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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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OMIM Resource Report Resource Website 5000+ mentions |
OMIM (RRID:SCR_006437) | OMIM, MIM | catalog, data or information resource, database | Online catalog of human genes and genetic disorders, for clinical features, phenotypes and genes. Collection of human genes and genetic phenotypes, focusing on relationship between phenotype and genotype. Referenced overviews in OMIM contain information on all known mendelian disorders and variety of related genes. It is updated daily, and entries contain copious links to other genetics resources. | gene, genetics, phenotype, genotype, genetic loci, mutation, clinical, trait, disorder, umls, ontology, gold standard, FASEB list |
is used by: Human Phenotype Ontology is used by: NIF Data Federation is used by: MitoMiner is used by: Schizo-Pi is used by: GEMINI is used by: MARRVEL is used by: HmtPhenome is listed by: BioPortal is listed by: OMICtools is related to: HomoloGene is related to: TopoSNP is related to: phenomeNET is related to: Integrated Gene-Disease Interaction is related to: OMIA - Online Mendelian Inheritance in Animals is related to: Europhenome Mouse Phenotyping Resource is related to: Homophila is related to: Biomine is related to: MalaCards is related to: PhenoTips is related to: KOBAS is related to: Integrated Manually Extracted Annotation is related to: aGEM is related to: biomaRt has parent organization: Johns Hopkins University School of Medicine; Baltimore, Maryland; USA has parent organization: NCBI works with: Human Mouse Disease Connection works with: Database of genes related to Repeat Expansion Diseases |
Genetic disorder, Mendelian disorder, Developmental disorder | PMID:22477700 PMID:22470145 PMID:21472891 PMID:19728286 PMID:18842627 PMID:18428346 PMID:17642958 PMID:17357067 PMID:15608251 PMID:15360913 PMID:11752252 PMID:10845565 PMID:10612823 PMID:9805561 PMID:7937048 PMID:1867277 |
Restricted | nif-0000-03216, r3d100010416, OMICS_00278 | http://www.ncbi.nlm.nih.gov/sites/entrez?db=omim, http://www.ncbi.nlm.nih.gov/Omim/, http://purl.bioontology.org/ontology/OMIM, https://doi.org/10.17616/R3188W | SCR_006437 | Online Mendelian Inheritance in Man, OMIM - Online Mendelian Inheritance in Man, MIM, The Online Mendelian Inheritance in Man Morbid Map | 2026-08-03 09:33:04 | 5456 | ||||
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Johns Hopkins University School of Medicine; Baltimore, Maryland; USA Resource Report Resource Website |
Johns Hopkins University School of Medicine; Baltimore, Maryland; USA (RRID:SCR_000973) | JHM | university | Johns Hopkins University School of Medicine is a medical graduate institution that provides physician, clinical fellowship and residency programs. | institution, university, baltimore, maryland, usa, medicine, medical school, med school, physician, clinical fellowship, fellowship, residency |
uses: Scizzle has parent organization: Johns Hopkins University; Maryland; USA is parent organization of: SAGE GENIE is parent organization of: Johns Hopkins NIMH Research Center Novel Therapeutics of HIV-associated Cognitive Disorders is parent organization of: Johns Hopkins University Pharmacology is parent organization of: DermAtlas. is parent organization of: DTI White Matter Atlas is parent organization of: Johns Hopkins Laboratory of Brain Anatomical MRI is parent organization of: OMIM is parent organization of: Johns Hopkins University Neuroscience is parent organization of: Johns Hopkins Alzheimer's Disease Research Center is parent organization of: Precursors of Premature Disease and Death is parent organization of: kmer-SVM is parent organization of: Johns Hopkins University - University of Maryland Diabetes Research Center Health and Populations Science Core is parent organization of: Johns Hopkins University - University of Maryland Diabetes Research Center Gene Editing Core is parent organization of: Johns Hopkins University - University of Maryland Diabetes Research Center Cell Biology Core is parent organization of: Johns Hopkins University - University of Maryland Diabetes Research Center Administrative Core is parent organization of: Johns Hopkins University - University of Maryland Diabetes Research Center is parent organization of: PhenoDB is parent organization of: Johns Hopkins Medical Institute Clinical and Translational Research Laboratory Core Facility is parent organization of: Johns Hopkins University School of Medicine Mass Spectrometry and Proteomics Core Facility is parent organization of: Johns Hopkins Reference Histology Core Facility is parent organization of: Johns Hopkins University School of Medicine Center for Proteomics Discovery CPD Core Facility |
, Wikidata: Q50363516, GRID: grid.469474.c, ISNI: 0000 0000 8617 4175, nlx_76328 | https://ror.org/037zgn354 | SCR_000973 | , Johns Hopkins Medicine, Johns Hopkins University School of Medicine (JHM), Johns Hopkins University School of Medicine | 2026-08-01 12:01:20 | 0 | |||||||
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NCBI Resource Report Resource Website 10000+ mentions |
NCBI (RRID:SCR_006472) | NCBI | nonprofit organization | A portal to biomedical and genomic information. NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information for the better understanding of molecular processes affecting human health and disease. | biomedical, genomic, molecular biology, health, disease, database, computational biology, bio.tools |
is used by: NIF Data Federation is listed by: NIDDK Information Network (dkNET) is listed by: bio.tools is listed by: Debian is related to: AmiGO is related to: NCBI Viral Genomes is related to: Clone DB is related to: PubReader is related to: OMIA - Online Mendelian Inheritance in Animals is related to: European Nucleotide Archive (ENA) is related to: Plant Co-expression Annotation Resource is related to: METAGENOTE is related to: Phyutility is related to: CaspBase is related to: Prokaryotic Genomes Automatic Annotation Pipeline has parent organization: National Library of Medicine is parent organization of: MedGen is parent organization of: dbSTS is parent organization of: PubMed Health is parent organization of: BLASTP is parent organization of: GQuery is parent organization of: BLASTN is parent organization of: GTEx eQTL Browser is parent organization of: BLASTX is parent organization of: Homology Maps Page is parent organization of: PEDHUNTER is parent organization of: Conserved Domain Database is parent organization of: NCBI Genome Survey Sequences Database is parent organization of: High Throughput Genomic Sequences Division is parent organization of: AceView is parent organization of: dbMHC is parent organization of: dbSNP is parent organization of: Entrez Gene is parent organization of: NCBI Genome is parent organization of: NCBI database of Genotypes and Phenotypes (dbGap) is parent organization of: GenBank is parent organization of: International HapMap Project is parent organization of: IgBLAST is parent organization of: Lowes Syndrome Mutation Database is parent organization of: HomoloGene is parent organization of: Influenza Virus Resource is parent organization of: Distant Regulatory Elements is parent organization of: e-PCR is parent organization of: MapViewer is parent organization of: Primer-BLAST is parent organization of: dbVar is parent organization of: NCBI Taxonomy is parent organization of: NCBI Protein Database is parent organization of: Gene Reference into Function is parent organization of: Protein Clusters is parent organization of: RefSeq is parent organization of: TPA is parent organization of: GENSAT at NCBI - Gene Expression Nervous System Atlas is parent organization of: COBALT: Constraint-based Multiple Alignment Tool is parent organization of: PubMed Central is parent organization of: UniLib is parent organization of: NCBI Structure is parent organization of: PubChem is parent organization of: Anopheles gambiae (African malaria mosquito) genome view is parent organization of: UniGene is parent organization of: NLM Catalog is parent organization of: Entrez GEO Profiles is parent organization of: Nucleotide database is parent organization of: NCBI BioSystems Database is parent organization of: CBLAST is parent organization of: NCBI BioProject is parent organization of: NCBI Probe is parent organization of: PubMed is parent organization of: NCBI BioSample is parent organization of: NCBI Nucleotide is parent organization of: NCBI Structure: Cn3D is parent organization of: NCBI BLAST is parent organization of: IBIS: Inferred Biomolecular Interactions Server is parent organization of: NCBI Sequence Read Archive (SRA) is parent organization of: Gene Expression Omnibus (GEO) is parent organization of: NCBI Popset is parent organization of: PIE the search is parent organization of: Genetic Testing Registry is parent organization of: NCBI Resource List is parent organization of: NCBI dbRBC is parent organization of: NCBI YouTube Channel is parent organization of: NCBI Epigenomics is parent organization of: ClinVar is parent organization of: Genome Reference Consortium is parent organization of: GeneReviews is parent organization of: Molecular Imaging and Contrast Agent Database is parent organization of: Consensus CDS is parent organization of: UniSTS is parent organization of: HIV-1 Human Protein Interaction Database is parent organization of: Assay Guidance Manual is parent organization of: Bookshelf is parent organization of: COG is parent organization of: Gene Expression Omnibus is parent organization of: Molecular Modelling DataBase is parent organization of: Organelle Genome Resources is parent organization of: SKY/M-FISH/CGH is parent organization of: dbEST is parent organization of: JournalReview.org is parent organization of: NCBI GenBank via FTP is parent organization of: PubChem Compound is parent organization of: Molecular Modeling DataBase is parent organization of: Vector Alignment Search Tool is parent organization of: PubChem BioAssay is parent organization of: NCBI Genome Workbench is parent organization of: TBLASTN is parent organization of: TBLASTX is parent organization of: Mega BLAST is parent organization of: Genetic Codes is parent organization of: HIV-1, Human Protein Interaction Database is parent organization of: PubReader is parent organization of: PubChem Substance is parent organization of: OMIA - Online Mendelian Inheritance in Animals is parent organization of: OMIM is parent organization of: 1000 Genomes: A Deep Catalog of Human Genetic Variation is parent organization of: GeneTests is parent organization of: NCBI Genome Survey Sequences Database is parent organization of: MagicBlast is parent organization of: RefSeq is parent organization of: Sequin is parent organization of: Batch Entrez is parent organization of: Entrez is parent organization of: tbl2asn is parent organization of: Whole Genome Shotgun (WGS) Project is parent organization of: Digital Differential Display (DDD) is parent organization of: BLASTClust is parent organization of: PASC is parent organization of: Open Reading Frame Finder is parent organization of: Genotyping works with: Human Mouse Disease Connection works with: A plasmid Editor works with: Database of genes related to Repeat Expansion Diseases |
Public, The community can contribute to this resource | nif-0000-00139, biotools:ncbi_resources | https://bio.tools/ncbi_resources | http://www.ncbi.nih.gov/ | SCR_006472 | National Center for Biotechnology Information, NCBI - National Center for Biotechnology Information | 2026-08-01 12:03:10 | 25993 | |||||
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PhenoTips Resource Report Resource Website 10+ mentions |
PhenoTips (RRID:SCR_006340) | PhenoTips | software resource, software application | A software tool providing a Web interface and a database back-end for collecting clinical symptoms and physical findings observed in patients with genetic disorders. The main goals of this software are * To allow for collecting patient data in standard formats, enabling effortless data exchange and automated search in annotated gene and disease databases, and * To provide advanced functionalities and a friendly user interface that help reduce the clinician''''s workload, permitting seamless use of this application within the clinician''''s routine. PhenoTips uses the Human Phenotype Ontology (HPO) to express clinical phenotypes, and provides a friendly interface with error-tolerant, predictive search of phenotypic descriptions. PhenoTips closely mirrors clinician workflows: observations can be recorded directly during the patient encounter, and the interface is compatible with any device that runs a modern Web browser. The clinician can record demographic information, family history, medical history, various standard measurements, phenotypic abnormalities detected in the patient, pertinent indications that were not observed and that can be helpful for differential diagnosis, relevant images depicting manifestations of the patient''''s disorders, and additional notes for each of these categories. The software automatically plots growth curves, selects phenotypes reflecting abnormal measurements, instantly finds OMIM disorders matching the phenotypic description and suggests other symptoms to investigate in order to reach a more accurate diagnosis. | clinical symptom, physical finding, clinical, phenotype, demographic information, family history, medical history, standard measurement, indication, image, note, growth curve |
is related to: Human Phenotype Ontology is related to: OMIM has parent organization: University of Toronto; Ontario; Canada |
Genetic disorder | Free | nlx_152049 | SCR_006340 | PhenoTips: phenotyping made easy | 2026-08-01 12:10:39 | 24 | ||||||
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KOBAS Resource Report Resource Website 1000+ mentions |
KOBAS (RRID:SCR_006350) | KOBAS | production service resource, data analysis service, analysis service resource, service resource, software resource | Web server to identify statistically enriched pathways, diseases, and GO terms for a set of genes or proteins, using pathway, disease, and GO knowledge from multiple famous databases. It allows for both ID mapping and cross-species sequence similarity mapping. It then performs statistical tests to identify statistically significantly enriched pathways and diseases. KOBAS 2.0 incorporates knowledge across 1327 species from 5 pathway databases (KEGG PATHWAY, PID, BioCyc, Reactome and Panther) and 5 human disease databases (OMIM, KEGG DISEASE, FunDO, GAD and NHGRI GWAS Catalog). A standalone command line version is also available, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | ortholog, pathway, disease, gene, protein, annotation, command line, FASEB list |
is listed by: OMICtools is related to: Gene Ontology is related to: KEGG is related to: OMIM is related to: Pathway Interaction Database is related to: BioCarta Pathways is related to: Reactome is related to: BioCyc is related to: PANTHER is related to: FunDO is related to: Genetic Association Database is related to: GWAS: Catalog of Published Genome-Wide Association Studies has parent organization: Peking University; Beijing; China |
PMID:21715386 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02228 | SCR_006350 | KEGG Orthology Based Annotation System | 2026-08-03 09:33:03 | 4787 | ||||||
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NIF Data Federation Resource Report Resource Website 10+ mentions |
NIF Data Federation (RRID:SCR_004834) | Data Federation | service resource, data or information resource, portal | Service that partners with the community to expose and simultaneously drill down into individual databases and data sets and return relevant content. This type of content, part of the so called hidden Web, is typically not indexed by existing web search engines. Every record links back to the originating site. In order for NIF to directly query these independently maintained databases and datasets, database providers must register their database or dataset with the NIF Data Federation and specify permissions. Databases are concept mapped for ease of sharing and to allow better understanding of the results. Learn more about registering your resource, http://neuinfo.org/nif_components/disco/interoperation.shtm Search results are displayed under the Data Federation tab and are categorized by data type and nervous system level. In this way, users can easily step through the content of multiple resources, all from the same interface. Each federated resource individually displays their query results with links back to the relevant datasets within the host resource. This allows users to take advantage of additional views on the data and tools that are available through the host database. The NIF site provides tutorials for each resource, indicated by the Professor Icon professor icon showing users how to navigate the results page once directed there through the NIF. Additionally, query results may be exported as an Excel document. Note: NIF is not responsible for the availability or content of these external sites, nor does NIF endorse, warrant or guarantee the products, services or information described or offered at these external sites. Integrated Databases: Theses virtual databases created by NIF and other partners combine related data indexed from multiple databases and combine them into one view for easier browsing. * Integrated Animal View * Integrated Brain Gene Expression View * Integrated Disease View * Integrated Nervous System Connectivity View * Integrated Podcasts View * Integrated Software View * Integrated Video View * Integrated Jobs * Integrated Blogs For a listing of the Federated Databases see, http://neuinfo.org/mynif/databaseList.php or refer to the Resources Listed by NIF Data Federation table below. | semantics, neuroscience, animal, annotation, antibody, biospecimen, brain activation foci, clinical trial, connectivity, dataset, disease, drug, grant, image, microarray, model, multimedia, negative data, pathway, people, plasmid, registry, software, brain region, cell, gene, molecule, multi-level, nervous system, nervous system function, model |
uses: MNI Podcasts uses: Educational Resources in Neuroscience uses: Mind Hacks uses: BAMS Nested Regions uses: Indeed uses: NINDS Disorder Index uses: Drug Design Data Resource uses: PubMed Health uses: This Week In Science uses: Science Talk uses: BAMS Connectivity uses: Lady Scientist uses: Psychology Corner uses: Wired Science uses: CENtral Science uses: RetractionWatch.com uses: The Guardian: Science Weekly uses: H2SO4Hurts uses: 60-Second Mind uses: PLoS Blogs uses: Clarity resources uses: Open Source Brain uses: Diabetic Complications Consortium uses: Integrated Animals uses: Kawasaki Disease Dataset uses: EEGbase uses: Integrated Models uses: Lifespan Observations Database uses: NIF Web Services uses: NIF Blog uses: ATCC uses: Cerebellar Platform uses: Brain Machine Interface Platform uses: Rafael Yustes Laboratory uses: ASAP uses: NIH VideoCasting uses: NIDA Data Share uses: Neurofed uses: Candida Genome Database uses: Addgene uses: ASPGD uses: Glomerular Activity Response Archive uses: WikiPathways uses: AmiGO uses: NeuroMorpho.Org uses: Cell Centered Database uses: Integrated uses: Community Structure-Activity Resource uses: ClinicalTrials.gov uses: Ensembl uses: GeneNetwork uses: Avian Brain Circuitry Database uses: EcoCyc uses: Entrez Gene uses: Zebrafish Information Network (ZFIN) uses: Arredondo ANT fNIRS dataset1 uses: Grants.gov uses: T3DB uses: Simtk.org uses: PharmGKB uses: DrugBank uses: Aging Genes and Interventions Database uses: Gene Expression Nervous System Atlas uses: SumsDB uses: bioDBcore uses: BioNumbers uses: Gene Ontology uses: Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat uses: Gramene uses: Retina Project uses: HomoloGene uses: ArrayExpress uses: Journal of Visualized Experiments uses: Allen Mouse Brain Reference Atlas uses: Gene Weaver uses: Visiome Platform uses: Developmental Therapeutics Program uses: NeuroMab uses: WormBase uses: NeuronDB uses: Integrated Grants uses: studyforrest.org uses: BrainInfo uses: Mouse Phenome Database (MPD) uses: NCBI Taxonomy uses: NCBI Protein Database uses: Psychoactive Drug Screening Program Ki Database uses: Nuclear Receptor Signaling Atlas uses: Brede Database uses: NeuroImaging Tools and Resources Collaboratory (NITRC) uses: Mouse Genome Informatics Transgenes uses: Reactome uses: Cell Image Library (CIL) uses: BAMS Cells uses: Synapse Web uses: Integrated Videos uses: NeuroVault uses: Royal College of Psychiatrists Podcasts uses: WU-Minn HCP 500 Subjects MR and MEG Release uses: Data.gov Science and Research Data Catalog uses: NITRC-IR uses: One Mind Biospecimen Bank Listing uses: Integrated Brain Gene Expression uses: BrainSpan uses: All In The Mind uses: Scientific American Cross-Check uses: PubChem uses: NeuroPod uses: BrainSpan uses: Health.Data.gov uses: Biointeractive uses: UniProtKB uses: Gray Matters uses: dkCOIN uses: Brain Science Podcast uses: NIGMS Human Genetic Cell Repository uses: DISCO uses: GeneDB Lmajor uses: TAIR uses: ScienceNOW uses: Daily Scan uses: SGD uses: Integrated Software uses: BrainPod uses: GeneDB Tbrucei uses: MPO uses: PANTHER uses: Neurology Podcast uses: Integrated Disease uses: VMD uses: UCSF Laboratory for Visual Neuroscience uses: NIMH Chemical Synthesis and Drug Supply Program uses: NIH Neuroscience Microarray Consortium uses: SGN uses: Protocol Online - Your labs reference book uses: Integrated Podcasts uses: OpenNeuro uses: National Academy of Sciences Podcasts uses: Beta Cell Biology Consortium uses: Naturejobs uses: Scientific American Guest Blog uses: jobs.ac.uk uses: New Scientist Jobs uses: Science Careers uses: Access-ScienceJobs.co.uk uses: ScienceBlogs: Life Science uses: ScienceBlogs: Brain and Behavior uses: TheScienceJobs.com uses: Nature Network Blogs uses: The Guardian: Science uses: LabSpaces uses: ScienceBlogs: Medicine and Health uses: Scientific American Observations uses: Scientific American Bering in Mind uses: QUEST uses: Daring Nucleic Adventures - genegeek uses: Oxford Science Blog uses: Sciblogs uses: New York Times - Well uses: SciLogs uses: Cassandras Tears uses: BioPortfolio uses: Now at NEJM uses: 1000 Functional Connectomes Project uses: Integrated Jobs uses: Integrated Blogs uses: JCVI CMR uses: SciCrunch Registry uses: Neuroskeptic uses: CRCNS uses: Expression Atlas of the Marmoset uses: IXI dataset uses: Integrated Auto-Extracted Annotation uses: EU Clinical Trials Register uses: Integrated Clinical Trials uses: Human Brain Atlas uses: goCognitive uses: Law and Neuroscience uses: International Mouse Phenotyping Consortium (IMPC) uses: ClinVar uses: Integrated Gene-Disease Interaction uses: XNAT Central uses: neuroelectro uses: Integrated Nervous System Connectivity uses: Antibody Registry uses: OMIA - Online Mendelian Inheritance in Animals uses: OMIM uses: Science Podcast uses: Mouse Genome Informatics (MGI) uses: Monster uses: NCBI uses: Wired Science Blogs uses: F1000 Posters uses: Neurophilosophy uses: Comparative Toxicogenomics Database (CTD) uses: FlyBase uses: GeneReviews uses: GeneDB Pfalciparum uses: Naturally Selected uses: PomBase uses: Pseudomonas Genome Database uses: The Guardian: Science Videos uses: Orphanet uses: Dictyostelium discoideum genome database uses: PeptideAtlas uses: NeuroSynth uses: neuropathology blog uses: Genomes Unzipped uses: National Institutes of Health Research Portfolio Online Reporting Tool uses: BrainMaps.org uses: It Takes 30 uses: Gait in Parkinson's Disease uses: Physiobank uses: Gait Dynamics in Neuro-Degenerative Disease Data Base uses: American Journal of Psychiatry Podcasts uses: Neurodatabase.org uses: Brain Architecture Management System uses: RanchoBiosciences uses: ModelDB uses: CoCoMac uses: Olfactory Bulb Odor Map DataBase (OdorMapDB) uses: Gene Expression Omnibus uses: Caenorhabditis Genetics Center uses: Labome uses: Open Access Series of Imaging Studies uses: Biological General Repository for Interaction Datasets (BioGRID) uses: Olfactory Receptor DataBase uses: T1DBase uses: Gemma uses: CellML Model Repository uses: ResearchCrossroads uses: Biocompare uses: BioNOT uses: Hays uses: Research Blogging uses: Discover Magazine uses: PolygenicBlog uses: Kawasaki Disease Dataset2 uses: Allen Mouse Brain Connectivity Atlas uses: Integrated Manually Extracted Annotation uses: Roadmap Epigenomics Project uses: Integrated Cell Lines uses: National Mouse Metabolic Phenotyping Centers uses: Mendelspod uses: Integrated Snippets uses: Integrated Datasets uses: Nature Podcast uses: GWAS: Catalog of Published Genome-Wide Association Studies uses: KEGG uses: USC Multimodal Connectivity Database uses: Inside NIA: A Blog for Researchers uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) uses: NIF Registry Automated Crawl Data uses: Genetic Analysis Software uses: anage uses: Intestinal Stem Cell Consortium uses: Animal QTLdb uses: elements of morphology uses: Human Life-Table Database uses: Clinical Genomic Database uses: NIDDK Central Repository uses: MONARCH Initiative uses: Human Phenotype Ontology is used by: SciCrunch is used by: NIDDK Information Network (dkNET) lists: AutDB lists: Drug Related Gene Database lists: Gene Ontology Tools lists: CHEBI is listed by: 3DVC is related to: International Mouse Strain Resource is related to: Internet Brain Volume Database is related to: Resource Identification Portal is related to: Rat Genome Database (RGD) is related to: VISTA Enhancer Browser is related to: NIH Human Pluripotent Stem Cell Registry is related to: Zebrafish International Resource Center is related to: Bloomington Drosophila Stock Center is related to: Journal of Comparative Neurology Antibody database has parent organization: Neuroscience Information Framework |
NIDA ; NIH Blueprint for Neuroscience Research ; U.S. Department of Health and Human Services HHSN27120080035C |
Refer to individual databases | nlx_81822 | http://neuinfo.org/nif/nifgwt.html?query=* | SCR_004834 | Neuroscience Information Framework Data Federation | 2026-08-03 09:32:44 | 28 | |||||
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Biomine Resource Report Resource Website 1+ mentions |
Biomine (RRID:SCR_003552) | Biomine | service resource, data or information resource, database | Service that integrates cross-references from several biological databases into a graph model with multiple types of edges, such as protein interactions, gene-disease associations and gene ontology annotations. Edges are weighted based on their type, reliability, and informativeness. In particular, it formulates protein interaction prediction and disease gene prioritization tasks as instances of link prediction. The predictions are based on a proximity measure computed on the integrated graph. | gene, protein, genetics, visualization, connection, biological entity, protein interaction, disease gene, link prediction |
is related to: Entrez Gene is related to: Gene Ontology is related to: HomoloGene is related to: InterPro is related to: OMIM is related to: STRING is related to: UniProtKB is related to: UniProt is related to: GoMapMan has parent organization: University of Helsinki; Helsinki; Finland |
PMID:22672646 | nlx_157687 | SCR_003552 | 2026-08-03 09:32:27 | 4 | ||||||||
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OMIA - Online Mendelian Inheritance in Animals Resource Report Resource Website 10+ mentions |
OMIA - Online Mendelian Inheritance in Animals (RRID:SCR_006436) | OMIA | data or information resource, database | Describes phenotype relationships with between breeds and genes. Catalogue/compendium of inherited disorders, other (single-locus) traits, and genes in 245 animal species. Database of genes, inherited disorders and traits in animal species other than human, mouse, and rats. Database contains textual information and references, as well as links to relevant records from OMIM, PubMed and Gene. | gene, inherited disorder, trait, disorder, genetic disorder, animal model, human disorder, homologue, phenotype, comparative biology, genotype, gold standard, FASEB list |
is used by: NIF Data Federation is related to: OMIM is related to: Ensembl Variation is related to: NCBI has parent organization: University of Sydney; Sydney; Australia has parent organization: NCBI |
Genetic disorder | H.G. Slater Foundation ; Australian Commonwealth ; International Livestock Centre for Africa ; Food and Agriculture Organization of the United Nations ; American Humane Association |
PMID:16381939 PMID:12520001 PMID:9638822 |
Free, Acknowledgement requested, The community can contribute to this resource, Non-commercial, Commercial with permission, Copyrighted | nif-0000-03215, r3d100010772 | https://doi.org/10.17616/R3VW5D | SCR_006436 | Online Mendelian Inheritance in Animals | 2026-08-03 09:33:07 | 39 | |||
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Europhenome Mouse Phenotyping Resource Resource Report Resource Website 10+ mentions |
Europhenome Mouse Phenotyping Resource (RRID:SCR_006935) | EuroPhenome | production service resource, data analysis service, service resource, database, analysis service resource, data or information resource | Open source software system for capturing, storing and analyzing raw phenotyping data from SOPs contained in EMPReSS, it provides access to raw and annotated mouse phenotyping data generated from primary pipelines such as EMPReSSlim and secondary procedures from specialist centers. Mutants of interest can be identified by searching the gene or the predicted phenotype. You can also access phenotype data from the EMPReSSlim Pipeline for inbred mouse strains. Initially EuroPhenome was developed within the EUMORPHIA programme to capture and store pilot phenotyping data obtained on four background strains (C57BL/6J, C3H/HeBFeJ, BALB/cByJ and 129/SvPas). EUMORPHIA (European Union Mouse Research for Public Health and Industrial Applications) was a large project comprising of 18 research centers in 8 European countries, with the main focus of the project being the development of novel approaches in phenotyping, mutagenesis and informatics to improve the characterization of mouse models for understanding human molecular physiology and pathology. The current version of EuroPhenome is capturing data from the EUMODIC project as well as the WTSI MGP, HMGU GMC pipeline and the CMHD. EUMODIC is undertaking a primary phenotype assessment of up to 500 mouse mutant lines derived from ES cells developed in the EUCOMM project as well as other lines. Lines showing an interesting phenotype will be subject to a more in depth assessment. EUMODIC is building upon the comprehensive database of standardized phenotyping protocols, called EMPReSS, developed by the EUMORPHIA project. EUMODIC has developed a selection of these screens, called EMPReSSslim, to enable comprehensive, high throughput, primary phenotyping of large numbers of mice. Phenovariants are annotated using a automated pipeline, which assigns a MP term if the mutant data is statistically different to the baseline data. This data is shown in the Phenomap and the mine for a mutant tool. Please note that a statistically significant result and the subsequent MP annotation does not necessarily mean a true phenovariant. There are other factors that could cause this result that have not been accounted for in the analysis. It is the responsibility of the user to download the data and use their expert knowledge or further analysis to decide whether they agree or not. EuroPhenome is primarily based in the bioinformatics group at MRC Harwell. The development of EuroPhenome is in collaboration with the Helmholtz Zentrum Munchen, Germany, the Wellcome Trust Sanger Institute, UK and the Institut Clinique de la Souris, France. | phenotype, gene, mutant mouse strain, inbred mouse strain, annotation, ortholog, high-throughput, phenovariant, disorder, c57bl/6j, c3h/hebfej, balb/cbyj, 129/svpas |
is related to: European Mouse Phenotyping Resource of Standardised Screens is related to: OMIM is related to: Understanding Human Disease Through Mouse Genetics is related to: European Conditional Mouse Mutagenesis Program is related to: European Mouse Phenotyping Resource of Standardised Screens has parent organization: MRC Mammalian Genetics Unit |
European Union FP6 contract LSHG-CT-2006-037188; MRC ; National Genome Research Network |
PMID:19933761 PMID:17905814 |
Open unspecified license, Acknowledgement requested | nif-0000-30535 | SCR_006935 | 2026-08-03 09:33:12 | 19 | ||||||
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aGEM Resource Report Resource Website 10+ mentions |
aGEM (RRID:SCR_013349) | aGEM | data or information resource, database | Database platform of an integrated view of eight databases (mouse gene expression resources: EMAGE, GXD, GENSAT, BioGPS, ABA, EUREXPRESS; human gene expression databases: HUDSEN, BioGPS and Human Protein Atlas) that allows the experimentalist to retrieve relevant statistical information relating gene expression, anatomical structure (space) and developmental stage (time). Moreover, general biological information from databases such as KEGG, OMIM and MTB is integrated too. It can be queried using gene and anatomical structure. Output information is presented in a friendly format, allowing the user to display expression maps and correlation matrices for a gene or structure during development. An in-depth study of a specific developmental stage is also possible using heatmaps that relate gene expression with anatomical components. This is a powerful tool in the gene expression field that makes easy the access to information related to the anatomical pattern of gene expression in human and mouse, so that it can complement many functional genomics studies. The platform allows the integration of gene expression data with spatial-temporal anatomic data by means of an intuitive and user friendly display., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, anatomy, gene expression, anatomical structure, developmental stage, functional genomics, genomics |
is related to: EMAGE Gene Expression Database is related to: Gene Expression Database is related to: Gene Expression Nervous System Atlas is related to: BioGPS: The Gene Portal Hub is related to: Allen Mouse Brain Reference Atlas is related to: Eurexpress is related to: HUDSEN is related to: The Human Protein Atlas is related to: OMIM is related to: KEGG has parent organization: Autonomous University of Madrid; Madrid; Spain |
National Institute for Bioinformatics ; AMIT Programme CDTI CEN-20101014; RESOLVE UE CE:FP7-202047; Ministerio de Ciencia e Innovacion BIO2010-16566; Biostruct-X FP7-Infrastructures-2011-1; Centrosoma 3D CSD2006-00023 |
PMID:22106336 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152022 | SCR_013349 | anatomic Gene Expression Mapping | 2026-08-03 09:35:12 | 12 | |||||
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Schizo-Pi Resource Report Resource Website 1+ mentions |
Schizo-Pi (RRID:SCR_014599) | data or information resource, database | An interactome of protein-protein interactions related to schizophrenia, it contains novel PPIs predicted with the HiPPIP model. Schizophrenia associated genes are gathered from GWAS genes, historical candidates, and OMIM. Members of the scientific community can also suggest genes to add to the interactome. | schizophrenia, protein protein interaction, interactome, novel ppi, novel protein protein interaction |
uses: OMIM uses: GWAS: Catalog of Published Genome-Wide Association Studies |
PMID:27336055 DOI:10.1038/npjschz.2016.12 |
Acknowledgement requested | SCR_014599 | Schizophrenia Protein Interactome, Schizo Pi | 2026-08-03 09:35:45 | 4 | ||||||||
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Database of genes related to Repeat Expansion Diseases Resource Report Resource Website 1+ mentions |
Database of genes related to Repeat Expansion Diseases (RRID:SCR_018086) | DRED | service resource, data or information resource, database | Database of genes related to Repeat Expansion Diseases, as comprehensive manually curated database that covers all reported repeat expansion diseases included in PubMed and OMIM. Detailed information about each repeat and its related genes/diseases can be found in database, links to OMIM, NCBI and Ensembl are also provided. Provides list of predicted genes containing unstable tandem repeats that may cause diseases via abnormal repeat expansion by support vector machine and random forest. | Gene, repeat expansion disease, unstable tandem repeat, abnormal repeat expansion, data |
works with: OMIM works with: NCBI works with: Ensembl |
Repeat Expansion Diseases | Free, Freely available | SCR_018086 | Database of genes related to Repeat Expansion Diseases | 2026-08-03 09:36:51 | 1 | |||||||
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GEMINI Resource Report Resource Website 500+ mentions |
GEMINI (RRID:SCR_014819) | software resource | Framework for exploring genetic variation in the context of the genome annotations available for the human genome. Users can load a VCF file into a database and each variant is automatically annotated by comparing it to several genome annotations from source such as ENCODE tracks, UCSC tracks, OMIM, dbSNP, KEGG, and HPRD. | framework, genetic variation, annotation, human, genome, vcf, database, , bio.tools, FASEB list |
uses: KEGG uses: ENCODE uses: OMIM uses: dbSNP uses: HPRD - Human Protein Reference Database is listed by: Debian is listed by: bio.tools has parent organization: University of Utah; Utah; USA |
DOI:10.1371/journal.pcbi.1003153 | Freely available | biotools:gemini | https://github.com/arq5x/gemini, https://bio.tools/gemini | SCR_014819 | GEnome MINIng (GEMINI), GEMINI - a flexible framework for exploring genome variation, Genome Mining, GEnome MINIng | 2026-08-01 12:05:18 | 515 | ||||||
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MitoMiner Resource Report Resource Website 50+ mentions |
MitoMiner (RRID:SCR_001368) | data or information resource, database | A database of mitochondrial proteomics data. It includes two sets of proteins: the MitoMiner Reference Set, which has 10477 proteins from 12 species; and MitoCarta, which has 2909 proteins from mouse and human mitochondrial proteins. MitoMiner provides annotation from the Gene Ontology (GO) and UniProt databases. This reference set contains all proteins that are annotated by either of these resources as mitochondrial in any of the species included in MitoMiner. MitoMiner data via is available via Application Programming Interface (API). The client libraries are provided in Perl, Python, Ruby and Java. | mitochondrion, proteomics, function, homolog, proteome, protein expression, mass-spectrometry, protein, metabolism, green fluorescent protein tag, ortholog, FASEB list |
uses: HomoloGene uses: UniProt uses: KEGG uses: OMIM uses: The Human Protein Atlas uses: Gene Ontology |
MRC | PMID:22121219 PMID:19208617 |
Public, Acknowledgement requested, Code: | nlx_152504 | SCR_001368 | MitoMiner - A database of the mitochondrial proteome | 2026-08-03 09:31:18 | 76 | ||||||
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MARRVEL Resource Report Resource Website 10+ mentions |
MARRVEL (RRID:SCR_016871) | MARRVEL | production service resource, data analysis service, data or information resource, database, analysis service resource, service resource | Web tool to search multiple public variant databases simultaneously and provide a unified interface to facilitate the search process. Used for integration of human and model organism genetic resources to facilitate functional annotation of the human genome. Used for analysis of human genes and variants by cross-disciplinary integration of records available in public databases to facilitate clinical diagnosis and basic research. | integration, database, model, genetic, resource, functional, annotation, genome, data, analysis, dataset, rare, variant, exploration, bio.tools |
uses: OMIM uses: ClinVar uses: DECIPHER uses: Geno2MP uses: Database of Genomic Variants is used by: Hypothesis Center is listed by: bio.tools is listed by: Debian |
NINDS 1U54NS093793; NIH Office of the Director R24 OD022005; The Robert and Janice McNair Foundation ; Baylor College of Medicine Medical Scientist Training Program ; NINDS U54 NS093793; NIGMS R01 GM067858; NIGMS R01 GM120033; NSF DMS 1263932; CPRIT RP170387; Houston Endowment ; Huffington Foundation ; Belfer Foundation ; T T Chao Family Foundation ; NIGMS R01 GM067761; NIGMS R01 GM084947; NCRR R24 RR032668; NIH Office of the Director R24 OD021997; NCI P30 CA06516; NHGRI U01 HG007709; Simons Foundation |
PMID:28502612 | Free, Public, Freely available | biotools:marrvel | https://bio.tools/marrvel | SCR_016871 | Model organism Aggregated Resources for Rare Variant ExpLoration | 2026-08-03 09:36:37 | 22 | ||||
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HmtPhenome Resource Report Resource Website |
HmtPhenome (RRID:SCR_017289) | network graph visualization software, database, software application, data processing software, service resource, data or information resource, software resource, data visualization software | Collection of data about variants, genes, phenotypes and diseases involved in mitochondrial functionality. Users can search for variant position, gene, phenotype or disease and retrieve all related information through integrated network of biological entities. | mitochondria, variant, gene, function, phenotype, data |
uses: Human Phenotype Ontology uses: Ensembl uses: OMIM uses: Orphanet uses: DisGeNET has parent organization: University of Bari; Bari; Italy |
DOI:10.1101/660282 | Free, Freely available | SCR_017289 | 2026-08-03 09:36:50 | 0 | |||||||||
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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, r3d100010781, OMICS_01544 | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene, https://doi.org/10.17616/R3889F | SCR_002924 | NCBI HomoloGene | 2026-08-03 09:32:05 | 437 | |||||
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biomaRt Resource Report Resource Website 1000+ mentions |
biomaRt (RRID:SCR_019214) | software resource, data processing software, software application, data analysis software | Software package that integrates BioMart data resources with data analysis software in Bioconductor. Can annotate range of gene or gene product identifiers including Entrez Gene and Affymetrix probe identifiers with information such as gene symbol, chromosomal coordinates, Gene Ontology and OMIM annotation. Enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis. | BioMart databases, Bioconductor, data analysis, BioMart data integration, gene annotation, gene product identifiers annotation, gene symbol retrival, chromosomal coordinates retrival, genomic sequence retrival, nucleotide polimorphism information, , bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: BioMart Project is related to: BioMart MartView is related to: Entrez Gene is related to: Affymetrix is related to: Gene Ontology is related to: OMIM is related to: Affymetrix |
PMID:16082012 | Free, Available for download, Freely available | biotools:biomart | https://bio.tools/biomart | SCR_019214 | biomaRt v 2.42.1 | 2026-08-03 09:37:13 | 2638 | ||||||
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Human Phenotype Ontology Resource Report Resource Website 50+ mentions |
Human Phenotype Ontology (RRID:SCR_006016) | HPO, HP | controlled vocabulary, data or information resource, ontology | Provides standardized vocabulary of phenotypic abnormalities encountered in human disease. Structured and controlled vocabulary for phenotypic features encountered in human hereditary and other disease. HPO is being developed in collaboration with members of OBO Foundry (Open Biological and Biomedical Ontologies), and logical definitions for HPO terms are being developed using PATO and a number of other ontologies including FMA, GO, ChEBI, and MPATH. | phenotype, genetics, disease, phenomizer, obo, clinical, phenome, pathological, organismal, FASEB list |
uses: OMIM uses: Phenexplorer is used by: DisGeNET is used by: HmtPhenome is used by: MONARCH Initiative is used by: NIF Data Federation is listed by: BioPortal is listed by: OBO is related to: Phenexplorer is related to: Phenomizer is related to: PhenoTips is related to: Neurocarta is related to: GWASdb is related to: Phenomizer has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany works with: Human Mouse Disease Connection |
Monogenic disease, Hereditary disease | PMID:20412080 | Free, Freely available | SCR_006219, nlx_151406, nlx_151835 | http://purl.bioontology.org/ontology/HP, http://compbio.charite.de/svn/hpo/trunk/src/ontology/human-phenotype-ontology.obo | SCR_006016 | Human Phenotype Ontology (HPO), Human Phenotype Ontology | 2026-08-03 09:32:58 | 73 | ||||
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phenomeNET Resource Report Resource Website 10+ mentions |
phenomeNET (RRID:SCR_006165) | PhenomeNet | production service resource, data analysis service, service resource, database, source code, analysis service resource, data or information resource, software resource | 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 | 2026-08-03 09:32:55 | 13 |
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