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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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Gene Ontology Resource Report Resource Website 10000+ mentions |
Gene Ontology (RRID:SCR_002811) | GO | consortium, data or information resource, knowledge environment resource, organization portal, portal, project portal | 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 is organization facet of: Alliance of Genome Resources |
European Union QLRI-CT-2001-00015; European Union QLRI-CT-2001-0098; 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 | SciCrunch Registry | the Gene Ontology, GO, Gene Ontology Resource, Gene Ontology | 2026-10-24 12:44:48 | 12993 | ||||
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OnEx - Ontology Evolution Explorer Resource Report Resource Website 1+ mentions |
OnEx - Ontology Evolution Explorer (RRID:SCR_000602) | OnEx | software resource, web application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Web-based application that integrates versions of 16 life science ontologies including the Gene Ontology, NCI Thesaurus and selected OBO ontologies with data leading back to 2002 in a common repository to explore ontology changes. It allows to study and apply the evolution of these integrated ontologies on three different levels. It provides global ontology evolution statistics and ontology-specific evolution trends for concepts and relationships and it allows the migration of annotations in case a new ontology version was released | ontology, gene, protein, function, process, component, ontology or annotation browser, evolution, trend, annotation, version |
is listed by: OMICtools is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: NCI Thesaurus is related to: OBO has parent organization: University of Leipzig; Saxony; Germany |
BMBF 01AK803E; DFG |
PMID:19678926 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02273, nlx_149129 | http://www.izbi.de/onex, http://aprilia.izbi.uni-leipzig.de:8080/onex/ | SCR_000602 | SciCrunch Registry | Ontology Evolution Explorer (OnEx), Ontology Evolution Explorer | 2026-10-24 12:44:20 | 1 | ||||
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Ontology Lookup Service Resource Report Resource Website 10+ mentions |
Ontology Lookup Service (RRID:SCR_006596) | OLS | data access protocol, data or information resource, database, software resource, source code, web service | Interactive and programmatic interfaces to query, browse and navigate an increasing number of biomedical ontologies and controlled vocabularies. It provides a web service interface to query multiple ontologies from a single location with a unified output format. It can integrate any ontology available in the Open Biomedical Ontology (OBO) format. The database can be queried to obtain information on a single term or to browse a complete ontology using AJAX. Auto-completion provides a user-friendly search mechanism. An AJAX-based ontology viewer is available to browse a complete ontology or subsets of it. A weekly MySQL database export file can be downloaded from the EBI public FTP directory. | ontology, ontology or annotation browser, ontology or annotation search engine, gold standard |
lists: Cell Type Ontology is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: OBO-Edit is related to: OBO has parent organization: European Bioinformatics Institute |
BBSRC ; iSPIDER ; European Union FP6 Felics contract 021902 (RII3) |
PMID:18467421 PMID:16507094 |
Apache License, v2, Acknowledgement requested | OMICS_02275, nif-0000-10390, r3d100010413 | https://doi.org/10.17616/R3GS9G | http://www.ebi.ac.uk/ols | SCR_006596 | SciCrunch Registry | OLS - Ontology Lookup Service, Ontology Lookup Service (OLS) | 2026-10-24 12:45:45 | 24 | |||
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OntoVisT Resource Report Resource Website 1+ mentions |
OntoVisT (RRID:SCR_005674) | OntoVisT | data or information resource, database, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 07, 2013. Web based ontological visualization tool for interactive visualization of any ontological hierarchy for a specific node of interest, up to the chosen level of children and/or ancestor. It takes any ontology file in OBO format as input and generates output as DAG hierarchical graph for the chosen query. To enhance the navigation capabilities of complex networks, we have embedded several features such as search criteria, zoom in/out, center focus, nearest neighbor highlights and mouse hover events. The application has been tested on all 72 data sets available in OBO format through OBO foundry. The results for few of them can be accessed through OntoVisT-Gallery. | ontology, visualization, web service, gene ontology, ontology or annotation browser, ontology or annotation search engine, ontology or annotation visualization, dag hierarchical form, dag, windows, mac os x, linux, unix |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: OBO has parent organization: Jawaharlal Nehru University; New Delhi; India |
Council of Scientific and Industrial Research; New Delhi; India ; Jawaharlal Nehru University; New Delhi; India ; Department of Biotechnology |
PMID:21738333 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02274, nlx_149113 | SCR_005674 | SciCrunch Registry | OntoVisT: A General purpose Ontological Visualization Tool | 2026-10-24 12:50:35 | 1 | |||||
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go-perl Resource Report Resource Website 10+ mentions |
go-perl (RRID:SCR_005730) | go-perl | software resource | go-perl is a set of Perl modules for parsing, manipulating and exporting ontologies and annotations. It includes parsers for the OBO and GO gene association file formats. It has a graph-based object model with methods for graph traversal. For more details, see the documentation included with the modules. go-perl comes bundled with XSL (Extensible Stylesheet Language) transforms (which can also be used independently of Perl, provided you have files in OBO-XML format), as well as scripts that can be used as standalone tools. Installation should be simple, provided you have some experience with Perl and CPAN; see the INSTALL file for details. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | ontology, annotation, software library, slimmer-type tool, parser |
is listed by: Gene Ontology Tools is related to: OBO is related to: go-moose is related to: go-db-perl has parent organization: Comprehensive Perl Archive Network has parent organization: Gene Ontology |
Free for academic use | nlx_149190 | SCR_005730 | SciCrunch Registry | 2026-10-24 12:45:32 | 11 | ||||||||
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OWLTools Resource Report Resource Website 10+ mentions |
OWLTools (RRID:SCR_005732) | OWLTools | software resource | OWLTools (aka OWL2LS - OWL2 Life Sciences) is a java API for accessing ontologies in either OBO or OWL. OWLTools provides a bio-ontologies friendly wrapper on top of the Manchester OWL API. It provides many features, including: * convenience methods for OBO-like properties such as synonyms, textual definitions, obsoletion, replaced_by * simple graph-like operations over ontologies * visualization using the QuickGO graphs libraries Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | software library, ontology |
is listed by: Gene Ontology Tools is related to: OBO has parent organization: Gene Ontology has parent organization: Google Project Hosting is parent organization of: OwlSim |
Open unspecified license - Free for academic use | nlx_149192 | SCR_005732 | SciCrunch Registry | OWL2LS - OWL2 Life Sciences, OWL Tools | 2026-10-24 12:45:31 | 18 | |||||||
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Berkeley Bioinformatics Open-Source Projects Resource Report Resource Website 1+ mentions |
Berkeley Bioinformatics Open-Source Projects (RRID:SCR_006704) | BBOP | data or information resource, portal, software resource, topical portal | The BBOP, located at the Lawrence Berkeley National Labs, is a diverse group of scientific researchers and software engineers dedicated to developing tools and applying computational technologies to solve biological problems. Members of the group contribute to a number of projects, including the Gene Ontology, OBO Foundry, the Phenotypic Quality Ontology, modENCODE, and the Generic Model Organism Database Project. Our group is focused on the development, use, and integration of ontolgies into biological data analysis. Software written or maintained by BBOP is accessible through the site. | ontology, biology, computation, data analysis |
is related to: AmiGO has parent organization: Lawrence Berkeley National Laboratory is parent organization of: Blip: Biomedical Logic Programming is parent organization of: OwlSim is parent organization of: OBO is parent organization of: go-moose is parent organization of: GO Online SQL Environment (GOOSE) |
NHGRI ; NIGMS |
nlx_149171 | SCR_006704 | SciCrunch Registry | Berkeley BOP | 2026-10-24 12:45:50 | 1 | |||||||
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COBrA Resource Report Resource Website 1000+ mentions |
COBrA (RRID:SCR_005677) | COBrA | software resource | COBrA is a Java-based ontology editor for bio-ontologies that distinguishes itself from other editors by supporting the linking of concepts between two ontologies, and providing sophisticated analysis and verification functions. In addition to the Gene Ontology and Open Biology Ontologies formats, COBrA can import and export ontologies in the Semantic Web formats RDF, RDFS and OWL. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | ontology, anatomy, browser, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: OBO has parent organization: University of Edinburgh; Scotland; United Kingdom |
BBSRC 15/BEP 17046 | PMID:15513995 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149117 | SCR_005677 | SciCrunch Registry | COBrA - An Ontology Browser for Anatomy, COBrA: a bio-ontology editor | 2026-10-24 12:45:30 | 1396 | |||||
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OBO-Edit Resource Report Resource Website 10+ mentions |
OBO-Edit (RRID:SCR_005668) | OBO-Edit | software application, software resource, source code | OBO-Edit is an open source, platform-independent application written in Java for viewing and editing any OBO format ontologies. OBO-Edit is a graph-based tool; its emphasis on the overall graph structure of an ontology provides a friendly interface for biologists, and makes OBO-Edit excellent for the rapid generation of large ontologies focusing on relationships between relatively simple classes. The UI components are cleanly separated from the data model and data adapters, so these can be reused in other applications. The oboedit foward-chaining reasoner can also be used independently (for example, for traversing ontology graphs). OBO-Edit uses the OBO format flat file. See the GO wiki, http://wiki.geneontology.org/index.php/OBO-Edit:_Getting_the_Source_Code, for instructions on downloading the source code. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | ontology, browser, search engine, visualization, editor, software library, ontology or annotation browser, ontology or annotation search engine, ontology or annotation visualization, ontology or annotation editor |
is listed by: Gene Ontology Tools is related to: OBO is related to: Ontology Lookup Service is related to: Phenote: A Phenotype Annotation Tool using Ontologies has parent organization: Gene Ontology |
PMID:17545183 | Open unspecified license - Free for academic use | nlx_149107 | http://org.geneontology.oboedit | SCR_005668 | SciCrunch Registry | OBO-Edit: The OBO Ontology Editor | 2026-10-24 12:50:35 | 21 | |||||
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LexGrid Resource Report Resource Website 1+ mentions |
LexGrid (RRID:SCR_006627) | LexGrid | software resource | LexGrid (Lexical Grid) provides support for a distributed network of lexical resources such as terminologies and ontologies via standards-based tools, storage formats, and access/update mechanisms. The Lexical Grid Vision is for a distributed network of terminological resources. It is the foundation of the National Center for Biomedical Ontology BioPortal interface and web-services, and can parse OBO format, as well as other formats such as OWL. Currently, there are many terminologies and ontologies in existence. Just about every terminology has its own format, its own set of tools, and its own update mechanisms. The only thing that most of these pieces have in common with each other is their incompatibility. This makes it very hard to use these resources to their full potential. We have designed the Lexical Grid as a way to bridge terminologies and ontologies with a common set of tools, formats and update mechanisms. The Lexical Grid is: * accessible through a set of common APIs * joined through shared indices * online accessible * downloadable * loosely coupled * locally extendable * globally revised * available in web-space on web-time * cross-linked The realization of this vision requires three interlocking components, which are: * Standards - access methods and formats need to be published and openly available * Tools - standards based tools must be readily available * Content - commonly used terminologies have to be available for access and download Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | software library, parse, ontology |
is listed by: BioPortal is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: OBO has parent organization: European Bioinformatics Institute has parent organization: National Cancer Institute |
NIH ; Cancer Biomedical Informatics Grid ; NLM LM07319 |
PMID:19261933 | Free for academic use | nlx_149194 | http://www.lexgrid.org/ | SCR_006627 | SciCrunch Registry | Lexical Grid | 2026-10-24 12:45:48 | 1 | ||||
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ONTO-PERL Resource Report Resource Website |
ONTO-PERL (RRID:SCR_005731) | ONTO-PERL | software resource, source code | ONTO-PERL is a collection of Perl modules to handle OBO-formatted ontologies (like the Gene Ontology). This code distribution gathers object-oriented modules (for dealing with ontology elements such as Term, Relationship and so forth), scripts (for typical tasks such as format conversions: obo2owl, owl2obo; besides, there are also many examples that can be easily adapted for specific applications), and a set of test files to ensure the suite''''s implementation quality. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | application programming interface, software library, ontology, analysis, development, biomedical |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: OBO has parent organization: Comprehensive Perl Archive Network has parent organization: Norwegian University of Science and Technology; Trondheim; Norway |
European Union FP6 LSHG-CT-2004-512143; European Union FP6 MEST-CT-2004-414632 |
PMID:18245124 | Free for academic use | nlx_149191 | SCR_005731 | SciCrunch Registry | 2026-10-24 12:52:08 | 0 | ||||||
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Wandora Resource Report Resource Website |
Wandora (RRID:SCR_005689) | Wandora | software application, software resource | Wandora is a general purpose information extraction, management and publishing application based on Topic Maps and Java. Wandora has graphical user interface, layered and merging information model, multiple visualization models, huge collection of information extraction, import and export options, embedded HTTP server with several output modules and open plug-in architecture. Wandora is a FOSS application with GNU GPL license. Wandora is well suited for constructing ontologies and information mashups. Wandora is capable of extracting and converting a wide range of open data feeds to topic map formats. Beyond topic map conversion, this feature allows Wandora user to aggregate multidimensional information mashups where information from Flickr interleaves with information from GeoNames and YouTube, for example. Wandora is a software application to build, edit, publish and visualize information graphs, especially topic maps. Wandora is written in Java and suits for * Collecting, combining, aggregating, managing, refining and publishing information and knowledge graphs * Designing information, information modeling and prototyping * Information mashups * Ontology creation and management * Mind and concept mapping * Language technology applications * Graph visualizations * Knowledge format conversions * Digital preservation * Data journalism * Open data projects * Linked data projects Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | visualization, ontology, ontology or annotation browser, knowledge management system |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: OBO |
Open unspecified license (GNU GPL v3) - Free for academic use | nlx_149134 | SCR_005689 | SciCrunch Registry | 2026-10-24 12:51:26 | 0 | ||||||||
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BioPerl Resource Report Resource Website 100+ mentions |
BioPerl (RRID:SCR_002989) | BioPerl | data or information resource, narrative resource, software repository, software resource, software toolkit, source code, wiki | BioPerl is a community effort to produce Perl code which is useful in biology. This toolkit of perl modules is useful in building bioinformatics solutions in Perl. It is built in an object-oriented manner so that many modules depend on each other to achieve a task. The collection of modules in the bioperl-live repository consist of the core of the functionality of bioperl. Additionally auxiliary modules for creating graphical interfaces (bioperl-gui), persistent storage in RDMBS (bioperl-db), running and parsing the results from hundreds of bioinformatics applications (Run package), software to automate bioinformatic analyses (bioperl-pipeline) are all available as Git modules in our repository. The BioPerl toolkit provides a library of hundreds of routines for processing sequence, annotation, alignment, and sequence analysis reports. It often serves as a bridge between different computational biology applications assisting the user to construct analysis pipelines. This chapter illustrates how BioPerl facilitates tasks such as writing scripts summarizing information from BLAST reports or extracting key annotation details from a GenBank sequence record. BioPerl includes modules written by Sohel Merchant of the GO Consortium for parsing and manipulating OBO ontologies. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | perl, biology, ontology, library, sequence, analysis, computational, application, pipeline, bioinformatics, sequence, annotation, module, life science, python, java, genome, software library, parse, manipulate, bio.tools |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite is related to: Gene Ontology is related to: OBO has parent organization: Duke University; North Carolina; USA has parent organization: European Bioinformatics Institute is required by: RelocaTE |
NIGMS T32 GM07754-22; NHGRI K22 HG00056; NHGRI K22 HG-00064-01; NHGRI HG00739; NHGRI P41HG02223 |
PMID:12368254 DOI:10.1101/gr.361602 |
Free, Available for download, Freely available | OMICS_04849, nif-0000-30188, biotools:bioperl | https://bio.tools/bioperl, https://sources.debian.org/src/bioperl/ | SCR_002989 | SciCrunch Registry | 2026-10-24 12:44:50 | 408 |
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