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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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BioStar Resource Report Resource Website 50+ mentions |
BioStar (RRID:SCR_002580) | Biostar | forum, discussion, narrative resource, community building portal, portal, data or information resource | A question answer forum for scientists, focusing on methods in bioinformatics, computational genomics and biological data analysis. They welcome detailed and specific posts, written clearly and simply. | bioinformatics, computational genomics, biological data analysis, data analysis, forum, question, answer |
is listed by: OMICtools is related to: NeuroStars |
NIH ; Luma Education ; NHGRI 5R25HG006243-02 |
PMID:22046109 | Free, Freely available | OMICS_01706, nlx_155982 | SCR_002580 | biostars.org | 2026-02-16 09:45:46 | 84 | |||||
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Gene Ontology Resource Report Resource Website 10000+ mentions |
Gene Ontology (RRID:SCR_002811) | GO | organization portal, portal, project portal, consortium, knowledge environment resource, data or information resource | Computable knowledge regarding functions of genes and gene products. GO resources include biomedical ontologies that cover molecular domains of all life forms as well as extensive compilations of gene product annotations to these ontologies that provide largely species-neutral, comprehensive statements about what gene products do. Used to standardize representation of gene and gene product attributes across species and databases. | gene, product, annotation, molecular, function, cellular, biological, role, database, query, obo, gold standard, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: GreenPhylDB is used by: LIPID MAPS Proteome Database is used by: Aging Portal is used by: ChannelPedia is used by: Open PHACTS is used by: CoPub is used by: PhenoGO is used by: Database for Annotation Visualization and Integrated Discovery is used by: MitoMiner is used by: dcGO is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is used by: barleyGO is used by: SynGO is used by: Functional Annotation is used by: SwissLipids is listed by: BioPortal is listed by: OBO is listed by: OMICtools is listed by: bio.tools is listed by: Debian is affiliated with: Mouse Genome Informatics: The Gene Ontology Project is related to: GenNav is related to: SynaptomeDB is related to: High-Throughput GoMiner is related to: Onto-Design is related to: OnEx - Ontology Evolution Explorer is related to: Avadis is related to: GONUTS is related to: PiNGO is related to: Automated Microarray Pipeline is related to: categoryCompare is related to: globaltest is related to: Semantic Measures Library is related to: WegoLoc is related to: AnimalTFDB is related to: MEME Suite - Motif-based sequence analysis tools is related to: Arabidopsis Hormone Database is related to: DAVID is related to: Arabidopsis thaliana Protein Interactome Database is related to: TM4 Microarray Software Suite - TIGR MultiExperiment Viewer is related to: pSTIING is related to: GoMiner is related to: FunSimMat is related to: GeneSpeed- A Database of Unigene Domain Organization is related to: Centre for Modeling Human Disease Gene Trap Resource is related to: Patterns of Gene Expression in Drosophila Embryogenesis is related to: Babelomics is related to: BioPerl is related to: GeneCruiser is related to: GOLEM An interactive, graphical gene-ontology visualization, navigation, and analysis tool is related to: GOToolBox Functional Investigation of Gene Datasets is related to: Cotton EST Database is related to: MouseNET is related to: PLANTTFDB is related to: T-profiler is related to: Physico-Chemical Process is related to: Integrated Molecular Interaction Database is related to: SEGS is related to: GOCat is related to: Quantitative Enrichment of Sequence Tags is related to: Neural-Immune Gene Ontology is related to: INMEX is related to: StRAnGER is related to: QuickGO is related to: Repository of molecular brain neoplasia data is related to: Cardiovascular Gene Ontology Annotation Initiative is related to: PANTHER is related to: Short Time-series Expression Miner (STEM) is related to: DATFAP is related to: GORetriever is related to: Gene Ontology Browsing Utility (GOBU) is related to: GeneTools is related to: GOSlimViewer is related to: go-moose is related to: Network Ontology Analysis is related to: Onto-Compare is related to: Onto-Express is related to: OntoVisT is related to: STRAP is related to: CGAP GO Browser is related to: COBrA is related to: Gene Class Expression is related to: GeneInfoViz is related to: GOfetcher is related to: GoFish is related to: GOProfiler is related to: GOanna is related to: Manatee is related to: Pandora - Protein ANnotation Diagram ORiented Analysis is related to: TAIR Keyword Browser is related to: Wandora is related to: GOTaxExplorer is related to: Onto-Miner is related to: Onto-Translate is related to: ToppGene Suite is related to: DBD - Slim Gene Ontology is related to: ONTO-PERL is related to: Blip: Biomedical Logic Programming is related to: OWL API is related to: CLENCH is related to: BiNGO: A Biological Networks Gene Ontology tool is related to: CateGOrizer is related to: FuSSiMeG: Functional Semantic Similarity Measure between Gene-Products is related to: ProteInOn is related to: GeneMerge is related to: GraphWeb is related to: ClueGO is related to: CLASSIFI - Cluster Assignment for Biological Inference is related to: GOHyperGAll is related to: FuncAssociate: The Gene Set Functionator is related to: GOdist is related to: FuncExpression is related to: FunCluster is related to: FIVA - Functional Information Viewer and Analyzer is related to: GARBAN is related to: GOEx - Gene Ontology Explorer is related to: SGD Gene Ontology Slim Mapper is related to: GOArray is related to: SNPsandGO is related to: GoSurfer is related to: GOtcha is related to: MAPPFinder is related to: GoAnnotator is related to: MetaGeneProfiler is related to: OntoGate is related to: ProfCom - Profiling of complex functionality is related to: SerbGO is related to: SOURCE is related to: Ontologizer is related to: THEA - Tools for High-throughput Experiments Analysis is related to: Generic GO Term Mapper is related to: GREAT: Genomic Regions Enrichment of Annotations Tool is related to: GoBean - a Java application for Gene Ontology enrichment analysis is related to: TXTGate is related to: GO-Module is related to: IT-GOM: Integrated Tool for IC-based GO Semantic Similarity Measures is related to: G-SESAME - Gene Semantic Similarity Analysis and Measurement Tools is related to: MalaCards is related to: FSST - Functional Similarity Search Tool is related to: Expression Profiler is related to: GOChase is related to: GoPubMed is related to: Whatizit is related to: REViGO is related to: WEGO - Web Gene Ontology Annotation Plot is related to: Blast2GO is related to: InterProScan is related to: PubSearch is related to: TrED is related to: CharProtDB: Characterized Protein Database is related to: VirHostNet: Virus-Host Network is related to: Pathbase is related to: GO Online SQL Environment (GOOSE) is related to: Neurobehavior Ontology is related to: InterSpecies Analysing Application using Containers is related to: KOBAS is related to: ConceptWiki is related to: GeneTerm Linker is related to: Bioconductor is related to: ErmineJ is related to: Gene Ontology For Functional Analysis (GOFFA) is related to: MGI GO Browser is related to: Comparative Toxicogenomics Database (CTD) is related to: GOEAST - Gene Ontology Enrichment Analysis Software Toolkit is related to: Ontology Lookup Service is related to: LexGrid is related to: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit is related to: g:Profiler is related to: OwlSim is related to: GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool is related to: YeTFaSCo is related to: FastSemSim is related to: RamiGO is related to: AutismKB is related to: GeneCodis is related to: FunSpec is related to: FunNet - Transcriptional Networks Analysis is related to: PhenoM - Phenomics of yeast Mutants is related to: agriGO is related to: GOblet is related to: DynGO is related to: SeqExpress is related to: ProbeExplorer is related to: ECgene: Gene Modeling with Alternative Splicing is related to: Organelle DB is related to: Gemma is related to: Candidate Genes to Inherited Diseases is related to: Proteome Analyst PA-GOSUB is related to: Network Analysis, Visualization and Graphing TORonto is related to: GOstat is related to: Onto-Express To Go (OE2GO) is related to: Tk-GO is related to: EGAN: Exploratory Gene Association Networks is related to: Spotfire is related to: GOMO - Gene Ontology for Motifs is related to: GFINDer: Genome Function INtegrated Discoverer is related to: Generic GO Term Finder is related to: Agile Protein Interactomes DataServer is related to: AgingDB is related to: UBERON is related to: Algal Functional Annotation Tool is related to: gsGator is related to: Flash Gviewer is related to: Cerebellar Development Transcriptome Database is related to: PlantNATsDB - Plant Natural Antisense Transcripts DataBase is related to: EASE: the Expression Analysis Systematic Explorer is related to: PiGenome is related to: L2L Microarray Analysis Tool is related to: MeGO is related to: CELDA Ontology is related to: Diabetes Disease Portal is related to: MatrixDB is related to: Kidney and Urinary Pathway Knowledge Base is related to: MouseCyc is related to: Candida Genome Database is related to: Honey Bee Brain EST Project is related to: ECO is related to: FlyMine is related to: Gramene is related to: 3D-Interologs is related to: Biomine is related to: UniProtKB is related to: NCBI BioSystems Database is related to: EBIMed is related to: Coremine Medical is related to: EMAGE Gene Expression Database is related to: GeneMANIA is related to: Yeast Search for Transcriptional Regulators And Consensus Tracking is related to: GeneTrail is related to: Magic is related to: Mouse Genome Informatics (MGI) is related to: FlyBase is related to: InterPro is related to: InnateDB is related to: canSAR is related to: HPRD - Human Protein Reference Database is related to: CRCView is related to: Integrated Manually Extracted Annotation is related to: LegumeIP is related to: Renal Disease Portal is related to: PhenoGO is related to: DOAF is related to: OBO is related to: biomaRt is related to: OncoboxPD is parent organization of: AmiGO is parent organization of: GOlr is parent organization of: RefGenome is parent organization of: OBO-Edit is parent organization of: OWLTools is parent organization of: Gene Ontology Tools is parent organization of: Gene Ontology Extension is parent organization of: SO is parent organization of: go-db-perl is parent organization of: go-perl works with: topGO works with: DIANA-mirPath works with: GOnet |
European Union QLRI-CT-2001-0098; European Union QLRI-CT-2001-00015; NHGRI P41 HG002273 |
PMID:23161678 PMID:10802651 |
Free, Freely available, Available for download | biotools:go, OMICS_02278, nif-0000-02915 | http://bioportal.bioontology.org/ontologies/GO https://bio.tools/go |
SCR_002811 | the Gene Ontology, GO, Gene Ontology Resource, Gene Ontology | 2026-02-16 09:45:54 | 10623 | ||||
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RNA Abundance Database Resource Report Resource Website 1+ mentions |
RNA Abundance Database (RRID:SCR_002771) | RAD | resource, data repository, database, storage service resource, service resource, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, Documented on March 24, 2014. A resource for gene expression studies, storing highly curated MIAME-compliant studies (i.e. experiments) employing a variety of technologies such as filter arrays, 2-channel microarrays, Affymetrix chips, SAGE, MPSS and RT-PCR. Data were available for querying and downloading based on the MGED ontology, publications or genes. Both public and private studies (the latter viewable only by users having appropriate logins and permissions) were available from this website. Specific details on protocols, biomaterials, study designs, etc., are collected through a user-friendly suite of web annotation forms. Software has been developed to generate MAGE-ML documents to enable easy export of studies stored in RAD to any other database accepting data in this format. RAD is part of a more general Genomics Unified Schema (http://gusdb.org), which includes a richly annotated gene index (http://allgenes.org), thus providing a platform that integrates genomic and transcriptomic data from multiple organisms. NOTE: Due to changes in technology and funding, the RAD website is no longer available. RAD as a schema is still very much active and incorporated in the GUS (Genomics Unified Schema) database system used by CBIL (EuPathDB, Beta Cell Genomics) and others. The schema for RAD can be viewed along with the other GUS namespaces through our Schema Browser. | gene expression, gene, affymetrix, biomaterial, genomics, microarray, mpss, ontology, rna, rt-pcr, sage, functional genomics, transcript abundance |
is listed by: OMICtools is related to: MIAME is related to: MGED Ontology is related to: MicroArray and Gene Expression Markup Language has parent organization: University of Pennsylvania; Philadelphia; USA |
NIH ; NHGRI RO1-HG-01539; NIDDK U01DK56947; NHGRI K25-HG-02296; NHGRI K25-HG-00052 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00133, OMICS_00869, r3d100000017 | https://doi.org/10.17616/R3QP4Q | SCR_002771 | RNA Abundance Database | 2026-02-16 09:45:49 | 4 | |||||
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Diseasome Resource Report Resource Website 1+ mentions |
Diseasome (RRID:SCR_002792) | Diseasome | book, narrative resource, data set, map, image, service resource, data or information resource | A disease / disorder relationships explorer and a sample of a map-oriented scientific work. It uses the Human Disease Network dataset and allows intuitive knowledge discovery by mapping its complexity. The Human Disease Network (official) dataset, a poster of the data and related book (Biology - The digital era, ISBN: 978-2-271-06779-1) are available. This kind of data has a network-like organization, and relations between elements are at least as important as the elements themselves. More data could be integrated to this prototype and could eventually bring closer phenotype and genotype. Results should be visual, but also printable. Creating posters can enhance collaborative work. It facilitates discussion and sharing of ideas about the data. This website initiative is an invitation to think about the benefits of networks exploration but above all it tries to outline future designs of scientific information systems. | disease, disorder, genotype, phenotype, poster, network |
is related to: Allen Institute Neurowiki has parent organization: Gephi |
Dana-Farber Cancer Institute ; W. M. Keck Foundation ; NHGRI ; NIGMS |
PMID:17502601 | Free, Freely Available | nif-0000-24580 | SCR_002792 | Diseaseome | 2026-02-16 09:45:50 | 1 | |||||
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Primer3Plus Resource Report Resource Website 1000+ mentions |
Primer3Plus (RRID:SCR_003081) | Primer3Plus | data analysis service, analysis service resource, software resource, source code, production service resource, service resource | A web interface to the Primer3 primer design program as an enhanced alternative for the CGI- scripts that come with Primer3. | primer, dna sequence, primer design, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Primer3 has parent organization: Wageningen University and Research Centre; Gelderland; Netherlands |
Howard Hughes Medical Institute ; NHGRI R01-HG00257; NHGRI P50-HG00098 |
PMID:17485472 | Free, Freely available | biotools:primer3plus, OMICS_02347 | https://bio.tools/primer3plus | SCR_003081 | Primer3Plus - pick primers from a DNA sequence | 2026-02-16 09:45:55 | 1673 | ||||
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ArrayExpress Resource Report Resource Website 5000+ mentions |
ArrayExpress (RRID:SCR_002964) | ArrayExpress | data repository, database, storage service resource, catalog, service resource, data or information resource | International functional genomics data collection generated from microarray or next-generation sequencing (NGS) platforms. Repository of functional genomics data supporting publications. Provides genes expression data for reuse to the research community where they can be queried and downloaded. Integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Contains a subset of curated and re-annotated Archive data which can be queried for individual gene expression under different biological conditions across experiments. Data collected to MIAME and MINSEQE standards. Data are submitted by users or are imported directly from the NCBI Gene Expression Omnibus. | gold, standard, functional, genomics, data, collection, microarray, next, generation, sequencing, NGS, repository |
uses: MIAME uses: MINSEQE uses: Gene Expression Omnibus is used by: NIF Data Federation is used by: BioSample Database at EBI is used by: Integrated Datasets is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: DataCite is listed by: OMICtools is listed by: re3data.org is related to: DDBJ Omics Archive is related to: MIAME is related to: Gene Expression Atlas is related to: Experimental Factor Ontology is related to: Bgee: dataBase for Gene Expression Evolution is related to: ISA Infrastructure for Managing Experimental Metadata is related to: FlyMine is related to: MAGE-TAB is related to: Experimental Factor Ontology is related to: Magic is related to: ArrayExpress (R) is related to: CancerMIRNome has parent organization: European Bioinformatics Institute |
European Union ; SLING 226073; European Commission ; Gen2Phen 200754; NHGRI P41 HG003619 |
PMID:23193272 PMID:21071405 |
Available Public or Private, Free, Available for download, The community can contribute to this resource, Acknowledgement requested, to access private data registration required | OMICS_01023, nif-0000-30123, r3d100010222 | http://www.ebi.ac.uk/microarray-as/ae https://doi.org/10.17616/R3302G |
SCR_002964 | , ArrayExpress, ArrayExpress - functional genomics data, ArrayExpress Archive | 2026-02-16 09:45:55 | 7529 | ||||
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SNPHunter Resource Report Resource Website |
SNPHunter (RRID:SCR_002968) | software application, data processing software, sequence analysis software, data analysis software, resource, software resource | A tool for SNP Search and downloading with local management. It also offers flanking sequence downloading and automatic SNP filtering. It requires Windows and .NET Framework. | population, genetics, software, management, single nucleotide polymorphism, population genetics, training tools, data acquisition |
is listed by: 3DVC has parent organization: Harvard University; Cambridge; United States |
NIH ; NHGRI R01HG002518; NIDDK R01DK062290; NIDDK R01DK066401; NHLBI R01HL073882 |
DOI:10.1186/1471-2105-6-60 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30137 | http://www.hsph.harvard.edu/ppg/software.htm | SCR_002968 | SNPHunter - dbSNP Search & Management, Program for Population Genetics Software | 2026-02-16 09:46:04 | 0 | |||||
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Lowes Syndrome Mutation Database Resource Report Resource Website 1+ mentions |
Lowes Syndrome Mutation Database (RRID:SCR_002907) | data repository, database, storage service resource, service resource, data or information resource | The Lowe Syndrome Mutation Database is now being maintained by the National Center for Biotechnology Information (NCBI) at the National Institutes of Health. A database of mutations causing Lowe syndrome. Information on new mutations may be submitted online. Lowe oculocerebrorenal syndrome is an X-linked disorder caused by mutations in the OCRL1 gene, which encodes a 105-kDa Golgi protein with phosphatidylinositol (4,5) bisphosphate 5-phosphatase activity. genetics | mutation | has parent organization: NCBI | Lowe syndrome | NHGRI | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00155 | http://research.nhgri.nih.gov/lowe/ | SCR_002907 | Lowe Syndrome Mutation Database | 2026-02-16 09:45:52 | 1 | |||||
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Patterns of Gene Expression in Drosophila Embryogenesis Resource Report Resource Website 50+ mentions |
Patterns of Gene Expression in Drosophila Embryogenesis (RRID:SCR_002868) | BDGP insitu | image collection, database, source code, software resource, data or information resource | Database of embryonic expression patterns using a high throughput RNA in situ hybridization of the protein-coding genes identified in the Drosophila melanogaster genome with images and controlled vocabulary annotations. At the end of production pipeline gene expression patterns are documented by taking a large number of digital images of individual embryos. The quality and identity of the captured image data are verified by independently derived microarray time-course analysis of gene expression using Affymetrix GeneChip technology. Gene expression patterns are annotated with controlled vocabulary for developmental anatomy of Drosophila embryogenesis. Image, microarray and annotation data are stored in a modified version of Gene Ontology database and the entire dataset is available on the web in browsable and searchable form or MySQL dump can be downloaded. So far, they have examined expression of 7507 genes and documented them with 111184 digital photographs. | embryo, embryogenesis, gene, anatomy, microarray, pattern, protocol, rna, gene expression, expression pattern, embryonic drosophila, in situ hybridization, annotation, est, FASEB list |
is related to: Gene Ontology has parent organization: Berkeley Drosophila Genome Project |
Howard Hughes Medical Institute ; NIH ; NIGMS R01 GM076655; NHGRI HG00750; NHGRI P41 HG00739 |
PMID:17645804 PMID:12537577 |
Free, Freely available, Available for download | nif-0000-25550, r3d100011327 | https://doi.org/10.17616/R32H0K | http://www.fruitfly.org/cgi-bin/ex/insitu.pl | SCR_002868 | BDGP Embryonic Expression Patterns | 2026-02-16 09:45:56 | 64 | |||
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pVACtools Resource Report Resource Website 10+ mentions |
pVACtools (RRID:SCR_025435) | software toolkit, software resource | Software toolkit to identify and visualize cancer neoantigens. Cancer immunotherapy tools suite consisting of following tools: pVACseq as cancer immunotherapy pipeline for identifying and prioritizing neoantigens from VCF file; pVACbind as cancer immunotherapy pipeline for identifying and prioritizing neoantigens from FASTA file; pVACfuse as tool for detecting neoantigens resulting from gene fusions; pVACvector as tool designed to aid specifically in construction of DNA-based cancer vaccines; pVACview as application based on R Shiny that assists users in reviewing, exploring and prioritizing neoantigens from results of pVACtools processes for personalized cancer vaccine design. | Cancer immunotherapy tools, identify and visualize cancer neoantigens, | NCI U01CA209936; NCI U01CA231844; NCI U24CA237719; NHGRI R00HG007940; V Foundation for Cancer Research |
PMID:31907209 | Free, Freely available | SCR_025435 | 2026-02-15 09:23:00 | 27 | |||||||||
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SomaticSeq Resource Report Resource Website 1+ mentions |
SomaticSeq (RRID:SCR_024891) | software toolkit, software resource | Software accurate somatic mutation detection pipeline implementing stochastic boosting algorithm to produce somatic mutation calls for both single nucleotide variants and small insertions and deletions. NGS variant calling and classification. | NGS variant calling and classification, somatic mutation detection, somatic mutation calls, single nucleotide variants, detect somatic mutations, | NIGMS R01 GM109836; NHGRI R01 HG007834 |
PMID:26381235 | SCR_024891 | 2026-02-15 09:23:52 | 6 | ||||||||||
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Guided Sparse Factor Analysis Resource Report Resource Website 1+ mentions |
Guided Sparse Factor Analysis (RRID:SCR_025023) | GSFA | software toolkit, software resource | Software R package that performs sparse factor analysis and differential gene expression discovery simultaneously on single cell CRISPR screening data. | sparse factor analysis, differential gene expression, discovery simultaneously, single cell CRISPR screening data, | NIMH R01MH110531; NHGRI R01HG010773; NIMH R01MH116281; NIGMS R01 GM126553; NHGRI R01 HG011883; NSF ; Sloan Research Fellowship |
PMID:37770710 | Free, Available for download, Freely available | SCR_025023 | 2026-02-15 09:23:44 | 1 | ||||||||
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Winnowmap Resource Report Resource Website 10+ mentions |
Winnowmap (RRID:SCR_025349) | source code, software resource | Software tool as long-read mapping algorithm optimized for mapping ONT and PacBio reads to repetitive reference sequences. Winnowmap2 computes each read mapping through collection of confident subalignments. This approach is more tolerant of structural variation and more sensitive to paralog-specific variants within repeats. | long-read mapping, ONT and PacBio reads, repetitive reference sequences, paralog specific variants within repeats, | NHGRI ; Indian Institute of Science |
PMID:35365778 | Free, Available for download, Freely available | SCR_025349 | Winnowmap2 | 2026-02-15 09:23:51 | 17 | ||||||||
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forqs Resource Report Resource Website |
forqs (RRID:SCR_000643) | forqs | software application, software resource, simulation software | Software for forward-in-time population genetics simulation that tracks individual haplotype chunks as they recombine each generation. It also also models quantitative traits and selection on those traits. | c++, linux, osx, windows, command line, simulation, recombination, quantitative trait, selection, haplotype pattern |
is listed by: OMICtools has parent organization: University of California at Los Angeles; California; USA has parent organization: Bitbucket |
NHGRI HG002536; NHGRI R01 HG007089; NSF EF-0928690 |
PMID:24336146 | Free, Available for download, Freely available | OMICS_02196 | SCR_000643 | Forward-in-time simulation of Recombination, and Selection, Quantitative traits | 2026-02-16 09:45:18 | 0 | |||||
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Drosophila anatomy and development ontologies Resource Report Resource Website |
Drosophila anatomy and development ontologies (RRID:SCR_001607) | FBbt | ontology, data or information resource, controlled vocabulary | A structured controlled vocabulary of the anatomy of Drosophila melanogaster. These ontologies are query-able reference sources for information on Drosophila anatomy and developmental stages. They also provide controlled vocabularies for use in annotation and classification of data related to Drosophila anatomy, such as gene expression, phenotype and images. They were originally developed by FlyBase, who continue to maintain them and have used them for over 200,000 annotations of phenotypes and expression. Extensive use of synonyms means that, given a suitably sophisticated autocomplete, users can find relevant content by searching with almost any anatomical term they find in the literature. These ontologies are developed in the web ontology language OWL2. Their extensive formalization in OWL can be used to drive sophisticated query systems. | anatomy, development, developmental stage, gene expression, phenotype, owl |
is related to: OBO is related to: Flannotator is related to: REDfly Regulatory Element Database for Drosophilia is related to: Bgee: dataBase for Gene Expression Evolution has parent organization: FlyBase has parent organization: SourceForge |
NHGRI P41 HG000739 | Free, Freely available | nlx_153871 | SCR_001607 | Drosophila anatomy & dev ontologies | 2026-02-16 09:45:32 | 0 | ||||||
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Biological Pathways Exchange Resource Report Resource Website 50+ mentions |
Biological Pathways Exchange (RRID:SCR_001681) | controlled vocabulary, project portal, portal, ontology, data or information resource | Community standard for pathway data sharing. Standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. Supports data exchange between pathway data groups and thus reduces complexity of interchange between data formats by providing accepted standard format for pathway data. Open and collaborative effort by community of researchers, software developers, and institutions. BioPAX is defined in OWL DL and is represented in RDF/XML format.Uses W3C standard Web Ontology Language, OWL. | Standard language, community standard, pathway data sharing, biological pathway data, data exchange, W3C standard, Web Ontology Language, OWL, |
is listed by: BioPortal is related to: cPath is related to: Biofactoid is related to: PathGuide: the pathway resource list |
U.S. Department of Energy Workshop ; NHGRI P41HG004118 |
PMID:20829833 | Free, Available for download, Freely available | SCR_009881, nlx_157327, nif-0000-10171 | http://purl.bioontology.org/ontology/BP | SCR_001681 | BioPAX, BioPAX: Biological Pathways Exchange | 2026-02-16 09:45:33 | 90 | |||||
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Type 1 Diabetes Genetics Consortium Resource Report Resource Website 1+ mentions |
Type 1 Diabetes Genetics Consortium (RRID:SCR_001557) | T1DGC | research forum portal, resource, topical portal, portal, data or information resource, disease-related portal | Data and biological samples were collected by this consortium organizing international efforts to identify genes that determine an individual risk of type 1 diabetes. It originally focused on recruiting families with at least two siblings (brothers and/or sisters) who have type 1 diabetes (affected sibling pair or ASP families). The T1DGC completed enrollment for these families in August 2009. They completed enrollment of trios (father, mother, and a child with type 1 diabetes), as well as cases (people with type 1 diabetes) and controls (people with no history of type 1 diabetes) from populations with a low prevalence of this disease in January 2010. T1DGC Data and Samples: Phenotypic and genotypic data as well as biological samples (DNA, serum and plasma) for T1DGC participants have been deposited in the NIDDKCentral Repositories for future research. | gene, genetics, genotyping, analytic, dna, serum, plasma, data set, biomaterial supply resource, phenotypic, genotypic, autoantibody, hla, phenotype, genotype |
is listed by: One Mind Biospecimen Bank Listing is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Central Repository |
Type 1 diabetes, Diabetes | NIDDK ; NIAID ; NHGRI ; JDRF |
PMID:17130525 | Free, Freely available | nlx_152867 | SCR_001557 | Type 1 Diabetes Genetics Consortium (T1DGC) | 2026-02-16 09:45:31 | 2 | ||||
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Liftoff Resource Report Resource Website 10+ mentions |
Liftoff (RRID:SCR_026535) | source code, software resource | Software genome annotation lift-over tool capable of mapping genes between two assemblies of the same or closely related species. Aligns genes from reference genome to target genome and finds the mapping that maximizes sequence identity while preserving the structure of each exon, transcript and gene. Used for accurate mapping of gene annotations. | Aligns genes, reference genome to target genome alignment, mapping of gene annotations, genome annotation lift-over, mapping genes between two assemblies of species, mapping genes, same or closely related species, | NHGRI R01 HG006677; NIGMS R35 GM130151 |
PMID:33320174 | Free, Available for download, Freely available | SCR_026535 | 2026-02-15 09:23:18 | 10 | |||||||||
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HiGlass Resource Report Resource Website 10+ mentions |
HiGlass (RRID:SCR_026687) | web application, source code, software resource | Web-based visual exploration and analysis of genome interaction maps. | visual exploration and analysis, genome interaction maps, | NCI U01CA200059; NHGRI R00 HG007583; NHGRI U54 HG007963 |
PMID:30143029 | Free, Available for download, Freely available | SCR_026687 | 2026-02-15 09:23:21 | 45 | |||||||||
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apeglm Resource Report Resource Website |
apeglm (RRID:SCR_026951) | software toolkit, software resource | Software package provides Bayesian shrinkage estimators for effect sizes for variety of GLM models, using approximation of posterior for individual coefficients. | Bayesian shrinkage estimators, | NHGRI R01 HG009125; NCI P01 CA142538; NIEHS P30 ES010126; NIGMS R01 GM070335 |
PMID:30395178 | Free, Available for download, Freely available, | SCR_026951 | , Approximate Posterior Estimation for generalized linear model, Approximate posterior estimation for GLM | 2026-02-15 09:24:04 | 0 |
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