESCent - National Evolutionary Synthesis Center has parent organization: Phenoscape is parent organization of: Teleost Taxonomy Ontology |
NSF DBI-1062404; NSF DBI-1062542; NSF EF-0905606; NSF BDI-0641025; NSF EF-0423641 |
PMID:22736877 PMID:20505755 |
Free, Freely available | nif-0000-24925 | SCR_002821 | 2026-09-05 06:31:18 | 14 | ||||||
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Familial Hypertrophic Cardiomyopathy DNA Mutation Database Resource Report Resource Website 1+ mentions |
Familial Hypertrophic Cardiomyopathy DNA Mutation Database (RRID:SCR_002346) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The aim of this locus-specific mutation database was to provide an online resource that contains summarized and updated information on familial hypertrophic cardiomyopathy (FHC)-associated mutations and related data, for researchers and clinicians. It also serves as a means of publishing previously unpublished data, which could be of value in understanding genotype/phenotype correlations. This database contains mutations in various genes known to cause familial hypertrophic cardiomyopathy, a genetic disorder associated with defects in the sarcomere [1]. Only gene symbols approved by HUGO are used and mutations are reported in accordance with guidelines recommended by the Mutation Database Initiative of HUGO and EBI. | familial, gene, gene-, genetic, cardiomyopathy, clinic, correlation, defect, disorder, genotype, hypertrophic, locus, mutation, or disease- specific databases, phenotype, research, sarcomere, system- | PMID:10502780 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21151 | SCR_002346 | FHC Mutation Database | 2026-09-05 06:31:17 | 2 | ||||||||
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DBTBS Resource Report Resource Website 10+ mentions |
DBTBS (RRID:SCR_002345) | DBTBS | data or information resource, database | Database of experimentally validated gene regulatory relations and the corresponding transcription factor binding sites upstream of Bacillus subtilis genes. The database allows the comparison of systematic experiments with individual experimental results in order to facilitate the elucidation of the complete B. subtilis gene regulatory network. The current version is constructed by surveying 947 references and contains the information of 120 binding factors and 1475 gene regulatory relations. For each promoter, all of its known cis-elements are listed according to their positions, while these cis-elements are aligned to illustrate the consensus sequence for each transcription factor. All probable transcription factors coded in the genome were classified using Pfam motifs. The DBTBS database was reorganized to show operons instead of individual genes as the building blocks of gene regulatory networks. It now contains 463 experimentally known operons, as well as their terminator sequences if identifiable. In addition, 517 transcriptional terminators were identified computationally. (De Hoon, M.J.L. et al., PLoS Comput. Biol. 1, e25 (2005)). A new section was added under "Motif conservation", which presents hexameric motifs found to be conserved to different extents between upstream intergenic regions of genus-specific subgroups of homologous proteins. | gene, gene regulatory network, transcription factor binding site, transcription factor, regulated operon, motif, promoter, motif conservation |
is listed by: OMICtools has parent organization: University of Tokyo; Tokyo; Japan |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | PMID:17962296 PMID:14681362 PMID:11125112 |
Acknowledgement requested | nif-0000-02736, OMICS_01859 | SCR_002345 | DBTBS: a database of Bacillus subtilis promoters and transcription factors., DBTBS: a database of Bacillus subtilis promoters and transcription factors | 2026-09-05 06:31:17 | 34 | |||||
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eggNOG Resource Report Resource Website 1000+ mentions |
eggNOG (RRID:SCR_002456) | eggNOG | data or information resource, database | A database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories). eggNOG's database currently counts 1.7 million orthologous groups in 3686 species, covering over 7.7 million proteins (built from 9.6 million proteins). (Jan 30, 2014) | orthologous gene, ortholog, gene, function, FASEB list |
is listed by: OMICtools has parent organization: European Molecular Biology Laboratory |
BMBF ; European Union FP6 |
PMID:24297252 PMID:22096231 |
Free, Available for download, Freely available | nif-0000-02789, OMICS_01689 | SCR_002456 | eggNOG: evolutionary genealogy of genes: Non-supervised Orthologous Groups, eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups), evolutionary genealogy of genes: Non-supervised Orthologous Groups | 2026-09-05 06:31:18 | 4095 | |||||
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EDAS - EST-Derived Alternative Splicing Database Resource Report Resource Website 1+ mentions |
EDAS - EST-Derived Alternative Splicing Database (RRID:SCR_002449) | EDAS | data or information resource, database | Databases of alternatively spliced genes with data on the alignment of proteins, mRNAs, and EST. It contains information on all exons and introns observed, as well as elementary alternatives formed from them. The database makes it possible to filter the output data by changing the cut-off threshold by the significance level. It contains splicing information on human, mouse, dog (not yet functional) and rat (not yet functional). For each database, users can search by keyword or by overall gene expression. They can also view genes based on chromosomal arrangement or other position in genome (exon, intron, acceptor site, donor site), functionality, position, conservation, and EST coverage. Also offered is an online Fisher test. | alternative splicing, gene, protein, mrna, est, exon, intron, rat, dog |
is listed by: OMICtools has parent organization: Moscow State University; Moscow; Russia |
PMID:16909834 | Free, Freely available | nif-0000-02786, OMICS_01885 | SCR_002449 | EDAS: EST Derived Alternative Splicing Database, EST Derived Alternative Splicing Database | 2026-09-05 06:31:18 | 1 | ||||||
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Retina Project Resource Report Resource Website 1+ mentions |
Retina Project (RRID:SCR_002884) | Retina Project | atlas, data or information resource, spatially referenced dataset | Collection of images from cell type-specific protein expression in retina using BAC transgenic mice. Images from cell type-specific protein expression in retina using BAC transgenic mice from GENSAT project. | electrophysiology, protein expression, fluorescent, gene, amacrine cell, astrocyte, bipolar cell, blood vessel, brain, cell, ganglion cell layer, central nervous system, circuit, horizontal cell, hybridization, microglia, adult mouse, muller cell, neocortex, neuronal, photoreceptor, protein, recombinase, retina, spinal cord, mutant mouse strain, bac, retinal cell, cell type, night vision, direction, neuronal circuitry, connectivity, image collection |
is used by: NIF Data Federation has parent organization: GENSAT at NCBI - Gene Expression Nervous System Atlas |
Department Of Health And Human Services ; NINDS N01 NS02331 |
PMID:19648912 | Free, Freely available | nif-0000-25587 | SCR_002884 | GENSAT Retina Project, Retina Project from GENSAT, The Retina Project, The Retina Project from GENSAT, GENSAT - Retina Project | 2026-09-05 06:31:19 | 2 | |||||
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Full-Malaria: Malaria Full-Length cDNA Database Resource Report Resource Website 1+ mentions |
Full-Malaria: Malaria Full-Length cDNA Database (RRID:SCR_002348) | data or information resource, database | FULL-malaria is a database for a full-length-enriched cDNA library from the human malaria parasite Plasmodium falciparum. Because of its medical importance, this organism is the first target for genome sequencing of a eukaryotic pathogen; the sequences of two of its 14 chromosomes have already been determined. However, for the full exploitation of this rapidly accumulating information, correct identification of the genes and study of their expression are essential. Using the oligo-capping method, this database has produced a full-length-enriched cDNA library from erythrocytic stage parasites and performed one-pass reading. The database consists of nucleotide sequences of 2490 random clones that include 390 (16%) known malaria genes according to BLASTN analysis of the nr-nt database in GenBank; these represent 98 genes, and the clones for 48 of these genes contain the complete protein-coding sequence (49%). On the other hand, comparisons with the complete chromosome 2 sequence revealed that 35 of 210 predicted genes are expressed, and in addition led to detection of three new gene candidates that were not previously known. In total, 19 of these 38 clones (50%) were full-length. From these observations, it is expected that the database contains approximately 1000 genes, including 500 full-length clones. It should be an invaluable resource for the development of vaccines and novel drugs. Full-malaria has been updated in at least three points. (i) 8934 sequences generated from the addition of new libraries added so that the database collection of 11,424 full-length cDNAs covers 1375 (25%) of the estimated number of the entire 5409 parasite genes. (ii) All of its full-length cDNAs and GenBank EST sequences were mapped to genomic sequences together with publicly available annotated genes and other predictions. This precisely determined the gene structures and positions of the transcriptional start sites, which are indispensable for the identification of the promoter regions. (iii) A total of 4257 cDNA sequences were newly generated from murine malaria parasites, Plasmodium yoelii yoelii. The genome/cDNA sequences were compared at both nucleotide and amino acid levels, with those of P.falciparum, and the sequence alignment for each gene is presented graphically. This part of the database serves as a versatile platform to elucidate the function(s) of malaria genes by a comparative genomic approach. It should also be noted that all of the cDNAs represented in this database are supported by physical cDNA clones, which are publicly and freely available, and should serve as indispensable resources to explore functional analyses of malaria genomes. Sponsors: This database has been constructed and maintained by a Grant-in-Aid for Publication of Scientific Research Results from the Japan Society for the Promotion of Science (JSPS). This work was also supported by a Special Coordination Funds for Promoting Science and Technology from the Science and Technology Agency of Japan (STA) and a Grant-in-Aid for Scientific Research on Priority Areas from the Ministry of Education, Science, Sports and Culture of Japan. | drug, eukaryotic, expression, function, gene, alignment, amino acid, cdna, chromosome, clone, coding, comparative, genome, genomic, human, malaria, medical, nucleotide, oligo-capping, organism, parasite, pathogen, physical, plasmodium falciparum, promoter, protein, region, sequence, sequencing, unicellular eukaryote genome databases, vaccine | has parent organization: University of Tokyo; Tokyo; Japan | PMID:18987005 PMID:14681428 |
nif-0000-21157 | SCR_002348 | Full-Malaria | 2026-09-05 06:31:17 | 2 | ||||||||
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Human Gene Connectome Server Resource Report Resource Website 1+ mentions |
Human Gene Connectome Server (RRID:SCR_002627) | HGCS | analysis service resource, data analysis service, production service resource, service resource | An interactive web server that enables researchers to prioritize any list of genes by their biological proximity to defined core genes (i.e. genes that are known to be associated with the phenotype), and to predict novel gene pathways. | gene, disease, phenotype, genome, connectome, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Human Gene Connectome |
PMID:23509278 | Free | nlx_156049, biotools:hgcs | https://bio.tools/hgcs | SCR_002627 | 2026-09-05 06:31:18 | 8 | ||||||
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Bioinformatic Harvester IV (beta) at Karlsruhe Institute of Technology Resource Report Resource Website 1000+ mentions |
Bioinformatic Harvester IV (beta) at Karlsruhe Institute of Technology (RRID:SCR_008017) | data acquisition software, data or information resource, data processing software, database, software application, software resource | Harvester is a Web-based tool that bulk-collects bioinformatic data on human proteins from various databases and prediction servers. It is a meta search engine for gene and protein information. It searches 16 major databases and prediction servers and combines the results on pregenerated HTML pages. In this way Harvester can provide comprehensive gene-protein information from different servers in a convenient and fast manner. As full text meta search engine, similar to Google trade mark, Harvester allows screening of the whole genome proteome for current protein functions and predictions in a few seconds. With Harvester it is now possible to compare and check the quality of different database entries and prediction algorithms on a single page. Sponsors: This work has been supported by the BMBF with grants 01GR0101 and 01KW0013. | function, gene, bioinformatics, data, database, human, meta search engine, prediction, protein, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Karlsruhe Institute of Technology; Karlsruhe; Germany |
biotools:harvester, nif-0000-10169 | https://bio.tools/harvester | SCR_008017 | Harvester IV | 2026-09-05 06:30:01 | 1480 | ||||||||
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CLC Genomics Workbench Resource Report Resource Website 100+ mentions |
CLC Genomics Workbench (RRID:SCR_011853) | data analysis software, data processing software, data visualization software, software application, software resource | Commercially available software for visualization and analysis of next generation sequencing data. Used for viewing, exploring, and sharing of NGS analysis results. Complete toolkit for genomics, transcriptomics, epigenomics, and metagenomics in one program. | ngs, next, generation, sequencing, gene, rna, visualisation, analysis |
is listed by: OMICtools is listed by: SoftCite works with: CLC Genomics Server |
Restricted | SCR_016245, OMICS_01124 | SCR_011853 | 2026-09-05 06:30:03 | 187 | |||||||||
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SNPFILE Resource Report Resource Website 1+ mentions |
SNPFILE (RRID:SCR_009402) | software application, software library, software resource, software toolkit | Software library and API for manipulating large SNP datasets with associated meta-data, such as marker names, marker locations, individuals'' phenotypes, etc. in an I/O efficient binary file format. In its core, SNPFile assumes very little about the metadata associated with markers and individuals, but leaves this up to application program protocols. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, linux, unix | is listed by: Genetic Analysis Software | nlx_154641 | SCR_009402 | 2026-09-05 06:30:02 | 1 | ||||||||||
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HDBase Resource Report Resource Website |
HDBase (RRID:SCR_007132) | HDBase | data or information resource, data set, disease-related portal, portal, topical portal | A community website for Huntington''s Disease (HD) research that currently contains Y2H and Mass spectrometry protein-protein interaction data centered around the HD protein (huntingtin) and information on therapeutic studies in mouse. Also available are raw Human and Mouse Affymetrix Microarray data. The protein interaction data is from several sources, including interactions curated from the literature by ISB staff, experimentally determined interactions produced by Bob Hughes and colleagues at Prolexys (currently password protected), and interactions reported in a recent publication by Goehler et al from Eric Wanker''s lab. Content areas that may be covered by the site include the following: * Therapeutic studies in mouse, primarily drug screens. * HD mouse models with a focus on timelines of disease progression. * Antibodies used in HD research. * Microarray gene expression studies. * Genes and proteins relevant to HD research. This includes HD itself, the growing list of proteins thought to interact directly or indirectly with huntingtin (Htt), and other genes and proteins implicated in the disease process. * Molecular pathways thought to be involved in the disease process. * Timelines of disease for Mouse models | drug, gene expression, huntingtin, mass spectrometry, microarray, protein interaction, protein-protein interaction, y2h, mouse model, treatment, disease, phenotype, brain, striatum, adipose, muscle, gene, protein, antibody, pathway |
uses: Cytoscape has parent organization: Institute for Systems Biology; Washington; USA |
Huntington''s disease, Control | Hereditary Disease Foundation | nif-0000-00153 | SCR_007132 | HDBase - A Community Website for Huntingtons Disease Research, HDBase - A Community Website for Huntington''s Disease Research | 2026-09-05 06:30:01 | 0 | ||||||
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Genetic and Rare Diseases Information Center Resource Report Resource Website 10+ mentions |
Genetic and Rare Diseases Information Center (RRID:SCR_008695) | GARD | data or information resource, disease-related portal, portal, topical portal | Genetic and Rare Diseases Information Center (GARD) is a collaborative effort of two agencies of the National Institutes of Health, The Office of Rare Diseases Research (ORDR) and the National Human Genome Research Institute (NHGRI) to help people find useful information about genetic conditions and rare diseases. GARD provides timely access to experienced information specialists who can furnish current and accurate information about genetic and rare diseases. So far, GARD has responded to 27,635 inquiries on about 7,147 rare and genetic diseases. Requests come not only from patients and their families, but also from physicians, nurses and other health-care professionals. GARD also has proved useful to genetic counselors, occupational and physical therapists, social workers, and teachers who work with people with a genetic or rare disease. Even scientists who are studying a genetic or rare disease and who need information for their research have contacted GARD, as have people who are taking part in a clinical study. Community leaders looking to help people find resources for those with genetic or rare diseases and advocacy groups who want up-to-date disease information for their members have contacted GARD. And members of the media who are writing stories about genetic or rare diseases have found the information GARD has on hand useful, accurate and complete. GARD has information on: :- What is known about a genetic or rare disease. :- What research studies are being conducted. :- What genetic testing and genetic services are available. :- Which advocacy groups to contact for a specific genetic or rare disease. :- What has been written recently about a genetic or rare disease in medical journals. GARD information specialists get their information from: :- NIH resources. :- Medical textbooks. :- Journal articles. :- Web sites. :- Advocacy groups, and their literature and services. :- Medical databases. | genetic, disease, information, genome, human, rare disease, health, physician, counselor, gene, journal, medical | has parent organization: National Institutes of Health | Office of Rare Diseases Research ; NHGRI |
nif-0000-37627 | SCR_008695 | Genetic Rare Diseases Information Center | 2026-09-05 06:30:02 | 16 | |||||||
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Pig Genome Mapping Resource Report Resource Website |
Pig Genome Mapping (RRID:SCR_012884) | PiGMaP | atlas, data or information resource, database, image collection | Map of identifyied genes controlling traits of economic and welfare significance in the pig. The project objectives were to produce a genetic map with markers spaced at approximately 20 centiMorgan intervals over at least 90% of the pig genome; to produce a physical map with at least one distal and one proximal landmark locus mapped on each porcine chromosome arm and also genetically mapped; to develop a flow karyotype for the pig based on FACS sorted chromosomes; to develop PCR based techniques to enable rapid genotyping for polymorphic markers; to evaluate synteny conservation between pigs, man, mice and cattle; to develop and evaluate the statistical techniques required to analyze data from QTL mapping experiments and to plan and initiate the mapping of QTLs in the pig; to map loci affecting traits of economic and biological significance in the pig; and to develop the molecular tools to allow the future identification and cloning of mapped loci. Animal breeders currently assume that economically important traits such as growth, carcass composition and reproductive performance are controlled by an infinite number of genes each of infinitessimal effect. Although this model is known to be unrealistic, it has successfully underpinned the genetic improvement of livestock, including pigs, over recent decades. A map of the pig genome would allow the development of more realistic models of the genetic control of economic traits and the ultimately the identification of the major trait genes. This would allow the development of more efficient marker assisted selection which may be of particular value for traits such as disease resistance and meat quality. | gene, genetic, artificial chromosome, bacteriophage, biological, carcass, cattle, cdna, comparative, disease, genome, genotype, growth, human, karyotpe, linkage, livestock, locus, map, mapping, marker, mice, molecular, p1, pig, quality, quantitative, sus scrofa, trait, yeast | has parent organization: Roslin Institute | PMID:7749223 | nif-0000-20987 | http://www.projects.roslin.ac.uk/pigmap/pigmap.html | SCR_012884 | PGM | 2026-09-05 06:30:04 | 0 | ||||||
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Ascidian Network for InSitu Expression and Embryological Data Resource Report Resource Website 50+ mentions |
Ascidian Network for InSitu Expression and Embryological Data (RRID:SCR_013030) | ANISEED | data or information resource, data repository, database, service resource, software resource, storage service resource |
Database of ascidian embryonic development at the level of the genome (cis-regulatory sequences, gene expression, protein annotation), of the cell (morphology, fate, induction, lineage) or of the whole embryo (anatomy, morphogenesis). Currently, four organism models are described in Aniseed: Ciona intestinalis, Ciona savignyi, Halocynthia roretzi and Phallusia mammillata. This version supports four sets of Ciona intestinalis transcript models: JGI v1.0, KyotoGrail 2005, KH and ENSEMBL, all functionally annotated, and grouped into Aniseedv3.0 gene models. Users can explore their expression profiles during normal or manipulated development, access validated cis-regulatory regions, get the molecular tools used to assay gene function, or all articles related to the function, or regulation of a given gene. Known transcriptional regulators and targets are listed for each gene, as are the gene regulatory networks acting in individual anatomical territories. ANISEED is a community tool, and the direct involvement of external contributors is important to optimize the quality of the submitted data. Virtual embryo: The 3D Virtual embryo is available to download in the download section of the website. |
embryology, embryo, gene, genome, anatomy, cis-regulatory, development, morphogenesis, morphology, protein, molecular neuroanatomy resource, cis-regulatory sequence, gene expression, protein annotation, cell, expression profile, function, regulation, blast, visualization, data analysis service, clone, FASEB list | CNRS ; French Ministry of Research ; Marseille-Nice Genopole ; ARC ; European Network QLK3-CT-2001-01890 |
PMID:20647237 | nif-0000-10155 | http://crfb.univ-mrs.fr/aniseed/index.php | SCR_013030 | Aniseed database | 2026-09-05 06:30:04 | 63 | ||||||
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National Institute on Drug Abuse Center for Genetic Studies Resource Report Resource Website 1+ mentions |
National Institute on Drug Abuse Center for Genetic Studies (RRID:SCR_013061) | NIDA Center for Genetic Studies | data or information resource, data repository, data set, service resource, storage service resource | Site for collection and distribution of clinical data related to genetic analysis of drug abuse phenotypes. Anonymous data on family structure, age, sex, clinical status, and diagnosis, DNA samples and cell line cultures, and data derived from genotyping and other genetic analyses of these clinical data and biomaterials, are distributed to qualified researchers studying genetics of mental disorders and other complex diseases at recognized biomedical research facilities. Phenotypic and Genetic data will be made available to general public on release dates through distribution mechanisms specified on website. | drug abuse, family, family structure, genetic analysis, genetics, addiction, age, biomaterial, cell line, citation, clinical, clinical status, data, diagnosis, dna, genotyping, human, mental disorder, mutation analysis, phenotype, publications, sex, clinical data, genotype, gene, GWAS |
is recommended by: National Library of Medicine is listed by: One Mind Biospecimen Bank Listing is related to: One Mind Biospecimen Bank Listing is related to: NIH Data Sharing Repositories has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA has parent organization: Rutgers University; New Jersey; USA |
NIDA ; NIH Blueprint for Neuroscience Research |
Free, Freely available | nif-0000-00181 | https://zork5.wustl.edu//nida/ | http://zork.wustl.edu/nida/ | SCR_013061 | National Institute of Drug Abuse (NIDA) Human Genetics Initiative, NIDA Center for Genetic Studies | 2026-09-05 06:30:04 | 7 | ||||
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PLINK/SEQ Resource Report Resource Website 50+ mentions |
PLINK/SEQ (RRID:SCR_013193) | software application, software library, software resource, software toolkit | An open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing projects, particularly whole-exome and whole-genome studies. However, the library could in principle be applied to other types of genetic studies, including whole-genome association studies of common SNPs. (entry from Genetic Analysis Software) | gene, genetic, genomic, c/c++, r, macos, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is related to: PLINK has parent organization: Harvard University; Cambridge; United States |
Open unspecified license | nlx_154213, biotools:plink-seq | https://bio.tools/plink-seq | SCR_013193 | 2026-09-05 06:30:04 | 77 |
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