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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Peptide Sequence Database Resource Report Resource Website |
Peptide Sequence Database (RRID:SCR_005764) | PepSeqDB | data or information resource, database | The Peptide Sequence Database contains putative peptide sequences from human, mouse, rat, and zebrafish. Compressed to eliminate redundancy, these are about 40 fold smaller than a brute force enumeration. Current and old releases are available for download. Each species'' peptide sequence database comprises peptide sequence data from releveant species specific UniGene and IPI clusters, plus all sequences from their consituent EST, mRNA and protein sequence databases, namely RefSeq proteins and mRNAs, UniProt''s SwissProt and TrEMBL, GenBank mRNA, ESTs, and high-throughput cDNAs, HInv-DB, VEGA, EMBL, IPI protein sequences, plus the enumeration of all combinations of UniProt sequence variants, Met loss PTM, and signal peptide cleavages. The README file contains some information about the non amino-acid symbols O (digest site corresponding to a protein N- or C-terminus) and J (no digest sequence join) used in these peptide sequence databases and information about how to configure various search engines to use them. Some search engines handle (very) long sequences badly and in some cases must be patched to use these peptide sequence databases. All search engines supported by the PepArML meta-search engine can (or can be patched to) successfully search these peptide sequence databases. | peptide, sequence | has parent organization: Edwards Lab | nlx_149230 | SCR_005764 | 2026-02-14 02:06:30 | 0 | |||||||||
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GeneTrail Resource Report Resource Website 100+ mentions |
GeneTrail (RRID:SCR_006250) | GeneTrail | data analysis service, production service resource, service resource, analysis service resource | A web-based application that analyzes gene sets for statistically significant accumulations of genes that belong to some functional category. Considered category types are: KEGG Pathways, TRANSPATH Pathways, TRANSFAC Transcription Factor, GeneOntology Categories, Genomic Localization, Protein-Protein Interactions, Coiled-coil domains, Granzyme-B clevage sites, and ELR/RGD motifs. The web server provides two statistical approaches, "Over-Representation Analysis" (ORA) comparing a reference set of genes to a test set, and "Gene Set Enrichment Analysis" (GSEA) scoring sorted lists of genes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | pathway, microarray, enrichment, genomic, proteomic, function, transcription factor, genomic localization, protein-protein interaction, coiled-coil domain, granzyme-b clevage site, motif, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: KEGG is related to: TRANSPATH is related to: TRANSFAC is related to: Gene Ontology has parent organization: Saarland University; Saarbrucken; Germany |
PMID:17526521 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:genetrail, OMICS_02236 | https://bio.tools/genetrail | SCR_006250 | 2026-02-14 02:06:26 | 106 | ||||||
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Zebrafish Gene Collection Resource Report Resource Website 1+ mentions |
Zebrafish Gene Collection (RRID:SCR_007054) | ZGC | biomaterial supply resource, material resource | Part of zebrafish genome project. ZGC project to produce cDNA libraries, clones and sequences to provide complete set of full-length (open reading frame) sequences and cDNA clones of expressed genes for zebrafish. All ZGC sequences are deposited in GenBank and clones can be purchased from distributors of IMAGE consortium. With conclusion of ZGC project in September 2008, GenBank records of ZGC sequences will be frozen, without further updates. Since definition of what constitutes full-length coding region for some of genes and transcripts for which we have ZGC clones will likely change in future, users planning to order ZGC clones will need to monitor for these changes. Users can make use of genome browsers and gene-specific databases, such as UCSC Genome browser, NCBI's Map Viewer, and Entrez Gene, to view relevant regions of genome (browsers) or gene-related information (Entrez Gene). | cdna library, clone, sequence, full-length open reading frame, cdna clone, frozen, fish, gene, genetic, genome, genomic |
is listed by: One Mind Biospecimen Bank Listing is related to: One Mind Biospecimen Bank Listing is related to: NIDDK Information Network (dkNET) is related to: Mammalian Gene Collection is related to: GenBank is related to: ATCC has parent organization: National Cancer Institute |
NIH Blueprint for Neuroscience Research | Free, Freely available | nif-0000-00567 | https://genecollections.nci.nih.gov/ZGC/ | SCR_007054 | Zebrafish Gene Collection | 2026-02-14 02:07:03 | 1 | |||||
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ZMP Resource Report Resource Website 10+ mentions |
ZMP (RRID:SCR_006161) | ZMP | biomaterial supply resource, material resource | Create knockout alleles in protein coding genes in the zebrafish genome, using a combination of whole exome enrichment and Illumina next generation sequencing, with the aim to cover them all. Each allele created is analyzed for morphological differences and published on the ZMP site. Transcript counting is performed on alleles with a morphological phenotype. Alleles generated are archived and can be requested from this site through the Zebrafish International Resource Center (ZIRC). You may register to receive updates on genes of interest, or browse a complete list, or search by Ensembl ID, gene name or human and mouse orthologue. | phenotype, genome, gene, disease model, allele, orthologue, mutant, chromosome, human orthologue, mouse orthologue, mutation, knockout, human, mouse, transcript |
is listed by: One Mind Biospecimen Bank Listing is related to: Zebrafish International Resource Center has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust Sanger Institute; Hinxton; United Kingdom ; NIH ; ZF-HEALTH |
Free and open | nlx_151662 | SCR_006161 | Zebrafish Mutation Project (ZMP), Zebrafish Mutation Project, ZMP - Zebrafish Mutation Project | 2026-02-14 02:07:02 | 25 | ||||||
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Zebrafish - SCORE Imaging: Specimen in a Corrected Optical Rotational Enclosure Resource Report Resource Website 10+ mentions |
Zebrafish - SCORE Imaging: Specimen in a Corrected Optical Rotational Enclosure (RRID:SCR_001300) | SCORE imaging | data or information resource, narrative resource | Narrative resource describing a visual data analysis and collection approach that takes advantage of the cylindrical nature of the zebrafish allowing for an efficient and effective method for image capture called, Specimen in a Corrected Optical Rotational Enclosure (SCORE) Imaging. To achieve a non-distorted image, zebrafish were placed in a fluorinated ethylene propylene (FEP) tube with a surrounding, optically corrected imaging solution: water. By similarly matching the refractive index of the housing (FEP tubing) to that of the inner liquid and outer liquid (water), distortion was markedly reduced, producing a crisp imagable specimen that is able to be fully rotated 360 degrees. A similar procedure was established for fixed zebrafish embryos using convenient, readily available borosilicate capillaries surrounded by 75% glycerol. The method described could be applied to chemical genetic screening and other, related high-throughput methods within the fish community and among other scientific fields. | format, authoring tool, embryo, microscopy, publishing format, image |
is listed by: FORCE11 has parent organization: Mayo Clinic Minnesota; Minnesota; USA has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
NIGMS GM63904; NIDA DA14546 |
PMID:20528262 | nif-0000-07749 | SCR_001300 | Specimen in a Corrected Optical Rotational Enclosure imaging | 2026-02-14 02:06:59 | 11 | ||||||
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Gemma Resource Report Resource Website 1000+ mentions |
Gemma (RRID:SCR_008007) | Gemma | data or information resource, database | Resource for reuse, sharing and meta-analysis of expression profiling data. Database and set of tools for meta analysis, reuse and sharing of genomics data. Targeted at analysis of gene expression profiles. Users can search, access and visualize coexpression and differential expression results. | chip, microarray, functional genomics, gene expression, coexpression, differential expression, FASEB list |
is used by: NIF Data Federation is used by: Integrated Data Annotation is listed by: Debian is listed by: SoftCite is related to: Gene Ontology is related to: Gene Expression Omnibus is related to: Phenocarta has parent organization: University of British Columbia; British Columbia; Canada is parent organization of: Neurocarta |
NIGMS GM076990; Canadian Foundation for Innovation ; Michael Smith Foundation for Health Research ; Canadian Institutes for Health Research |
PMID:22782548 | Free, Freely available | nif-0000-08127, r3d100012747 | https://sources.debian.org/src/gemma/ https://doi.org/10.17616/R36R54 https://doi.org/10.17616/R36R54 |
SCR_008007 | 2026-02-14 02:06:41 | 1112 | |||||
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APPRIS Resource Report Resource Website 50+ mentions |
APPRIS (RRID:SCR_012019) | APPRIS | data or information resource, database | A database that houses annotations of human splice isoforms. It adds reliable protein structural and functional data and information from cross-species conservation. A visual representation of the annotations for each gene allows users to easily identify functional changes brought about by splicing events. In addition to collecting, integrating and analyzing reliable predictions of the effect of splicing events, it also selects a single reference sequence for each gene, termed the principal isoform, based on the annotations of structure, function and conservation for each transcript. | isoform, function, annotation, splice, reference sequence, structure, conservation, transcript, FASEB list |
is listed by: OMICtools has parent organization: Spanish National Cancer Research Center |
PMID:23161672 | Free | OMICS_01881 | SCR_012019 | APPRIS - A system for annotating alternative splice isoforms | 2026-02-14 02:06:21 | 85 | ||||||
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BonZeb project Resource Report Resource Website |
BonZeb project (RRID:SCR_021388) | data or information resource, portal, project portal | Portal provides tools for investigating visuomotor integration specific to high speed kinematic tracking in small model organisms in closed loop experiments. University of Toronto scientists developed suite of Bonsai modules for specifically tracking and analyzing zebrafish movements and integrating these data with closed-loop experiments. BonZeb modules can also be used in an open-loop fashion for collecting, analyzing, and integrating data from multiple sources in real time, or from offline sources for batch processing of pre-recorded data. | Tacking and analyzing zebrafish movements, integrating zebrafish movements data with closed loop experiments, zebrafish movements, OpenBehavior |
is listed by: OpenBehavior is related to: BonZeb has parent organization: University of Toronto; Ontario; Canada |
Free, Freely available | SCR_021388 | BonZeb | 2026-02-14 02:05:43 | 0 | |||||||||
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phenomeNET Resource Report Resource Website 10+ mentions |
phenomeNET (RRID:SCR_006165) | PhenomeNet | data analysis service, analysis service resource, data or information resource, production service resource, source code, service resource, software resource, database | PhenomeNet is a cross-species phenotype similarity network. It contains the experimentally observed phenotypes of multiple species as well as the phenotypes of human diseases. PhenomeNet provides a measure of phenotypic similarity between the phenotypes it contains. The latest release (from 22 June 2012) contains 124,730 complex phenotype nodes taken from the yeast, fish, worm, fly, rat, slime mold and mouse model organism databases as well as human disease phenotypes from OMIM and OrphaNet. The network is a complete graph in which edge weights represent the degree of phenotypic similarity. Phenotypic similarity can be used to identify and prioritize candidate disease genes, find genes participating in the same pathway and orthologous genes between species. To compute phenotypic similarity between two sets of phenotypes, we use a weighted Jaccard index. First, phenotype ontologies are used to infer all the implications of a phenotype observation using several phenotype ontologies. As a second step, the information content of each phenotype is computed and used as a weight in the Jaccard index. Phenotypic similarity is useful in several ways. Phenotypic similarity between a phenotype resulting from a genetic mutation and a disease can be used to suggest candidate genes for a disease. Phenotypic similarity can also identify genes in a same pathway or orthologous genes. PhenomeNet uses the axioms in multiple species-dependent phenotype ontologies to infer equivalent and related phenotypes across species. For this purpose, phenotype ontologies and phenotype annotations are integrated in a single ontology, and automated reasoning is used to infer equivalences. Specifically, for every phenotype, PhenomeNet infers the related mammalian phenotype and uses the Mammalian Phenotype Ontology for computing phenotypic similarity. Tools: * PhenomeBLAST - A tool for cross-species alignments of phenotypes * PhenomeDrug - method for drug-repurposing | phenotype, disease, gene, genotype, allele, model organism, human disease, candidate disease gene, pathway, orthologous gene, ortholog, ontology, semantic similarity, mutant phenotype, disease pathway, alignment, pharmacogenomics, drug |
is related to: OMIM is related to: Orphanet is related to: PharmGKB is related to: MPO has parent organization: University of Cambridge; Cambridge; United Kingdom |
European Union 7th FPRICORDO project 248502; NHGRI R01 HG004838-02; BBSRC BBG0043581 |
PMID:21737429 | The source code and all data are freely available on http://phenomeblast.googlecode.com | nlx_151667 | SCR_006165 | PhenomeNet - Cross Species Phenotype Network | 2026-02-14 02:01:05 | 13 | |||||
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Comparative Toxicogenomics Database (CTD) Resource Report Resource Website 1000+ mentions |
Comparative Toxicogenomics Database (CTD) (RRID:SCR_006530) | CTD | data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | A public database that enhances understanding of the effects of environmental chemicals on human health. Integrated GO data and a GO browser add functionality to CTD by allowing users to understand biological functions, processes and cellular locations that are the targets of chemical exposures. CTD includes curated data describing cross-species chemical–gene/protein interactions, chemical–disease and gene–disease associations to illuminate molecular mechanisms underlying variable susceptibility and environmentally influenced diseases. These data will also provide insights into complex chemical–gene and protein interaction networks. | environment, chemical, disease, gene, pathway, protein, interaction, animal model, ontology, annotation, toxin, ontology or annotation browser, FASEB list |
is used by: DisGeNET is used by: NIF Data Federation is listed by: 3DVC is listed by: Gene Ontology Tools is related to: PharmGKB Ontology is related to: Gene Ontology is related to: BioRAT is related to: Integrated Gene-Disease Interaction is related to: OMICtools is related to: Integrated Manually Extracted Annotation has parent organization: Mount Desert Island Biological Laboratory has parent organization: North Carolina State University; North Carolina; USA is parent organization of: Interaction Ontology |
Pfizer ; American Chemistry Council ; NIEHS ES014065; NIEHS R01 ES019604; NCRR P20 RR016463; NIEHS U24 ES033155 |
PMID:16902965 PMID:16675512 PMID:14735110 PMID:12760826 |
Free, Freely available | OMICS_01578, nif-0000-02683, r3d100011530 | http://ctd.mdibl.org https://doi.org/10.17616/R3KS7N |
SCR_006530 | CTD - Comparative Toxicogenomics Database | 2026-02-14 02:01:19 | 1188 | ||||
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Edwards Lab Resource Report Resource Website 1+ mentions |
Edwards Lab (RRID:SCR_008860) | Edwards Lab | portal, laboratory portal, data or information resource, organization portal, topical portal | The Edwards lab conducts research in various aspects of computational biology and bioinformatics, particularly proteomics and mass spectrometry informatics and DNA and protein based signatures for pathogen detection. Some tools provided by Edwards Lab are the PepArML Meta-Search Engine, PeptideMapper Web-Service, Peptide Sequence Databases, Rapid Microorganism Identification Database (RMIDb), and GlycoPeptideSearch. Our primary area of research is the analysis of mass spectrometry experiments for proteomics. Proteomics, the qualitative and quantitative analysis of the expressed proteins of a cell, makes it possible to detect and compare the protein abundance profiles of different samples. Proteins observed to be under or over expressed in disease samples can lead to diagnostic markers or drug targets. The observation of mutated or alternatively spliced protein isoforms may provide domain experts with clues to the mechanisms by which a disease operates. The detection of proteins by mass spectrometry can even signal the presence of airborne microorganisms, such as anthrax, in the detect-to-protect time-frame. Recent research has focused on the discovery of novel peptides in proteomics datasets, improving the sensitivity and specificity of peptide identification using spectral matching with hidden Markov models, and unsupervised machine-learning based peptide identification result combining. Outside of proteomics, we work on computational tools for the design of highly specific oligonucleotides useful for pathogen signatures and PCR assay design. Recent research has focused on precomputing all human oligos of length 20 that are unique up to 4 string edits; and all bacterial 20-mer oligos that are species specific up to 4 string edits. | peptide, proteomics, computational biology, bioinformatics, mass spectrometry, informatics, oligonucleotide, peptide sequence |
has parent organization: Georgetown University; Washington D.C.; USA is parent organization of: PeptideMapper is parent organization of: Peptide Sequence Database is parent organization of: GlycoPeptideSearch |
nlx_149188 | SCR_008860 | Georgetown - Edwards Lab, Georgetown University - Edwards Lab, GU - Edwards Lab | 2026-02-14 02:01:46 | 1 | ||||||||
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EGAN: Exploratory Gene Association Networks Resource Report Resource Website 1+ mentions |
EGAN: Exploratory Gene Association Networks (RRID:SCR_008856) | EGAN | data analysis software, software resource, data processing software, software application | Exploratory Gene Association Networks (EGAN) is a software tool that allows a bench biologist to visualize and interpret the results of high-throughput exploratory assays in an interactive hypergraph of genes, relationships (protein-protein interactions, literature co-occurrence, etc.) and meta-data (annotation, signaling pathways, etc.). EGAN provides comprehensive, automated calculation of meta-data coincidence (over-representation, enrichment) for user- and assay-defined gene lists, and provides direct links to web resources and literature (NCBI Entrez Gene, PubMed, KEGG, Gene Ontology, iHOP, Google, etc.). EGAN functions as a module for exploratory investigation of analysis results from multiple high-throughput assay technologies, including but not limited to: * Transcriptomics via expression microarrays or RNA-Seq * Genomics via SNP GWAS or array CGH * Proteomics via MS/MS peptide identifications * Epigenomics via DNA methylation, ChIP-on-Chip or ChIP-Seq * In-silico analysis of sequences or literature EGAN has been built using Cytoscape libraries for graph visualization and layout, and is comparable to DAVID, GSEA, Ingenuity IPA and Ariadne Pathway Studio. There are pre-collated EGAN networks available for human (Homo sapiens), mouse (Mus musculus), rat (Rattus norvegicus), chicken (Gallus gallus), zebrafish (Danio rerio), fruit fly (Drosophila melanogaster), nematode (Caenorhabditis elegans), mouse-ear cress (Arabidopsis thaliana), rice (Oryza sativa) and brewer's yeast (Saccharomyces cerevisiae). There is now an EGAN module available for GenePattern (human-only). Platform: Windows compatible, Mac OS X compatible, Linux compatible | gene, gene association, network, protein-protein interaction, pathway, interaction, annotation, signaling pathway, enrichment, cytoscape, visualization |
is listed by: 3DVC is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: Cytoscape has parent organization: UCSF Helen Diller Family Comprehensive Cancer Center Biostatistics Core |
NCI P30 CA92103 | PMID:19933825 | Free for academic use | nlx_149222 | SCR_008856 | Exploratory Gene Association Networks, Exploratory Gene Association Networks (EGAN) | 2026-02-14 02:01:48 | 8 | |||||
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Zebrafish RNAi Database Resource Report Resource Website |
Zebrafish RNAi Database (RRID:SCR_008965) | Zebrafish RNAi Database | data repository, storage service resource, organism-related portal, portal, data or information resource, service resource, topical portal | Community built zebrafish RNAi platform that contains plasmids, successfully targeted genes and shRNA sequences, and a forum for discussion. This is a true community platform with users who add data, modify entiries, request features and share using the discussion board. | plasmid, gene, shrna sequence, rnai, method | has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; | nlx_152032 | SCR_008965 | 2026-02-14 02:01:39 | 0 | |||||||||
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WebGestalt: WEB-based GEne SeT AnaLysis Toolkit Resource Report Resource Website 1000+ mentions |
WebGestalt: WEB-based GEne SeT AnaLysis Toolkit (RRID:SCR_006786) | WebGestalt | data access protocol, software resource, web service, web application | Web based gene set analysis toolkit designed for functional genomic, proteomic, and large-scale genetic studies from which large number of gene lists (e.g. differentially expressed gene sets, co-expressed gene sets etc) are continuously generated. WebGestalt incorporates information from different public resources and provides a way for biologists to make sense out of gene lists. This version of WebGestalt supports eight organisms, including human, mouse, rat, worm, fly, yeast, dog, and zebrafish. | proteomic, gene expression, genome wide association study, statistical analysis, functional genomics, protein protein interaction, pathway, regulatory module, analysis toolkit, web application |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: Entrez Gene is related to: KEGG is related to: Pathway Commons is related to: WikiPathways is related to: PheWAS Catalog is related to: webgestaltr has parent organization: Vanderbilt University; Tennessee; USA |
NIAAA U01 AA016662; NIAAA U01 AA013512; NIDA P01 DA015027; NIMH P50 MH078028; NIMH P50 MH096972; NCI U24 CA159988; NIGMS R01 GM088822 |
PMID:24233776 PMID:15980575 PMID:14975175 |
Free, Freely available | OMICS_02222, nif-0000-30622 | http://bioinfo.vanderbilt.edu/webgestalt/ | SCR_006786 | GOTM, Gene Ontology Tree Machine, WebGestalt2, WEB-based GEne SeT AnaLysis Toolkit, WebGestalt | 2026-02-14 02:01:23 | 2760 | ||||
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GeneInfoViz Resource Report Resource Website |
GeneInfoViz (RRID:SCR_005680) | GeneInfoViz | data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | GeneInfoViz is a web based tool for batch retrieval of gene function information, visualization of GO structure and construction of gene relation networks. It takes a input list of genes in the form of LocusLink ID, UniGeneID, gene symbol, or accession number and returns their functional genomic information. Based on the GO annotations of the given genes, GeneInfoViz allows users to visualize these genes in the DAG structure of GO, and construct a gene relation network at a selected level of the DAG. Platform: Online tool | gene network, gene ontology, visualization, gene, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of Tennessee Health Science Center; Tennessee; USA |
PMID:15724283 | Free for academic use | nlx_149121 | SCR_005680 | GeneInfoViz: Constructing and Visualizing Gene Relation Networks | 2026-02-14 02:01:10 | 0 | ||||||
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Zebrafish Anatomical Ontology Resource Report Resource Website 1+ mentions |
Zebrafish Anatomical Ontology (RRID:SCR_005887) | ZFA | data or information resource, ontology, controlled vocabulary | A structured controlled vocabulary of the anatomy and development of the Zebrafish (Danio rerio). It includes a list of structures, organized hierarchically into an ontology, with descriptions of each structure. The current version is being written by a consortium of researchers, each serving as an expert for a particular set of anatomical structures. Additional anatomical information derived from the current literature is provided by the ZFIN curation group. Development of a complete and uniform anatomical ontology for the zebrafish is vital to the success of zebrafish science. The anatomical ontology is necessary for: * Effective data dissemination and informatics. * A reference framework. * Interoperability. | anatomy, structure, anatomical structure, obo |
is used by: Teleost Anatomy Ontology is recommended by: Zebrafish Brain Atlas is listed by: BioPortal is related to: OBO is related to: Bgee: dataBase for Gene Expression Evolution has parent organization: Zebrafish Information Network (ZFIN) |
nlx_149454 | SCR_005887 | Zebrafish Anatomy and Development Ontology, ZFIN - Zebrafish Anatomical Ontology | 2026-02-14 02:01:01 | 4 | ||||||||
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NeuroMorpho.Org Resource Report Resource Website 50+ mentions |
NeuroMorpho.Org (RRID:SCR_002145) | data repository, storage service resource, data or information resource, service resource, database | Centrally curated inventory of digitally reconstructed neurons associated with peer-reviewed publications that contains some of the most complete axonal arborizations digitally available in the community. Each neuron is represented by a unique identifier, general information (metadata), the original and standardized ASCII files of the digital morphological reconstruction, and a set of morphometric features. It contains contributions from over 100 laboratories worldwide and is continuously updated as new morphological reconstructions are collected, published, and shared. Users may browse by species, brain region, cell type or lab name. Users can also download morphological reconstructions for research and analysis. Deposition and distribution of reconstruction files ultimately prevents data loss. Centralized curation and annotation aims at minimizing the effort required by data owners while ensuring a unified format. It also provides a one-stop entry point for all available reconstructions, thus maximizing data visibility and impact. | neuron, morphological reconstruction, morphometry, axonal arborization, digital neuronal reconstruction, neuronal reconstruction, neuronal morphology, data sharing, annotation, brain region, neocortex, digital reconstruction, neurogenetics, neurochemistry, neuroscience, neurology, FASEB list |
is used by: NIF Data Federation is used by: BICCN is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: DONE: Detection of Outlier NEurons is related to: NIF Literature is related to: Computational Neurobiology and Imaging Center is related to: Integrated Manually Extracted Annotation is related to: xyz2swc is related to: Allen Institute for Brain Science has parent organization: George Mason University; Virginia; USA is parent organization of: NeuroMorpho.Org species ontology is parent organization of: NeuroMorpho.Org species ontology old |
NINDS R01 NS39600; MURI ONR N000141010198 |
PMID:17728438 PMID:16552417 PMID:18949582 |
Free, Available for download, Freely available | nif-0000-00006, r3d100010107 | http://www.nitrc.org/projects/neuromorpho_org http://neuromorpho.org/ https://doi.org/10.17616/R3WW2K |
SCR_002145 | Neuro Morpho, NeuroMorpho.org, NeuroMorpho | 2026-02-14 02:00:22 | 96 | |||||
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Zebrafish Information Server Resource Report Resource Website |
Zebrafish Information Server (RRID:SCR_002237) | ZIS | data or information resource, organism-related portal, portal, topical portal | A portal to different zebrafish resources such as jobs, book, journals, database, meetings, and K-12 programs. Most information leads to ZFIN: The Zebrafish Model Organism Database. | database, job, k12 program, journal, monitor, zebrafish, book, meeting, method | has parent organization: University of South Carolina; South Carolina; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21003 | SCR_002237 | 2026-02-14 02:00:20 | 0 | ||||||||
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Ensembl Resource Report Resource Website 10000+ mentions |
Ensembl (RRID:SCR_002344) | data or information resource, database | Collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species. | collection, genome, dataset, database, vertebrate, eukaryotic, DNA, protein, sequence, search, automaticly, annotate, data, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: Animal QTLdb is used by: ChannelPedia is used by: Blueprint Epigenome is used by: HmtPhenome lists: Ensembl Covid-19 is listed by: OMICtools is listed by: Biositemaps is listed by: re3data.org is listed by: LabWorm is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Ensembl Genomes is related to: GermOnline is related to: CandiSNPer is related to: Human Splicing Finder is related to: NGS-SNP is related to: Sanger Mouse Resources Portal is related to: DECIPHER is related to: Ensembl Genomes is related to: PeptideAtlas is related to: AnimalTFDB is related to: Bgee: dataBase for Gene Expression Evolution is related to: FlyMine is related to: Rat Gene Symbol Tracker is related to: UniParc at the EBI is related to: go-db-perl is related to: UniParc is related to: g:Profiler is related to: RIKEN integrated database of mammals is related to: VBASE2 is related to: p300db is related to: ShinyGO has parent organization: European Bioinformatics Institute has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom is parent organization of: Ensembl Metazoa is parent organization of: Ensembl Variation is parent organization of: Pre Ensembl is parent organization of: Variant Effect Predictor is parent organization of: Ensembl Bacteria is parent organization of: Ensembl Plants is parent organization of: Ensembl Fungi is parent organization of: Ensembl Protists is parent organization of: Ensembl Genome Browser works with: Genotate works with: CellPhoneDB works with: Open Regulatory Annotation Database works with: Database of genes related to Repeat Expansion Diseases works with: TarBase |
Wellcome Trust ; EMBL ; European Union ; FP7 ; FP6 ; MRC ; NHGRI ; BBSRC |
PMID:24316576 PMID:23203987 |
nif-0000-21145, OMICS_01647, biotools:ensembl, r3d100010228 | https://bio.tools/ensembl https://sources.debian.org/src/ensembl/ https://doi.org/10.17616/R39K5B |
SCR_002344 | ENSEMBL | 2026-02-14 02:00:23 | 11652 | ||||||
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MONARCH Initiative Resource Report Resource Website 10+ mentions |
MONARCH Initiative (RRID:SCR_000824) | Monarch | data or information resource, database | Repository of information about model organisms, in vitro models, genes, pathways, gene expression, protein and genetic interactions, orthology, disease, phenotypes, publications, and authors, and ability to navigate multi-scale spatial and temporal phenotypes across in vivo and in vitro model systems in context of genetic and genomic data, using semantics and statistics. Discovery system provides basic and clinical science researchers, informaticists, and medical professionals with integrated interface and set of discovery tools to reveal genetic basis of disease, facilitate hypothesis generation, and identify novel candidate drug targets. Database that indexes authoritative information on experimental models of disease from MGI, RGD and ZFIN. | disease, animal model, phenotype, model organism, in vitro model, gene, pathway, gene expression, protein interaction, genetic interaction, orthology, disease, publication, author, genetic, genomic, model system, genotype, drug, in vivo model |
uses: Animal QTLdb uses: Ensembl Variation uses: Human Phenotype Ontology is used by: NIF Data Federation is related to: Mouse Genome Informatics (MGI) is related to: Rat Genome Database (RGD) is related to: Zebrafish Information Network (ZFIN) is related to: openSNP is related to: Ancora is related to: PhenoGen Informatics is related to: Lifespan Observations Database has parent organization: Oregon Health and Science University; Oregon; USA is parent organization of: monarch-ontologies |
NIH Office of the Director R24 OD011883 | PMID:26269093 | Free, Freely available | r3d100011594, nlx_152525, SCR_001373, nlx_152748 | https://orip.nih.gov/comparative-medicine/programs/genetic-biological-and-information-resources https://doi.org/10.17616/R31M09 |
SCR_000824 | MONARCH Integrated Disease Model, MONARCH Integrated Disease Models View, MONARCH Disease Models View, The MONARCH Initiative | 2026-02-14 01:59:54 | 12 |
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