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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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L2L Microarray Analysis Tool Resource Report Resource Website 1+ mentions |
L2L Microarray Analysis Tool (RRID:SCR_013440) | L2L | software application, data analysis service, data processing software, software resource, database, service resource, storage service resource, production service resource, data repository, data or information resource, analysis service resource, data analysis software |
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on August 26, 2019. Database of published microarray gene expression data, and a software tool for comparing that published data to a user''''s own microarray results. It is very simple to use - all you need is a web browser and a list of the probes that went up or down in your experiment. If you find L2L useful please consider contributing your published data to the L2L Microarray Database in the form of list files. L2L finds true biological patterns in gene expression data by systematically comparing your own list of genes to lists of genes that have been experimentally determined to be co-expressed in response to a particular stimulus - in other words, published lists of microarray results. The patterns it finds can point to the underlying disease process or affected molecular function that actually generated the observed changed in gene expression. Its insights are far more systematic than critical gene analyses, and more biologically relevant than pure Gene Ontology-based analyses. The publications included in the L2L MDB initially reflected topics thought to be related to Cockayne syndrome: aging, cancer, and DNA damage. Since then, the scope of the publications included has expanded considerably, to include chromatin structure, immune and inflammatory mediators, the hypoxic response, adipogenesis, growth factors, hormones, cell cycle regulators, and others. Despite the parochial origins of the database, the wide range of topics covered will make L2L of general interest to any investigator using microarrays to study human biology. In addition to the L2L Microarray Database, L2L contains three sets of lists derived from Gene Ontology categories: Biological Process, Cellular Component, and Molecular Function. As with the L2L MDB, each GO sub-category is represented by a text file that contains annotation information and a list of the HUGO symbols of the genes assigned to that sub-category or any of its descendants. You don''''t need to download L2L to use it to analyze your microarray data. There is an easy-to-use web-based analysis tool, and you have the option of downloading your results so you can view them at any time on your own computer, using any web browser. However, if you prefer, the entire L2L project, and all of its components, can be downloaded from the download page. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible |
microarray, gene expression, adipogenesis, biological, biological process, cancer, cell cycle regulator, cellular component, chromatin, cockayne syndrome, dna damage, growth factor, hormone, human biology, hypoxic response, immune mediator, inflammatory mediator, molecular function, molecular neuroanatomy resource, adipocyte, development, hypoxia, immune, inflammation, metabolism, mitogen, neuro, rna, vascular, transcription, tissue, splicing, mouse, human, rat, source code, statistical analysis, gene, chromatin structure |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of Washington; Seattle; USA |
Cockayne syndrome, DNA damage, Other, Aging, Cancer | Cora May Poncin Foundation ; NIGMS GM41624 |
PMID:16168088 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10463 | http://depts.washington.edu/l2l/about.html | SCR_013440 | L2L Microarray Database, L2L Microarray Analysis Tool: A simple tool for discovering the hidden biological significance in microarray expression data, L2L MDB | 2026-02-15 09:20:28 | 1 | |||
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PiGenome Resource Report Resource Website |
PiGenome (RRID:SCR_013394) | PiGenome | data analysis service, database, service resource, production service resource, data or information resource, analysis service resource | Database for ESTs (Expressed Sequence Tags), consensus sequences, bacterial artificial chromosome (BAC) clones, BES (BAC End Sequences). They have generated 69,545 ESTs from 6 full-length cDNA libraries (Porcine Abdominal Fat, Porcine Fat Cell, Porcine Loin Muscle, Liver and Pituitary gland). They have also identified a total of 182 BAC contigs from chromosome 6. It is very valuable resources to study porcine quantitative trait loci (QTL) mapping and genome study. Users can explore genomic alignment of various data types, including expressed sequence tags (ESTs), consensus sequences, singletons, QTL, Marker, UniGene and BAC clones by several options. To estimate the genomic location of sequence dataset, their data aligned BES (BAC End Sequences) instead of genomic sequence because Pig Genome has low-coverage sequencing data. Sus scrofa Genome Database mainly provide comparative map of four species (pig, cattle, dog and mouse) in chromosome 6. | gene expression, genome, sequence, gene, expressed sequence tag, consensus sequence, bac clone, bac end sequence, bac contig, quantitative trait loci, singleton, marker, unigene, chromosome 6, blast, transcript, bacterial artificial chromosome, snp, alignment |
is related to: Gene Ontology has parent organization: National Institute of Animal Science; Gyeonggi-do; South Korea |
National Institute of Animal Science; Gyeonggi-do; Korea ; Korean Rural Development Administration ; Biogreen21 Project 20050301034467 |
PMID:19082661 | nlx_153888 | http://pigenome.nabc.go.kr/ | SCR_013394 | Sus scrofa Genome database, Pig Genome Database, Pigenome database | 2026-02-15 09:20:43 | 0 | |||||
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PlantNATsDB - Plant Natural Antisense Transcripts DataBase Resource Report Resource Website 1+ mentions |
PlantNATsDB - Plant Natural Antisense Transcripts DataBase (RRID:SCR_013278) | PlantNATsDB | data analysis service, database, service resource, production service resource, data or information resource, analysis service resource | Natural Antisense Transcripts (NATs), a kind of regulatory RNAs, occur prevalently in plant genomes and play significant roles in physiological and/or pathological processes. PlantNATsDB (Plant Natural Antisense Transcripts DataBase) is a platform for annotating and discovering NATs by integrating various data sources involving approximately 2 million NAT pairs in 69 plant species. PlantNATsDB also provides an integrative, interactive and information-rich web graphical interface to display multidimensional data, and facilitate plant research community and the discovery of functional NATs. GO annotation and high-throughput small RNA sequencing data currently available were integrated to investigate the biological function of NATs. A ''''Gene Set Analysis'''' module based on GO annotation was designed to dig out the statistical significantly overrepresented GO categories from the specific NAT network. PlantNATsDB is currently the most comprehensive resource of NATs in the plant kingdom, which can serve as a reference database to investigate the regulatory function of NATs. | natural antisense transcript, annotation, high-throughput, small rna sequencing, function, regulatory function, predict, sequence, small rna, blast, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: Gene Expression Omnibus has parent organization: Zhejiang University; Zhejiang; China |
National Natural Sciences Foundation of China 30971743; National Natural Sciences Foundation of China 31050110121; National Natural Sciences Foundation of China 31071659; Ministry of Science and Technology of China 2009DFA32030; Program for New Century Excellent Talents in University of China NCET-07-0740; Huazhong Agricultural University Scientific and Technological Self-innovation Foundation 2010SC07 |
PMID:22058132 | Free | nlx_151492, biotools:plantnatsdb | https://bio.tools/plantnatsdb | SCR_013278 | Plant Natural Antisense Transcripts DataBase | 2026-02-15 09:20:26 | 9 | ||||
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GOnet Resource Report Resource Website 1+ mentions |
GOnet (RRID:SCR_018977) | software resource, data access protocol, web service, service resource, production service resource, analysis service resource | Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists. | Gene Ontology, interactive analysis, data, gene, protein, gene list, protein list, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools works with: Gene Ontology |
NIH Common Fund ; NIGMS ; NHGRI R24 HG010032; NIAID U19 AI118610; NIAID U19 AI118626 |
PMID:30526489 | biotools:GOnet | https://github.com/mikpom/gonet https://bio.tools/GOnet |
SCR_018977 | 2026-02-15 09:22:25 | 3 | |||||||
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SynGO Resource Report Resource Website 100+ mentions |
SynGO (RRID:SCR_017330) | data analysis service, ontology, service resource, production service resource, data or information resource, controlled vocabulary, analysis service resource | Evidence based, expert curated knowledge base for synapse. Universal reference for synapse research and online analysis platform for interpretation of omics data. Interactive knowledge base that accumulates available research about synapse biology using Gene Ontology annotations to novel ontology terms. | Synapse, evidence, curated, base, reference, analysis, omics, data, ontology, gene, annotation | uses: Gene Ontology | Stanley Center for Psychiatric Research at The Broad Institute of MIT and Harvard ; European Union ; CERCA Program/Generalitat de Catalunya ; NINDS NS36251; German Federal Ministry of Education and Research |
PMID:31171447 | Free, Freely available | SCR_017330 | Synaptic Gene Ontologies | 2026-02-15 09:21:18 | 134 | |||||||
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Gene Ontology Browsing Utility (GOBU) Resource Report Resource Website |
Gene Ontology Browsing Utility (GOBU) (RRID:SCR_005662) | GOBU | source code, software resource | Gene Ontology Browsing Utility (GOBU) (GOBU) is a Java-based software program for integrating biological annotation catalogs under an extendable software architecture. Users may interact with the Gene Ontology and user-defined hierarchy data of genes, and then use its plugins to (and not limited to) (1) browse the GO hierarchy with user defined data, (2) browse GO-oriented expression levels in the user data, (3) compute GO enrichment, and/or (4) customize data reporting. A set of classes and utility functions has been established so that a customized program can be made as a plugin or a command-line tool that programmically manipulate the Gene Ontology and specified user data. See the source code repository for examples. Reference Lin WD, Chen YC, Ho JM, Hsiao CD. GOBU: Toward an Integration Interface for Biological Objects. Journal of Information Science and Engineering. 2006 22(1):19-29. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | annotation, gene, browser, computation, visualization, software library, statistical analysis, term enrichment, ontology or annotation browser, ontology or annotation visualization |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Academia Sinica; Taipei; Taiwan |
Open unspecified license - Free for academic use | nlx_149098 | SCR_005662 | Gene Ontology Browsing Utility | 2026-02-15 09:19:09 | 0 | |||||||
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OWL API Resource Report Resource Website 10+ mentions |
OWL API (RRID:SCR_005734) | OWL API | source code, software resource | The OWL API is a Java API and reference implementation for creating, manipulating and serializing OWL Ontologies. The latest version of the API is focused towards OWL 2. The OWLAPI underpins ontology browsing and editing tools and platforms such as SWOOP and Protege4. Note that this API, or any other OWL-based API, can be used without an integrated OWL parser if you download a pre-converted OWL file generated from OBO. See OBO Ontologies List for all OBO ontologies converted to OWL (we do not list the full complement of OWL-based APIs here, only those of direct relevance to GO). The OWL API includes the following components: * An API for OWL 2 and an efficient in-memory reference implementation * RDF/XML parser and writer * OWL/XML parser and writer * OWL Functional Syntax parser and writer * Turtle parser and writer * KRSS parser * OBO Flat file format parser * Reasoner interfaces for working with reasoners such as FaCT++, HermiT, Pellet and Racer Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | ontology, owl, api, java, software library, parser, writer |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of Manchester; Manchester; United Kingdom has parent organization: SourceForge |
Open unspecified license - Free for academic use; available under either the LGPL or Apache Licenses | nlx_149195 | SCR_005734 | The OWL API, OWLAPI | 2026-02-15 09:19:02 | 15 | |||||||
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Quantitative Enrichment of Sequence Tags Resource Report Resource Website 10+ mentions |
Quantitative Enrichment of Sequence Tags (RRID:SCR_004065) | QuEST | software resource | A Kernel Density Estimator-based package for analysis of massively parallel sequencing data from chromatin immunoprecipitation (ChIP-seq) experiments. | genome-wide, transcription factor binding site, chip-seq, transcription factor, binding site, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: Stanford University; Stanford; California |
PMID:19160518 | OMICS_00458, biotools:quest | https://bio.tools/quest | SCR_004065 | Quantitative Enrichment of Sequence Tags: QuEST | 2026-02-14 02:00:40 | 49 | ||||||
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Neural-Immune Gene Ontology Resource Report Resource Website 1+ mentions |
Neural-Immune Gene Ontology (RRID:SCR_004120) | NIGO | data or information resource, ontology, controlled vocabulary | Ontology that is a subset of GO directed for neurological and immunological systems. It was created by clipping those GO terms that are not associated to any gene in human, rat and mouse, and by clipping terms not found to be relevant to the neural and/or immune domains. | obo |
is listed by: BioPortal is related to: Gene Ontology |
nlx_157506 | SCR_004120 | 2026-02-14 02:00:37 | 1 | |||||||||
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SO Resource Report Resource Website 10+ mentions |
SO (RRID:SCR_004374) | SO | data or information resource, ontology, controlled vocabulary | A collaborative ontology for the definition of sequence features used in biological sequence annotation. SO was initially developed by the Gene Ontology Consortium. Contributors to SO include the GMOD community, model organism database groups such as WormBase, FlyBase, Mouse Genome Informatics group, and institutes such as the Sanger Institute and the EBI. Input to SO is welcomed from the sequence annotation community. The OBO revision is available here: http://sourceforge.net/p/song/svn/HEAD/tree/ SO includes different kinds of features which can be located on the sequence. Biological features are those which are defined by their disposition to be involved in a biological process. Biomaterial features are those which are intended for use in an experiment such as aptamer and PCR_product. There are also experimental features which are the result of an experiment. SO also provides a rich set of attributes to describe these features such as polycistronic and maternally imprinted. The Sequence Ontologies use the OBO flat file format specification version 1.2, developed by the Gene Ontology Consortium. The ontology is also available in OWL from Open Biomedical Ontologies. This is updated nightly and may be slightly out of sync with the current obo file. An OWL version of the ontology is also available. The resolvable URI for the current version of SO is http://purl.obolibrary.org/obo/so.owl. | annotation, sequence, biological sequence, sequence variation, genome, genome annotation, owl, FASEB list |
is listed by: BioPortal is related to: ASOoViR is related to: VAGrENT has parent organization: OBO has parent organization: Gene Ontology |
NHGRI HG02273 | PMID:20796305 PMID:20226267 PMID:18629179 PMID:15892872 |
The community can contribute to this resource | nlx_38918 | SCR_004374 | Sequence Ontology Project, Sequence Types and Features Ontology, Sequence Ontology | 2026-02-14 02:00:58 | 44 | |||||
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Tk-GO Resource Report Resource Website |
Tk-GO (RRID:SCR_008855) | TkGO | software resource | Tk-GO is a GUI wrapping the basic functions of the GO AppHandle library from BDGP. GO terms are presented in an explorer-like browser, and behavior can be configured by altering Perl scripts. All available documentation is included in the download. Tk-GO uses the GO database (connects directly to the BDGP database by default) but is user-configurable. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | browser, gene, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Illumina |
MIT License - Free for academic use | nlx_149133 | SCR_008855 | 2026-02-14 02:01:46 | 0 | ||||||||
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Spotfire Resource Report Resource Website 100+ mentions |
Spotfire (RRID:SCR_008858) | Spotfire | software resource | The Spotfire Gene Ontology Advantage Application integrates GO annotations with gene expression analysis in Spotfire DecisionSite for Functional Genomics. Researchers can select a subset of genes in DecisionSite visualizations and display their distribution in the Gene Ontology hierarchy. Similarly, selection of any process, function or cellular location in the Gene Ontology hierarchy automatically marks the corresponding genes in DecisionSite visualizations. Platform: Windows compatible | analysis, predictive analytics, big data, visualization, gene ontology, annotation, gene expression, functional genomics, gene, function, cellular location, statistical analysis, genomics |
is listed by: Gene Ontology Tools is listed by: Metabolomics Workbench is related to: Gene Ontology |
Commercial license. Spotfire is available for purchase (individual license / enterprise use) / Free trial. | nlx_149169 | SCR_008858 | Tibco Spotfire, Spotfire Inc., Spotfire Gene Ontology Advantage Application, Spotfire - TIBCO Software | 2026-02-14 02:01:47 | 474 | |||||||
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DynGO Resource Report Resource Website 1+ mentions |
DynGO (RRID:SCR_007009) | DynGO | software resource | DynGO is a client-server application that provides several advanced functionalities in addition to the standard browsing capability. DynGO allows users to conduct batch retrieval of GO annotations for a list of genes and gene products, and semantic retrieval of genes and gene products sharing similar GO annotations (which requires more disk and memory to handle the semantic retrieval). The result are shown in an association tree organized according to GO hierarchies and supported with many dynamic display options such as sorting tree nodes or changing orientation of the tree. For GO curators and frequent GO users, DynGO provides fast and convenient access to GO annotation data. DynGO is generally applicable to any data set where the records are annotated with GO terms, as illustrated by two examples. Requirements: Java Platform: Windows compatible, Linux compatible, Unix compatible | gene, annotation, browser, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology |
NSF IIS-0430743 | PMID:16091147 | Free for academic use | nlx_149118 | http://gauss.dbb.georgetown.edu/liblab | SCR_007009 | DynGO: a tool for visualizing and mining of Gene Ontology and its associations | 2026-02-14 02:01:26 | 6 | ||||
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OBO Resource Report Resource Website 100+ mentions |
OBO (RRID:SCR_007083) | OBO | ontology, knowledge environment, data or information resource, controlled vocabulary, narrative resource, standard specification | A collaboration involving developers of science-based ontologies who are establishing a set of principles for ontology development with the goal of creating a suite of orthogonal interoperable reference ontologies in the biomedical domain. In addition to a listing of OBO ontologies, this site provides a statement of the OBO Foundry principles, discussion fora, technical infrastructure, and other services to facilitate ontology development. Feedback is welcome and participation encouraged. | biomedical, metadata standard, gold standard, FASEB list |
lists: CHEBI lists: NCI Thesaurus lists: Porifera Ontology lists: Gazetteer lists: Human Disease Ontology lists: Information Artifact Ontology lists: Teleost Anatomy Ontology lists: Gene Ontology lists: Spider Ontology lists: Mental Functioning Ontology lists: Ascomycete Phenotype Ontology lists: Beta Cell Genomics Ontology lists: Biological Collections Ontology lists: Emotion Ontology lists: Chemical Methods Ontology lists: Chemical Information Ontology lists: Clinical Measurement Ontology lists: Common Anatomy Reference Ontology lists: Experimental Conditions Ontology lists: Dictyostelium Discoideum Anatomy Ontology lists: Fission Yeast Phenotype Ontology lists: Fly Taxonomy lists: FlyBase Controlled Vocabulary lists: Hymenoptera Anatomy Ontology lists: Influenza Ontology lists: Lipid Ontology lists: Kinetic Simulation Algorithm Ontology lists: Malaria Ontology lists: Measurement Method Ontology lists: Minimal Anatomical Terminology lists: Ontology for Genetic Interval lists: Ontology for Parasite LifeCycle lists: Ontology of Adverse Events lists: Ontology of Medically Related Social Entities lists: Ontology of Vaccine Adverse Events lists: Rat Strain Ontology lists: Plant Environmental Conditions lists: Plant Trait Ontology lists: Population and Community Ontology lists: RNA Ontology lists: Rat Strain Ontology lists: Subcellular Anatomy Ontology lists: Software Ontology lists: Suggested Ontology for Pharmacogenomics lists: Vertebrate Taxonomy Ontology lists: Physico-Chemical Process lists: Adverse Event Reporting Ontology lists: Xenopus Anatomy Ontology lists: Cell Line Ontology lists: Human Phenotype Ontology lists: Neurobehavior Ontology lists: Ontology for Biomedical Investigations lists: Comparative Data Analysis Ontology lists: Ontology for General Medical Science lists: Physico-Chemical Methods and Properties lists: Gene Regulation Ontology is listed by: FORCE11 is related to: MeGO is related to: Drosophila anatomy and development ontologies is related to: Cell Type Ontology is related to: OBO-Edit is related to: go-perl is related to: OWLTools is related to: Zebrafish Anatomical Ontology is related to: OBO Tracker: Plant Ontology (PO) TERM requests is related to: eVOC is related to: OnEx - Ontology Evolution Explorer is related to: BioPerl is related to: dkCOIN is related to: Standards-based Infrastructure with Distributed Resources is related to: OntoVisT is related to: COBrA is related to: Wandora is related to: ONTO-PERL is related to: Genomic Standards Consortium is related to: Ontology Lookup Service is related to: LexGrid is related to: SBO is related to: RIKEN integrated database of mammals is related to: DOAF is related to: Gene Ontology is related to: African Population Ontology has parent organization: Berkeley Bioinformatics Open-Source Projects is parent organization of: OBO Relation Ontology is parent organization of: SO is parent organization of: PATO is parent organization of: MPO is parent organization of: AEO is parent organization of: UBERON |
PMID:17989687 | nlx_22892 | SCR_007083 | The Open Biomedical Ontologies, OBO Foundry, Open Biological and Biomedical Ontologies, Open Biological and Biomedical Ontology Foundry | 2026-02-14 02:01:27 | 169 | |||||||
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go-db-perl Resource Report Resource Website 1+ mentions |
go-db-perl (RRID:SCR_005721) | go-db-perl | software resource | Software resource that extends the functionality of go-perl (on which it depends) with GO Database access functionality. go-db-perl comes bundled with various scripts and a shell command line interface that can be used as standalone tools. Installation is more involved than for go-perl; you will need a MySQL database plus the requisite DBI and DBD Perl modules. Full installation instructions are included in the download. go-db-perl is in use both to drive AmiGO and internally within Ensembl. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | software library, database, gene ontology, database or data warehouse |
is listed by: Gene Ontology Tools is related to: AmiGO is related to: go-moose is related to: Ensembl is related to: go-perl has parent organization: Comprehensive Perl Archive Network has parent organization: Gene Ontology |
Free for academic use | nlx_149180 | SCR_005721 | 2026-02-14 02:01:10 | 1 | ||||||||
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Manatee Resource Report Resource Website 50+ mentions |
Manatee (RRID:SCR_005685) | Manatee | software resource | Manatee is a web-based gene evaluation and genome annotation tool; Manatee can store and view annotation for prokaryotic and eukaryotic genomes. The Manatee interface allows biologists to quickly identify genes and make high quality functional assignments, such as GO classifications, using search data, paralogous families, and annotation suggestions generated from automated analysis. Manatee can be downloaded and installed to run under the CGI area of a web server, such as Apache. Platform: Online tool, Linux compatible, Solaris | gene, genome, annotation, ontology or annotation browser, ontology or annotation editor |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: J. Craig Venter Institute has parent organization: University of Maryland School of Medicine; Maryland; USA has parent organization: SourceForge |
Open unspecified license - Free for academic use | nlx_149128 | SCR_005685 | 2026-02-14 02:01:10 | 64 | ||||||||
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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 | 2026-02-14 02:01:00 | 10 | ||||||||
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BiNGO: A Biological Networks Gene Ontology tool Resource Report Resource Website 500+ mentions |
BiNGO: A Biological Networks Gene Ontology tool (RRID:SCR_005736) | BiNGO | software resource | The Biological Networks Gene Ontology tool (BiNGO) is an open-source Java tool to determine which Gene Ontology (GO) terms are significantly overrepresented in a set of genes. BiNGO can be used either on a list of genes, pasted as text, or interactively on subgraphs of biological networks visualized in Cytoscape. BiNGO maps the predominant functional themes of the tested gene set on the GO hierarchy, and takes advantage of Cytoscape''''s versatile visualization environment to produce an intuitive and customizable visual representation of the results. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene ontology, gene, ontology, statistical analysis, term enrichment, biological network, plugin, bio.tools |
is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Cytoscape has parent organization: Ghent University; Ghent; Belgium |
PMID:15972284 | Open unspecified license - Free for academic use | nlx_149196, biotools:bingo | https://bio.tools/bingo | SCR_005736 | Biological Networks Gene Ontology | 2026-02-14 02:01:00 | 790 | |||||
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Gene Ontology Extension Resource Report Resource Website |
Gene Ontology Extension (RRID:SCR_010327) | GO-EXT | data or information resource, ontology, controlled vocabulary | An extension of the Gene Ontology. | obo |
is listed by: BioPortal has parent organization: Gene Ontology |
nlx_157414 | SCR_010327 | 2026-02-14 02:01:57 | 0 | |||||||||
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CELDA Ontology Resource Report Resource Website |
CELDA Ontology (RRID:SCR_001601) | CELDA | data or information resource, ontology, controlled vocabulary | Structured vocabulary to organize cell-associated data and to place these data in clearly defined semantic relations to other biological facts. It describes cell types, their properties and origin and links this information to other existing ontologies like the Cell Ontology (CL), Foundational Model of Anatomy (FMA), Gene Ontology (GO), Mouse Anatomy and others using the top-level ontology BioTop. | cell, expression, localization, development, anatomy, cell type, development, organ, kidney, liver, skin |
is related to: Cell Type Ontology is related to: FMA is related to: Gene Ontology has parent organization: CellFinder |
Seoul National University; Seoul; South Korea ; Research Institute for Veterinary Science ; DFG KU 851/3-1; DFG LE 1428/3-1; DFG JA 1904/2-1 |
PMID:23865855 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153858 | SCR_001601 | Cell: Expression Localization Development Anatomy, CellFinder Ontology, CELDA Ontology | 2026-02-14 02:00:06 | 0 |
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