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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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GermOnline Resource Report Resource Website 10+ mentions |
GermOnline (RRID:SCR_002807) | GermOnline | data or information resource, database | Cross-species microarray expression database focusing on high-throughput expression data relevant for germline development, meiosis and gametogenesis as well as the mitotic cell cycle. The database contains a unique combination of information: 1) High-throughput expression data obtained with whole-genome high-density oligonucleotide microarrays (GeneChips). 2) Sample annotation (mouse over the sample name and click on it) using the Multiomics Information Management and Annotation System (MIMAS 3.0). 3) In vivo protein-DNA binding data and protein-protein interaction data (available for selected species). 4) Genome annotation information from Ensembl version 50. 5) Orthologs are identified using data from Ensembl and OMA and linked to each other via a section in the report pages. The portal provides access to the Saccharomyces Genomics Viewer (SGV) which facilitates online interpretation of complex data from experiments with high-density oligonucleotide tiling microarrays that cover the entire yeast genome. The database displays only expression data obtained with high-density oligonucleotide microarrays (GeneChips). | fertility, development, germline, microarray, annotation, in vivo, protein-dna binding, protein-protein interaction, genome, ortholog, high-density oligonucleotide microarray, gene expression, genome annotation, gene orthology, genechip, tiling array, development, meiosis, gametogenesis, mitotic cell cycle, data set, data repository, bio.tools |
is listed by: 3DVC is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Ensembl is related to: OMA Browser has parent organization: National Institute of Health and Medical Research; Rennes; France |
Swiss Institute of Bioinformatics ; bioinformatics platform of Biogenouest ; National Institute of Health and Medical Research; Rennes; France ; University of Rennes 1; Rennes; France |
PMID:21149299 | Free, Acknowledgement requested, The community can contribute to this resource | biotools:germonline, nif-0000-02906 | https://bio.tools/germonline | SCR_002807 | 2025-04-03 11:02:09 | 17 | |||||
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Zebrafish Information Network (ZFIN) Resource Report Resource Website 500+ mentions |
Zebrafish Information Network (ZFIN) (RRID:SCR_002560) | ZFIN | data or information resource, database | Model organism database that serves as central repository and web-based resource for zebrafish genetic, genomic, phenotypic and developmental data. Data represented are derived from three primary sources: curation of zebrafish publications, individual research laboratories and collaborations with bioinformatics organizations. Data formats include text, images and graphical representations.Serves as primary community database resource for laboratory use of zebrafish. Developed and supports integrated zebrafish genetic, genomic, developmental and physiological information and link this information extensively to corresponding data in other model organism and human databases. | expression, gene, anatomy, development, disease, genomic, model, molecular, mutant, neuronal, organism, phenotype, physiological, synteny, zebrafish, gene expression, genome sequence, molecular neuroanatomy resource, genotype, anatomical structure, publication, genome, image collection, gold standard, bio.tools, FASEB list |
uses: InterMOD is used by: NIF Data Federation is used by: Resource Identification Portal is used by: Morpholino Database is used by: Integrated Animals is used by: NIH Heal Project is recommended by: Resource Identification Portal is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: OMICtools is listed by: InterMOD is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: AmiGO is related to: Phenoscape Knowledgebase is related to: MONARCH Initiative is related to: Bgee: dataBase for Gene Expression Evolution is related to: NIH Data Sharing Repositories is related to: HomoloGene is related to: Zebrafish International Resource Center is related to: Integrated Manually Extracted Annotation is related to: Zebrafish Genome Project has parent organization: University of Oregon; Oregon; USA is parent organization of: ZFIN Antibody Database is parent organization of: Zebrafish Anatomical Ontology is parent organization of: ZFIN Protocol Wiki is parent organization of: ZFIN Antibody Wiki |
NHGRI P41 HG002659; NHGRI R01 HG004834 |
PMID:23074187 PMID:21036866 PMID:16381936 |
Restricted | OMICS_01666, nif-0000-21427, biotools:zfin, SCR_017504 | http://zfin.org/ZFIN/misc_html/tips.html#newrecord https://wiki.zfin.org/display/general/ZFIN+Data+Submissions https://bio.tools/zfin |
SCR_002560 | Zebrafish Database, The Zebrafish Model Organism Database, Zebra Model Organism Database, ZebraFish Information Network, ZFIN | 2025-04-03 11:01:46 | 841 | ||||
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HomoloGene Resource Report Resource Website 100+ mentions |
HomoloGene (RRID:SCR_002924) | HomoloGene | service resource, data or information resource, database | Automated system for constructing putative homology groups from complete gene sets of wide range of eukaryotic species. Databse that provides system for automatic detection of homologs, including paralogs and orthologs, among annotated genes of sequenced eukaryotic genomes. HomoloGene processing uses proteins from input organisms to compare and sequence homologs, mapping back to corresponding DNA sequences. Reports include homology and phenotype information drawn from Online Mendelian Inheritance in Man, Mouse Genome Informatics, Zebrafish Information Network, Saccharomyces Genome Database and FlyBase. | homolog, paralog, ortholog, genome, gene, protein, protein alignment, phenotype, conserved domain, homology, amino acid sequence, cell, dna, gold standard |
is used by: NIF Data Federation is used by: Nowomics is used by: MitoMiner is listed by: OMICtools is listed by: re3data.org is related to: OMIM is related to: Mouse Genome Informatics (MGI) is related to: Zebrafish Information Network (ZFIN) is related to: SGD is related to: FlyBase is related to: ProbeMatchDB 2.0 is related to: Biomine is related to: Consensus CDS has parent organization: NCBI |
PMID:23193264 | Free, Freely availalbe | nif-0000-02975, OMICS_01544 | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene | SCR_002924 | NCBI HomoloGene | 2025-04-03 11:02:19 | 403 | |||||
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MapViewer Resource Report Resource Website 100+ mentions |
MapViewer (RRID:SCR_003092) | Map Viewer | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023. Database that provides special browsing capabilities for a subset of organisms in Entrez Genomes. Map Viewer allows users to view and search an organism's complete genome, display chromosome maps, and zoom into progressively greater levels of detail, down to the sequence data for a region of interest. If multiple maps are available for a chromosome, it displays them aligned to each other based on shared marker and gene names, and, for the sequence maps, based on a common sequence coordinate system. | genome, mapping, sequencing, chromosome |
is listed by: OMICtools is related to: NCBI Genome is related to: Consensus CDS has parent organization: NCBI |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00921, nif-0000-03103 | SCR_003092 | Entrez Map Viewer, NCBI Map Viewer | 2025-04-03 11:02:40 | 240 | |||||||
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Information Hyperlinked Over Proteins Resource Report Resource Website 10+ mentions |
Information Hyperlinked Over Proteins (RRID:SCR_004829) | iHOP | service resource, data or information resource, database | Information system that provides a network of concurring genes and proteins extends through the scientific literature touching on phenotypes, pathologies and gene function. It provides this network as a natural way of accessing millions of PubMed abstracts. By using genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed can be converted into one navigable resource, bringing all advantages of the internet to scientific literature research. Moreover, this literature network can be superimposed on experimental interaction data (e.g., yeast-two hybrid data from Drosophila melanogaster and Caenorhabditis elegans) to make possible a simultaneous analysis of new and existing knowledge. The network contains half a million sentences and 30,000 different genes from humans, mice, D. melanogaster, C. elegans, zebrafish, Arabidopsis thaliana, yeast and Escherichia coli. | phenotype, gene, protein, interaction, pathology, physiology, gene network, network, literature, gene function, text-mining, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: PubMed has parent organization: Autonomous University of Madrid; Madrid; Spain |
European Union IST-2001- 32688; European Union QLRT-2001-00015 |
PMID:15226743 | Creative Commons Attribution-NoDerivs License, Works v3 | biotools:ihop, nif-0000-00232, OMICS_01185 | https://bio.tools/ihop | SCR_004829 | iHOP - Information Hyperlinked over Proteins | 2025-04-03 11:03:42 | 24 | ||||
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Boston Children's Hospital Center of Excellence in Molecular Hematology Resource Report Resource Website |
Boston Children's Hospital Center of Excellence in Molecular Hematology (RRID:SCR_015348) | data or information resource, portal, service resource, resource, access service resource, topical portal, disease-related portal | Research center investigating molecular hematology through mouse and zebrafish models. | hematology research, hematology research center, online portal |
is listed by: NIDDK Information Network (dkNET) is parent organization of: Boston Children's Hospital Center of Excellence in Molecular Hematology Zebrafish Core is parent organization of: Boston Children's Hospital Center of Excellence in Molecular Hematology Stem Cell Engineering and Analysis Core is parent organization of: Boston Children's Hospital Center of Excellence in Molecular Hematology Mouse Embryonic Stem(ES) Cell and Gene Targeting Core has organization facet: Boston Children's Hospital Center of Excellence in Molecular Hematology Mouse Embryonic Stem(ES) Cell and Gene Targeting Core has organization facet: Boston Children's Hospital Center of Excellence in Molecular Hematology Zebrafish Core has organization facet: Boston Children's Hospital Center of Excellence in Molecular Hematology Stem Cell Engineering and Analysis Core is organization facet of: Hematology Centers |
NIDDK U54DK110805 | Available to the research community | SCR_015348 | 2025-04-03 11:11:32 | 0 | |||||||||
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Zebrafish Atlas Resource Report Resource Website 1+ mentions |
Zebrafish Atlas (RRID:SCR_006722) | Zebrafish Atlas | reference atlas, data or information resource, atlas | Atlas containing 2- and 3-dimensional, anatomical reference slides of the lifespan of the zebrafish to support research and education worldwide. Hematoxylin and eosin histological slides, at various points in the lifespan of the zebrafish, have been scanned at 40x resolution and are available through a virtual slide viewer. 3D models of the organs are reconstructed from plastic tissue sections of embryo and larvae. The size of the zebrafish, which allows sections to fall conveniently within the dimensions of the common 1 x 3 glass slide, makes it possible for this anatomical atlas to become as high resolution as for any vertebrate. That resolution, together with the integration of histology and organ anatomy, will create unique opportunities for comparisons with both smaller and larger model systems that each have their own strengths in research and educational value. The atlas team is working to allow the site to function as a scaffold for collaborative research and educational activity across disciplines and model organisms. The Zebrafish Atlas was created to answer a community call for a comprehensive, web-based, anatomical and pathological atlas of the zebrafish, which has become one of the most widely used vertebrate animal models globally. The experimental strengths of zebrafish as a model system have made it useful for a wide range of investigations addressing the missions of the NIH and NSF. The Zebrafish Atlas provides reference slides for virtual microscopic viewing of the zebrafish using an Internet browser. Virtual slide technology allows the user to choose their own field of view and magnification, and to consult labeled histological sections of zebrafish. We are planning to include a complete set of embryos, larvae, juveniles, and adults from approximately 25 different ages. Future work will also include a variety of comparisons (e.g. normal vs. mutant, normal vs. diseased, multiple stages of development, zebrafish with other organisms, and different types of cancer). | embryo, eosin, expression, genetic, adult, anatomical, anatomy, cancer, development, hematoxylin, histological, histology, juvenile, larvae, lifespan, model, slide, sagittal, coronal, transverse, stage, embryonic zebrafish, juvenile zebrafish, immature zebrafish, larval zebrafish, young zebrafish, adult zebrafish | has parent organization: Pennsylvania State University | Normal, Mutant, Cancer | NCRR | nif-0000-24352 | SCR_006722 | Penn State Zebrafish Atlas, Zebrafish Atlas - A Lifespan Atlas of the Zebrafish, PSU Zebrafish Atlas | 2025-04-03 11:05:35 | 3 | ||||||
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Integrated Gene-Disease Interaction Resource Report Resource Website |
Integrated Gene-Disease Interaction (RRID:SCR_006173) | data or information resource, database | Virtual database currently indexing interaction between genes and diseases from Online Mendelian Inheritance in Man (OMIM) and Comparative Toxicogenomics Database (CTD). | gene, phenotype, disease, interaction, integrated, database |
is used by: NIF Data Federation is related to: OMIM is related to: Comparative Toxicogenomics Database (CTD) has parent organization: Integrated |
NIDA ; NIH Blueprint for Neuroscience Research |
Data are licensed by their respective owners, Use and distribution is subject to the Terms of Use by the original resource | nlx_151674 | https://legacy.neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-7 http://neuinfo.org/nif/nifgwt.html?query=nlx_151674, https://www.neuinfo.org/mynif/search.php?q=*&t=indexable&nif=nlx_151674-1, https://neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-7 | SCR_006173 | Gene-Disease Interaction, NIF Integrated Gene-Disease Interaction, Integrated GDI, NIF Integrated Gene-Disease Interaction View, NIF Gene-Disease Interaction, Integrated Gene-Disease Interaction View | 2025-04-03 11:05:07 | 0 | ||||||
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BioGPS: The Gene Portal Hub Resource Report Resource Website 500+ mentions |
BioGPS: The Gene Portal Hub (RRID:SCR_006433) | BioGPS | data or information resource, database | An extensible and customizable gene annotation portal that emphasizes community extensibility and user customizability. It is a complete resource for learning about gene and protein function. Community extensibility reflects a belief that any BioGPS user should be able to add new content to BioGPS using the simple plugin interface, completely independently of the core developer team. User customizability recognizes that not all users are interested in the same set of gene annotation data, so the gene report layouts enable each user to define the information that is most relevant to them. Currently, BioGPS supports eight species: Human (Homo sapiens), Mouse (Mus musculus), Rat (Rattus norvegicus), Fruitfly (Drosophila melanogaster), Nematode (Caenorhabditis elegans), Zebrafish (Danio rerio), Thale-cress (Arabidopsis thaliana), Frog (Xenopus tropicalis), and Pig (Sus scrofa). BioGPS presents data in an ortholog-centric format, which allows users to display mouse plugins next to human ones. Our data for defining orthologs comes from NCBI's HomoloGene database. | gene, ortholog, plug-in, report, literature, genetics, expression, reagent, protein, pathway, snp, genomics, gene annotation, function, FASEB list |
is listed by: Biositemaps is related to: bioDBcore is related to: aGEM has parent organization: Scripps Research Institute |
Novartis Research Foundation ; NIGMS R01GM083924 |
PMID:19919682 | Free, The community can contribute to this resource | nif-0000-10168 | http://biogps.gnf.org/ | SCR_006433 | 2025-04-03 11:05:29 | 683 | |||||
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ECgene: Gene Modeling with Alternative Splicing Resource Report Resource Website 10+ mentions |
ECgene: Gene Modeling with Alternative Splicing (RRID:SCR_007634) | ECgene | data or information resource, database | Database of functional annotation for alternatively spliced genes. It uses a gene-modeling algorithm that combines the genome-based expressed sequence tag (EST) clustering and graph-theoretic transcript assembly procedures. It contains genome, mRNA, and EST sequence data, as well as a genome browser application. Organisms included in the database are human, dog, chicken, fruit fly, mouse, rhesus, rat, worm, and zebrafish. Annotation is provided for the whole transcriptome, not just the alternatively spliced genes. Several viewers and applications are provided that are useful for the analysis of the transcript structure and gene expression. The summary viewer shows the gene summary and the essence of other annotation programs. The genome browser and the transcript viewer are available for comparing the gene structure of splice variants. Changes in the functional domains by alternative splicing can be seen at a glance in the transcript viewer. Two unique ways of analyzing gene expression is also provided. The SAGE tags deduced from the assembled transcripts are used to delineate quantitative expression patterns from SAGE libraries available publicly. The cDNA libraries of EST sequences in each cluster are used to infer qualitative expression patterns. | est cluster, genome, alternative splicing, splice, gene, mrna, est, annotation, gene modeling, structure, function, gene expression, transcript, genome browser, differential expression, snp |
is listed by: OMICtools is related to: Gene Ontology has parent organization: Ewha Womans University; Seoul; South Korea |
PMID:17132829 PMID:15805497 PMID:15608289 |
nif-0000-02780, OMICS_01884 | http://genome.ewha.ac.kr/ECgene/ | SCR_007634 | ECgene - Genome Annotation for Alternative Splicing | 2025-04-03 11:06:15 | 12 | ||||||
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Genomicus Resource Report Resource Website 10+ mentions |
Genomicus (RRID:SCR_011791) | Genomicus | data or information resource, database | A genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time. | genome, gene, synteny, browser, FASEB list | is listed by: OMICtools | PMID:23193262 | OMICS_00914 | SCR_011791 | 2025-04-03 11:09:02 | 48 | ||||||||
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HomeoDB Resource Report Resource Website 10+ mentions |
HomeoDB (RRID:SCR_015492) | data or information resource, database | Database of homeobox genes in humans, mice, chickens, frogs, zebrafishes, amphioxuses, fruitflies, beetles, honeybees, and nematodes. | homeobox gene, homeobox gene database, gene database |
has parent organization: Peking University; Beijing; China has parent organization: University of Oxford; Oxford; United Kingdom |
Marie Curie International Incoming Fellowship | Open source | SCR_015492 | 2025-04-03 11:11:44 | 19 | |||||||||
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Dfam Resource Report Resource Website 50+ mentions |
Dfam (RRID:SCR_021168) | data or information resource, database | Open collection of Transposable Element DNA sequence alignments, hidden Markov Models, consensus sequences, and genome annotations.Dfam 3.2 provides early access to uncurated, de novo generated families. | Transposable Element, DNA sequence alignments, hidden Markov Models, consensus sequences, genome annotations | is related to: RepeatModeler | NHGRI U24 HG010136; NHGRI R01 HG002939 |
DOI:10.1186/s13100-020-00230-y | Free, Freely available | SCR_021168 | Dfam 3.2 | 2025-04-03 11:15:10 | 67 | |||||||
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Zebrafish Neuroscience Research Consortium Resource Report Resource Website |
Zebrafish Neuroscience Research Consortium (RRID:SCR_000298) | ZNRC | training resource, group | A group of scientists who collaborate and promote zebrafish neuroscience research. The consortium has opportunities for networking, scholarly publications and zebrafish-related symposia and conferences. The consortium is a supporter of the Zebrafish Neurophenome Project (ZNP), an initiative for a database of zebrafish behavioral and physiological data in an online, open source format. | zebrafish, consortium, research, publication, scholar, neuroscience, behavioral activity | is parent organization of: Zebrafish Neurophenome Project Database | Available to the research community, Interested labs may join | nlx_151974 | SCR_000298 | Zebrafish Neuroscience Research Consortium (ZNRC) | 2025-04-03 11:00:05 | 0 | |||||||
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Duke O'Brien Center for Kidney Research Animal Models Core Resource Report Resource Website |
Duke O'Brien Center for Kidney Research Animal Models Core (RRID:SCR_015267) | service resource, resource, access service resource, core facility | Core facility that provides access to a range of experimental models of kidney, heart and vascular diseases. It also provides comprehensive phenotyping services for kidney functions, blood pressure and other cardiovascular functions. | animal model, experimental kidney model, experimental heart model, experimental vascular model |
is listed by: NIDDK Information Network (dkNET) has parent organization: Duke O'Brien Center for Kidney Research has parent organization: Duke University School of Medicine; North Carolina; USA has parent organization: Duke University; North Carolina; USA is organization facet of: Duke O'Brien Center for Kidney Research |
kidney disease, heart disease, hypertension, muscle disease | NIDDK P30DK096493 | Available to the research community | SCR_015267 | 2025-04-03 11:11:25 | 0 | ||||||||
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UAB Hepatorenal Fibrocystic Diseases Core Center Engineered Models Resource Resource Report Resource Website |
UAB Hepatorenal Fibrocystic Diseases Core Center Engineered Models Resource (RRID:SCR_015310) | service resource, resource, access service resource, core facility | Core whose goals include Generation of New Animal and Cell Models of HRFDs, to establish In Vivo Biosensors to Study Signaling Pathways Involved in HRFD Ciliopathies, and to generate and distribute HRFD Related Biologicals to the Center?s Investigator Base. | HRFD genes, engineered models |
is listed by: NIDDK Information Network (dkNET) has parent organization: UAB Hepatorenal Fibrocystic Diseases Core Center is organization facet of: UAB Hepatorenal Fibrocystic Diseases Core Center |
Hepatorenal Fibrocystic Disease | NIDDK P30DK074038 | Available to the research community, Acknowledgement requested | SCR_015310 | 2025-04-03 11:11:29 | 0 | ||||||||
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Translational Polycystic Kidney Disease (PKD) Center at Mayo Clinic Rochester Model Systems Core Resource Report Resource Website |
Translational Polycystic Kidney Disease (PKD) Center at Mayo Clinic Rochester Model Systems Core (RRID:SCR_015312) | service resource, resource, access service resource, core facility | Core that makes available PKD model systems and technologies to PKD researchers at Mayo and at other institutions. Its services include C. elegans PKD-targeted services, Zebrafish PKD-targeted services, and Rodent PKD-targeted services. | model systems, c. elegans, zebrafish, rodents, PKD genes |
is listed by: NIDDK Information Network (dkNET) has parent organization: Mayo Clinic Minnesota; Minnesota; USA has parent organization: Translational Polycystic Kidney Disease (PKD) Center at Mayo Clinic Rochester is organization facet of: Translational Polycystic Kidney Disease (PKD) Center at Mayo Clinic Rochester |
Polycystic Kidney Disease | NIDDK P30DK090728 | Available to the research community | SCR_015312 | 2025-04-03 11:11:29 | 0 |
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