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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MAIA Resource Report Resource Website 100+ mentions |
MAIA (RRID:SCR_007153) | MAIA | data analysis software, data processing software, software application, software resource | Software package of programs for complex segregation analysis in animal pedigrees. | gene, genetic, genomic, segregation, analysis, animal, pedigree |
is listed by: Genetic Analysis Software has parent organization: Institute of Cytology and Genetics of the Siberian Branch of the RAS; Novosibirsk; Russia |
Free, Non-commercial, Change of source code requires permission | nlx_154435 | SCR_007153 | 2026-09-05 06:26:07 | 359 | ||||||||
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Protein Information Resource Resource Report Resource Website 50+ mentions |
Protein Information Resource (RRID:SCR_002837) | PIR | data or information resource, portal, topical portal | Integrated public bioinformatics resource to support genomic, proteomic and systems biology research and scientific studies. Provides databases and protein sequence analysis tools to scientific community, including Protein Sequence Database which grew out from the Atlas of Protein Sequence and Structure. Conducts research in biomedical text mining and ontology, computational systems biology, and bioinformatics cyberinfrastructure. In 2002 PIR, along with its international partners, EBI (European Bioinformatics Institute) and SIB (Swiss Institute of Bioinformatics), were awarded a grant from NIH to create UniProt, a single worldwide database of protein sequence and function, by unifying the PIR-PSD, Swiss-Prot, and TrEMBL databases. Currently, PIR major activities include: i) UniProt (Universal Protein Resource) development, ii) iProClass protein data integration and ID mapping, iii) PRO protein ontology, and iv) iProLINK protein literature mining and ontology development. The FTP site provides free download for iProClass, PIRSF, and PRO. | annotation, genomic, mining, protein, protein bioinformatics, proteomic, research, sequence, structure, systems biology, gold standard, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: NCBI Protein Database has parent organization: University of Delaware; Delaware; USA has parent organization: Georgetown University; Washington D.C.; USA is parent organization of: PRO is parent organization of: PIRSF is parent organization of: PR is parent organization of: UniProt |
NLM P41 LM05798 | PMID:12520019 | Free, Freely available | biotools:pir, nif-0000-21327, nif-0000-00143, SCR_008229 | https://bio.tools/pir, http://pir.georgetown.edu/ | SCR_002837 | PIR - Protein Information Resource | 2026-09-05 06:24:54 | 85 | ||||
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HGNC Resource Report Resource Website 1000+ mentions |
HGNC (RRID:SCR_002827) | controlled vocabulary, data or information resource, database | Only worldwide authority that provides standardized nomenclature, i.e. gene names and symbols (short form abbreviations), for all known human genes, and stores all approved symbols in the HGNC database. Approved human gene nomenclature. Database of gene symbols and names. Manually curated genes into groups based on shared characteristics such as homology, function or phenotype. Data for protein-coding genes, pseudogenes and non-coding RNAs. | gene, owl, gene symbol, phenotype, nomenclature, gene family, gene groups, genomic, proteomic, ortholog, web service, locus, protein coding, genetics, gold standard, bio.tools, FASEB list, GCBR, ELIXIR Core Data Resource, DRKB |
is used by: Nowomics is used by: Cytokine Registry is listed by: BioPortal is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Rat Gene Symbol Tracker is related to: INFEVERS is related to: VGNC has parent organization: University of Cambridge School of Clinical Medicine; Cambridge; United Kingdom |
NHGRI U24HG003345 | PMID:36243972 PMID:32747822 PMID:34615987 PMID:33152070 |
Free, Freely available | biotools:genenames.org, nif-0000-02955, r3d100010901 | http://bioportal.bioontology.org/ontologies/HUGO, https://bio.tools/genenames.org, https://doi.org/10.17616/R3XC80 | SCR_002827 | HUGO symbols, HGNC Database, HGNC - HUGO Gene Nomenclature Committee, HUGO Gene Nomenclature Committee, Human Genome Organization Gene Symbols | 2026-09-05 06:24:54 | 1134 | |||||
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Haploview Resource Report Resource Website 5000+ mentions |
Haploview (RRID:SCR_003076) | Haploview | data processing software, software application, software resource, source code | A Java based software tool designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses. Haploview currently allows users to examine block structures, generate haplotypes in these blocks, run association tests, and save the data in a number of formats. All functionalities are highly customizable. (entry from Genetic Analysis Software) * LD & haplotype block analysis * haplotype population frequency estimation * single SNP and haplotype association tests * permutation testing for association significance * implementation of Paul de Bakker's Tagger tag SNP selection algorithm. * automatic download of phased genotype data from HapMap * visualization and plotting of PLINK whole genome association results including advanced filtering options Haploview is fully compatible with data dumps from the HapMap project and the Perlegen Genotype Browser. It can analyze thousands of SNPs (tens of thousands in command line mode) in thousands of individuals. Note: Haploview is currently on a development and support freeze. The team is currently looking at a variety of options in order to provide support for the software. Haploview is an open source project hosted by SourceForge. The source can be downloaded at the SourceForge project site. | linkage disequilibrium, haplotype, genotype, visualization, analysis, single nucleotide polymorphism, gene, genetic, genomic, java |
is listed by: Genetic Analysis Software is listed by: SoftCite is related to: International HapMap Project is related to: PLINK has parent organization: Broad Institute |
PMID:15297300 PMID:21356869 PMID:20147036 |
Free, Available for download, Freely available | nif-0000-30472 | http://www.broad.mit.edu/personal/jcbarret/haploview/ | SCR_003076 | 2026-09-05 06:24:57 | 7041 | ||||||
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JASPAR Resource Report Resource Website 5000+ mentions |
JASPAR (RRID:SCR_003030) | JASPAR | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Open source database of curated, non-redundant set of profiles derived from published collections of experimentally defined transcription factor binding sites for multicellular eukaryotes. Consists of open data access, non-redundancy and quality. JASPAR CORE is smaller set that is non-redundant and curated. Collection of transcription factor DNA-binding preferences, modeled as matrices. These can be converted into Position Weight Matrices (PWMs or PSSMs), used for scanning genomic sequences. Web interface for browsing, searching and subset selection, online sequence analysis utility and suite of programming tools for genome-wide and comparative genomic analysis of regulatory regions. New functions include clustering of matrix models by similarity, generation of random matrices by sampling from selected sets of existing models and a language-independent Web Service applications programming interface for matrix retrieval. | structural class, transcription factor binding site, profile, regulatory region, genome, genomic, matrix, transcription factor, binding site, dna, FASEB list |
is listed by: OMICtools is listed by: re3data.org is related to: Babelomics has parent organization: University of Copenhagen; Copenhagen; Denmark has parent organization: Karolinska Institute; Stockholm; Sweden |
Carlsberg Foundation ; EMBRACEa Sixth Framework Network of Excellence ; European Union ; Novo Nordisk Foundation ; Sars Centre |
PMID:18006571 PMID:16381983 PMID:14681366 |
Free, Freely available | r3d100010091, OMICS_00538, nif-0000-03061 | https://doi.org/10.17616/R3QC7R | http://129.177.120.189/cgi-bin/jaspar2010/jaspar_db.pl, http://jaspar.cgb.ki.se | SCR_003030 | JASPAR, JASPAR CORE, JASPAR CORE database, JASPAR database | 2026-09-05 06:24:56 | 5785 | |||
|
r3Cseq Resource Report Resource Website 10+ mentions |
r3Cseq (RRID:SCR_003198) | r3Cseq | data analysis software, data processing software, software application, software resource | An R/Bioconductor package to identify chromosomal interaction regions generated by chromosome conformation capture (3C) coupled to next-generation sequencing (NGS), a technique termed 3C-seq. It performs data analysis for a number of different experimental designs, as it can analyze 3C-seq data with or without a control experiment and it can be used to facilitate data analysis for experiments with multiple replicates. The r3Cseq package provides functions to perform data normalization, statistical analysis for cis/trans interactions and visualization in order to help scientists identify genomic regions that physically interact with the given viewpoints of interest. This tool greatly facilitates hypothesis generation and the interpretation of experimental results. | next-generation sequencing, genomic, interaction, chromosome conformation capture, chromosome, 3c-seq, r |
is listed by: OMICtools has parent organization: University of Bergen; Bergen; Norway has parent organization: Bioconductor |
PMID:23671339 | Free, Freely available | OMICS_01560 | SCR_003198 | 2026-09-05 06:24:59 | 24 | |||||||
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QGene Resource Report Resource Website 100+ mentions |
QGene (RRID:SCR_003209) | QGene | data analysis software, data processing software, simulation software, software application, software resource, source code | A free, open-source, computationally efficient Java program for comparative analyses of QTL mapping data and population simulation that runs on any computer operating system. (entry from Genetic Analysis Software) It is written with a plug-in architecture for ready extensibility. The software accommodates line-cross mating designs consisting of any arbitrary sequence of selfing, backcrossing, intercrossing and haploid-doubling steps that includes map, population, and trait simulators; and is scriptable. Source code is available on request. | gene, genetic, genomic, java, qtl mapping, trait analysis, trait, population, simulation, map, quantitative trait locus, comparison, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Kansas State University; Kansas; USA |
NSF DBI 0109879; USDA-NRI Applied Plant Genomics Program 2004-35317-14867 |
PMID:18940826 | Free, Available for download, Freely available | biotools:qgene, nif-0000-31383 | https://bio.tools/qgene | http://coding.plantpath.ksu.edu/qgene | SCR_003209 | QGene - Software for QTL data exploration | 2026-09-05 06:24:59 | 129 | |||
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Sage Bionetworks Resource Report Resource Website 100+ mentions |
Sage Bionetworks (RRID:SCR_003384) | nonprofit organization | Non-profit biomedical research organization developing predictors of disease and accelerating health research through creation of open systems, incentives, and standards. Formed to coordinate and link academic and commercial biomedical researchers through Commons that represents new paradigm for genomics intellectual property, researcher cooperation, and contributor evolved resources. | bionetwork, medical, research, human, treatment, disease, biological, biomedical, genomic, development, diagnostic, therapeutic, molecular, meta-data, model, clinical, bioinformatics, drug, consortium, data sharing, software |
is listed by: Consortia-pedia is parent organization of: CommonMind Consortium is parent organization of: Sage Bionetworks Podcasts is parent organization of: Key Driver Analysis is parent organization of: Synapse |
Free, Freely available | Wikidata: Q891621, nif-0000-32903, grid.430406.5, SCR_004425, ISNI: 0000 0004 6023 5303, nlx_42820 | https://ror.org/049ncjx51 | http://sagebase.org/commons/repository.php | SCR_003384 | 2026-09-05 06:25:02 | 119 | |||||||
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MGH-USC Human Connectome Project Resource Report Resource Website 100+ mentions |
MGH-USC Human Connectome Project (RRID:SCR_003490) | MGH/UCLA HCP | data or information resource, instrument manufacture, material service resource, portal, production service resource, service resource | A multi-center project comprising two distinct consortia (Mass. Gen. Hosp. and USC; and Wash. U. and the U. of Minn.) seeking to map white matter fiber pathways in the human brain using leading edge neuroimaging methods, genomics, architectonics, mathematical approaches, informatics, and interactive visualization. The mapping of the complete structural and functional neural connections in vivo within and across individuals provides unparalleled compilation of neural data, an interface to graphically navigate this data and the opportunity to achieve conclusions about the living human brain. The HCP is being developed to employ advanced neuroimaging methods, and to construct an extensive informatics infrastructure to link these data and connectivity models to detailed phenomic and genomic data, building upon existing multidisciplinary and collaborative efforts currently underway. Working with other HCP partners based at Washington University in St. Louis they will provide rich data, essential imaging protocols, and sophisticated connectivity analysis tools for the neuroscience community. This project is working to achieve the following: 1) develop sophisticated tools to process high-angular diffusion (HARDI) and diffusion spectrum imaging (DSI) from normal individuals to provide the foundation for the detailed mapping of the human connectome; 2) optimize advanced high-field imaging technologies and neurocognitive tests to map the human connectome; 3) collect connectomic, behavioral, and genotype data using optimized methods in a representative sample of normal subjects; 4) design and deploy a robust, web-based informatics infrastructure, 5) develop and disseminate data acquisition and analysis, educational, and training outreach materials. | human, structural, functional, neural, white matter, fiber, brain, in vivo, genomic, neuroimaging, visualization, neuroanatomy, genotype, connectivity, connectivity model, neural pathway, phenomic, connectomics, quantification, scanner, eeg, meg, shape analysis, spatial transformation, diffusion spectrum, q-ball, tensor metric, fiber tracking, connectome, behavior, scanner, web resource, diffusion spectrum, q-ball, tensor metric, quantification, shape analysis, spatial transformation, fiber tracking, FASEB list |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: Laboratory of Neuro Imaging has parent organization: Harvard Medical School; Massachusetts; USA has parent organization: NIH Human Connectome Project is parent organization of: USC Multimodal Connectivity Database |
Normal | NIH ; NIH Blueprint for Neuroscience Research |
Open unspecified license, (BSD/MIT-Style), LONI Software License, Public Domain | nif-0000-35789 | http://www.nitrc.org/projects/hcp_mgh-ucla | SCR_003490 | Harvard/MGH-UCLA Human Connectome Project, Harvard/MGH-UCLA Consortium: Human Connectome Project, HCP Harvard/MGH-UCLA, MGH/UCLA Consortium: Human Connectome Project | 2026-09-05 06:25:04 | 186 | ||||
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BioBank Central Resource Report Resource Website |
BioBank Central (RRID:SCR_008645) | BioBank Central | biospecimen repository, material storage repository, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 27, 2013. Web-based portal to connect all the constituencies in the global biobank community. The project seeks to increase the transparency and accessibility of the scientific research process by connecting researchers with an additional source of funding - microinvestments received from the broader online community. In exchange for these public investments, researchers will maintain research logs detailing the play-by-play progress made in their project, as well as publishing all of their data in a public database under a science commons license. These research projects, in turn, will serve to continually update a research-based neuroscience-based human brain & body curriculum. Biobanks are the meeting point of two major information trends in biomedical research: the generation of huge amounts of genomic and other laboratory data, and the electronic capture and integration of patient clinical records. They are comprised of large numbers of human biospecimens supplemented with clinical data. Biobanks when implemented effectively can harness the power of both genomic and clinical data and serve as a critical bridge between basic and applied research, linking laboratory to patient and getting to cures faster. As science and technology leaders work to address the many challenges facing U.S. biobanks logistical, technical, ethical, financial, intellectual property, and IT BioBank Central will serve as an accurate and timely source of knowledge and news about biorepositories and their role in research and drug development. The Web site also provides a working group venue, patient and public education programs, and a forum for international collaboration and harmonization of best practices. | biobank, community, biomedical, data, genomic, integration, patient, clinical, human, biospecimen, science, technology, biorepository, drug, development, education | has parent organization: Open Source Science Project | FasterCures ; Feinstein Kean Healthcare ; IBM Healthcare and Life Sciences ; Affymetrix ; Bioaccelerate Holdings Inc. ; Invitrogen Corporation |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-32933 | SCR_008645 | 2026-09-05 06:26:26 | 0 | |||||||
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Ingenuity Pathway Analysis Resource Report Resource Website 5000+ mentions Rating or validation data |
Ingenuity Pathway Analysis (RRID:SCR_008653) | IPA | pathway analysis tool | A web-based software application that enables users to analyze, integrate, and understand data derived from gene expression, microRNA, and SNP microarrays, metabolomics, proteomics, and RNA-Seq experiments, and small-scale experiments that generate gene and chemical lists. Users can search for targeted information on genes, proteins, chemicals, and drugs, and build interactive models of experimental systems. IPA allows exploration of molecular, chemical, gene, protein and miRNA interactions, creation of custom molecular pathways, and the ability to view and modify metabolic, signaling, and toxicological canonical pathways. In addition to the networks and pathways that can be created, IPA can provide multiple layering of additional information, such as drugs, disease genes, expression data, cellular functions and processes, or a researchers own genes or chemicals of interest. | software, drug, gene, analysis, chemical, metabolic, model, pathway, protein, signal, molecular signaling, genomic, pathway analysis tool |
uses: Ingenuity Pathways Knowledge Base is listed by: Biositemaps is listed by: OMICtools is listed by: SoftCite |
Commercial license | nif-0000-33144, OMICS_00399 | http://www.ingenuity.com/products/ipa, http://www.ingenuity.com/products/ipa/microrna-research | SCR_008653 | QIAGEN Ingenuity Pathway Analysis | 2026-09-05 06:26:26 | 6828 | ||||||
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genes2mind Resource Report Resource Website 1+ mentions |
genes2mind (RRID:SCR_008872) | genes2mind | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | genes2mind is a tool for rapid exploratory analysis of psychotropic drug-induced gene expression in the brain. We present here an open resource containing comparison of effects of various classes of psychotropic drugs on transcriptional alterations of ~20,000 genes in the mouse brain (C57BL/6J). Data stored in the database include raw gene expression values as well as results of drug comparison. * Genomic Signature Identification section allows for the identification of drug-specific genomic signatures. * Genomic Signature Analysis section allows for further inspection and visualization of the signatures using multidimensional data analysis (PCA), co-expression analysis and heatmaps. * Single Gene Inspection allows for brief review of expression of specific candidate genes using barplots. | psychotropic drug, gene expression, gene, brain, drug, c57bl/6j, genomic | has parent organization: Polish Academy of Sciences Poznan; Poznan; Poland | Institute of Pharmacology PAS ; Polish Ministry of Science and Higher Education DeMeTer 3.1 POIG; Polish Ministry of Science and Higher Education NN405 274137; European Union FP6 GENADDICT LSHM-CT-2004-005166 |
nlx_149344 | SCR_008872 | 2026-09-05 06:26:30 | 3 | ||||||||
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ALLELIX Resource Report Resource Website 1+ mentions |
ALLELIX (RRID:SCR_009115) | ALLELIX | analysis service resource, data analysis service, production service resource, service resource, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on September 23, 2013. Software application / data analysis service where one can enter the alleles of commonly used STR by clicking the mouse. The algorithm calculates the paternity index and the Essen-Moeller probability of kinship for the deficiency- and the trio case. Everybody can use the network-software online after registering. The usage on the internet is free. Academic users can ask me to unlock an option to display the details (formulas/frequencies etc.) and to have an export-funktion to MS Word. The program is in German and (non-professional) English. An expansion to other languages is easy, if somebody helps us with the translation. For those who are interested to have the software running on their own intranet (for database security reasons) an individual agreement can be found. (entry from Genetic Analysis Software) (German version is: http://www.allelix.de) | gene, genetic, genomic, c++, java script, ms-windows, (2000 &iis/me & personal webserver) | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154216 | SCR_009115 | Allelix - Paternity Linkage Analysis Online | 2026-09-05 06:26:32 | 2 | |||||||
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BARS Resource Report Resource Website 10+ mentions |
BARS (RRID:SCR_009123) | BARS | software application, software resource | Software application that is a statistical method that bridges the gap between single-locus and haplotype-based tests of association. It is based on the non-parametric regression techniques embodied by Bayesian Adaptive Regression Splines. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, r, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154204, biotools:bars, nlx_154228, SCR_009106 | https://bio.tools/bars | SCR_009123 | Bayesian Adaptive Regression Splines | 2026-09-05 06:26:32 | 39 | ||||||
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CMAP Resource Report Resource Website 100+ mentions |
CMAP (RRID:SCR_009034) | CMap | data analysis software, data processing software, software application, software resource | Web-based tool that allows users to view comparisons of genetic and physical maps. The package also includes tools for curating map data. (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, unix, solaris, freebsd, linux, sequence, FASEB list |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: SoftCite has parent organization: Generic Model Organism Database Project works with: Drug Gene Budger |
PMID:19648141 | GNU General Public License | nlx_153998, OMICS_00933 | https://sourceforge.net/projects/gmod/files/cmap/ | http://www.gmod.org/cmap/, http://gmod.org/wiki/Cmap | SCR_009034 | , GMOD Comparative Mapping (CMap) tool, Comparative Mapping tool, genetic and comparative maps | 2026-09-05 06:26:32 | 417 | ||||
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caGWAS Resource Report Resource Website |
caGWAS (RRID:SCR_009617) | caGWAS | software resource | Too that allows researchers to integrate, query, report, and analyze significant associations between genetic variations and disease, drug response or other clinical outcomes. SNP array technologies make it possible to genotype hundreds of thousands of single nucleotide polymorphisms (SNPs) simultaneously, enabling whole genome association studies. Within the Clinical Genomic Object Model (CGOM), the caIntegrator team created a domain model for Whole Genome Association Study Analysis. CGOM-caGWAS is a A semantically annotated domain model that captures associations between Study, Study Participant, Disease, SNP Association Analysis, SNP Population Frequency and SNP annotations. caGWAS APIs and web portal provide: * a semantically annotated domain model, database schema with sample data, seasoned middleware, APIs, and web portal for GWAS data; * platform and disease agnostic CGOM-caGWAS model and associated APIs; * the opportunity for developers to customize the look and feel of their GWAS portal; * a foundation of open source technologies; * a well-tested and performance-enhanced platform, as the same software is being used to house the CGEMS data portal; * accelerated analysis of results from various biomedical studies; and * a single application through which researchers and bioinformaticians can access and analyze clinical and experimental data from a variety of data types, as caGWAS objects are part of the CGOM, which includes microarray, genomic, immunohistochemistry, imaging, and clinical data. | application, computational neuroscience, genetic association, genomic analysis, imaging genomics, java, snp, gene, software, web environment, microarray, genomic, immunohistochemistry, imaging, clinical |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: National Cancer Institute |
BSD License | nlx_155841 | http://www.nitrc.org/projects/cagwas | SCR_009617 | caGWAS (Cancer Genome-Wide Association Studies), Cancer Genome-Wide Association Studies, CGOM-caGWAS | 2026-09-05 06:26:35 | 0 | ||||||
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Gene Regulation Ontology Resource Report Resource Website |
Gene Regulation Ontology (RRID:SCR_010590) | GRO, BOOTStrep | controlled vocabulary, data or information resource, ontology | Ontology that is a conceptual model for the domain of gene regulation. It covers processes that are linked to the regulation of gene expression as well as physical entities that are involved in these processes (such as genes and transcription factors) in terms of ontology classes and semantic relations between classes. GRO is intended to represent common knowledge about gene regulation in a formal way rather than representing extremely fine-grained classes as can be found in ontologies such as the Gene Ontology (GO) (created for data base annotation purposes) and various relevant databases. The main purpose of the ontology is to support NLP applications. It has a particular focus on the relations between processes and the molecules (participants) involved. The basic structure of the GRO is a direct acyclic graph (DAG) with ontology classes as nodes and is-a relations between classes as edges. The taxonomic backbone is further enriched by several semantic relation types (part-of, from-species, participates-in with the two sub-relations agent-of and patient-of). | owl, genomic, proteomic, biological process, gene regulation, gene expression, gene, transcription factor, process, molecule, biological_process |
is listed by: BioPortal is listed by: OBO has parent organization: European Bioinformatics Institute |
nlx_157415, nlx_46399 | http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html, http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO_latest | SCR_010590 | Gene Regulation Ontology - Ontological resource from the BOOTStrep project for the representation of gene regulation events | 2026-09-05 06:26:43 | 0 | |||||||
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GEISHA - Gallus Expression in Situ Hybridization Analysis: A Chicken Embryo Gene Expression Database Resource Report Resource Website 1+ mentions |
GEISHA - Gallus Expression in Situ Hybridization Analysis: A Chicken Embryo Gene Expression Database (RRID:SCR_007440) | GEISHA | atlas, data or information resource, data repository, database, experimental protocol, narrative resource, service resource, storage service resource | Online repository for chicken in situ hybridization information. This site presents whole mount in situ hybridization images and corresponding probe and genomic information for genes expressed in chicken embryos in Hamburger Hamilton stages 1-25 (0.5-5 days). The GEISHA project began in 1998 to investigate using high throughput whole mount in situ hybridization to identify novel, differentially expressed genes in chicken embryos. An initial expression screen of approximately 900 genes demonstrated feasibility of the approach, and also highlighted the need for a centralized repository of in situ hybridization expression data. Objectives: The goals of the GEISHA project are to obtain whole mount in situ hybridization expression information for all differentially expressed genes in the chicken embryo between HH stages 1-25, to integrate expression data with the chicken genome browsers, and to offer this information through a user-friendly graphical user interface. In situ hybridization images are obtained from three sources: 1. In house high throughput in situ hybridization screening: cDNAs obtained from several embryonic cDNA libraries or from EST repositories are screened for expression using high throughput in situ hybridization approaches. 2. Literature curation: Agreements with journals permit posting of published in situ hybridization images and related information on the GEISHA site. 3. Unpublished in situ hybridization information from other laboratories: laboratories generally publish only a small fraction of their in situ hybridization data. High quality images for which probe identity can be verified are welcome additions to GEISHA. | expression data, expression pattern, gene, gene expression, genome, chicken, chicken embryo, genomic, in situ hybridization, mapping, microarray, microrna, model organism, oligo, probe, stage, image, molecular neuroanatomy resource, embryo, embryonic chicken | has parent organization: University of Arizona; Arizona; USA | NIH ; NICHD R01HD044767 |
nif-0000-01251, r3d100012509 | https://doi.org/10.17616/R3RB6B | SCR_007440 | Gallus Expression in Situ Hybridization Analysis, GEISHA - Gallus Expression in Situ Hybridization Analysis | 2026-09-05 06:26:12 | 2 | ||||||
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Animal Genome Size Database Resource Report Resource Website 100+ mentions |
Animal Genome Size Database (RRID:SCR_007551) | Genomesize | catalog, data or information resource, data repository, database, service resource, storage service resource | Comprehensive catalogue of animal genome size data. Haploid DNA contents (C-values, in picograms) are available for 4972 species (3231 vertebrates and 1741 non-vertebrates) based on 6518 records from 669 published sources. Data may be submitted directly to the database or reprints and notifications of new papers may be sent to database curation staff. | genome size, haploid dna, non-vertebrate, vertebrate, genome structure, comparative biodiversity, sequencing, genome, genomic, FASEB list | has parent organization: University of Guelph; Ontario; Canada | Natural Sciences and Engineering Research Council of Canada | PMID:17090588 | Data taken from the database must not be reproduced in published lists, Online databases, Or other such formats, Nor redistributed without permission. The information is provided solely for personal and academic use., Please cite, The community can contribute to this resource | nif-0000-02548, r3d100012517 | https://doi.org/10.17616/R3R782, https://doi.org/10.17616/R3R782 | SCR_007551 | 2026-09-05 06:26:14 | 190 | |||||
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ALTree Resource Report Resource Website 1+ mentions |
ALTree (RRID:SCR_007562) | data analysis software, data processing software, software application, software resource | Software package to perform phylogeny based association and localization analysis.Used for association detection and localization of susceptibility sites using haplotype phylogenetic trees. Performs these two phylogeny-based analysis: tests association between candidate gene and disease; pinpoints markers (SNPs) that are putative disease susceptibility loci. | phylogeny based association, association detection, susceptibility sites, haplotype phylogenetic trees, gene, genetic, genomic |
is listed by: Genetic Analysis Software is listed by: Debian |
PMID:16595555 DOI:10.1093/bioinformatics/btl131 |
Free, Available for download, Freely available | OMICS_13032, nlx_154221 | https://sources.debian.org/src/altree/, https://gitlab.inria.fr/NGS/ALTree, | SCR_007562 | ALTREE | 2026-09-05 06:26:14 | 3 |
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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.
