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http://ophid.utoronto.ca/navigator/

A software package for visualizing and analyzing protein-protein interaction networks. NAViGaTOR can query OPHID / I2D - online databases of interaction data - and display networks in 2D or 3D. To improve scalability and performance, NAViGaTOR combines Java with OpenGL to provide a 2D/3D visualization system on multiple hardware platforms. NAViGaTOR also provides analytical capabilities and supports standard import and export formats such as GO and the Proteomics Standards Initiative (PSI). NAViGaTOR can be installed and run on Microsoft Windows, Linux / UNIX, and Mac OS systems. NAViGaTOR is written in Java and uses JOGL (Java bindings for OpenGL) to support scalability, highlighting or suppressing of information, and other advanced graphic approaches.

Proper citation: Network Analysis, Visualization and Graphing TORonto (RRID:SCR_008373) Copy   

•   Source: SciCrunch Registry

http://www.conceptwiki.org

A community owned repository of concepts used to define all concepts unambiguously. Users can edit and add their own concepts to the wiki.

Proper citation: ConceptWiki (RRID:SCR_006362) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.ubc.ca/ermineJ/

Data analysis software for gene sets in expression microarray data or other genome-wide data that results in rankings of genes. A typical goal is to determine whether particular biological pathways are doing something interesting in the data. The software is designed to be used by biologists with little or no informatics background. A command-line interface is available for users who wish to script the use of ermineJ. Major features include: * Implementation of multiple methods for gene set analysis: ** Over-representation analysis ** A resampling-based method that uses gene scores ** A rank-based method that uses gene scores ** A resampling-based method that uses correlation between gene expression profiles (a type of cluster-enrichment analysis). * Gene sets receive statistical scores (p-values), and multiple test correction is supported. * Support of the Gene Ontology terminology; users can choose which aspects to analyze. * User files use simple text formats. * Users can modify gene sets or create new ones. * The results can be visualized within the software. * It is simple to compare multiple analyses of the same data set with different settings. * User-definable hyperlinks are provided to external sites to allow more efficient browsing of the results. * For programmers, there is a command line interface as well as a simple application programming interface that can be used to plug ermineJ functionality into your own code Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: ErmineJ (RRID:SCR_006450) Copy   

•   Source: SciCrunch Registry

http://ctdbase.org/

A public database that enhances understanding of the effects of environmental chemicals on human health. Integrated GO data and a GO browser add functionality to CTD by allowing users to understand biological functions, processes and cellular locations that are the targets of chemical exposures. CTD includes curated data describing cross-species chemical–gene/protein interactions, chemical–disease and gene–disease associations to illuminate molecular mechanisms underlying variable susceptibility and environmentally influenced diseases. These data will also provide insights into complex chemical–gene and protein interaction networks.

Proper citation: Comparative Toxicogenomics Database (CTD) (RRID:SCR_006530) Copy   

•   Source: SciCrunch Registry

http://flybase.org/

Database of Drosophila genetic and genomic information with information about stock collections and fly genetic tools. Gene Ontology (GO) terms are used to describe three attributes of wild-type gene products: their molecular function, the biological processes in which they play a role, and their subcellular location. Additionally, FlyBase accepts data submissions. FlyBase can be searched for genes, alleles, aberrations and other genetic objects, phenotypes, sequences, stocks, images and movies, controlled terms, and Drosophila researchers using the tools available from the "Tools" drop-down menu in the Navigation bar.

Proper citation: FlyBase (RRID:SCR_006549) Copy   

•   Source: SciCrunch Registry

http://www.cmhd.ca/genetrap/

Generate gene trap insertions using mutagenic polyA trap vectors, followed by sequence tagging to develop a library of mutagenized ES cells freely available to the scientific community. This library is searchable by sequence or key word searches including gene name or symbol, chromosome location, or Gene Ontology (GO) terms. In addition,they offer a custom email alert service in which researchers are able to submit search criteria. Researchers will receive automated e-mail notification of matching gene trap clones as they are entered into the library and database. The resource features the use of complementary second and third generation polyA trap vectors developed by the Stanford lab and the laboratory of Professor Yasumasa Ishida of the Nara Institute of Science and Technology (NAIST) in Japan to mutagenize murine embryonic stem (ES) cells. CMHD gene trap clones are distributed by the Canadian Mouse Mutant Repository(CMMR). Information about ordering, services, and pricing can be found on their web site (http://www.cmmr.ca/services/index.html)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

Proper citation: Centre for Modeling Human Disease Gene Trap Resource (RRID:SCR_002785) Copy   

•   Source: SciCrunch Registry

http://bioportal.bioontology.org/

Open repository of biomedical ontologies that provides access via Web browsers and Web services to ontologies. It supports ontologies in OBO format, OWL, RDF, Rich Release Format (RRF), Protege frames, and LexGrid XML. Functionality includes the ability to browse, search and visualize ontologies as well as to comment on, and create mappings for ontologies. Any registered user can submit an ontology. The NCBO Annotator and NCBO Resource Index can also be accessed via BioPortal. Additional features: * Add Reviews: rate the ontology according to several criteria and describe your experience using the ontology. * Add Mappings: submit point-to-point mappings or upload bulk mappings created with external tools. Notification of new Mappings is RSS-enabled and Mappings can be browsed via BioPortal and accessed via Web services. * NCBO Annotator: Tool that tags free text with ontology terms. NCBO uses the Annotator to generate ontology annotations, creating an ontology index of these resources accessible via the NCBO Resource Index. The Annotator can be accessed through BioPortal or directly as a Web service. The annotation workflow is based on syntactic concept recognition (using the preferred name and synonyms for terms) and on a set of semantic expansion algorithms that leverage the ontology structure (e.g., is_a relations). * NCBO Resource Index: The NCBO Resource Index is a system for ontology based annotation and indexing of biomedical data; the key functionality of this system is to enable users to locate biomedical data linked via ontology terms. A set of annotations is generated automatically, using the NCBO Annotator, and presented in BioPortal. This service uses a concept recognizer (developed by the National Center for Integrative Biomedical Informatics, University of Michigan) to produce a set of annotations and expand them using ontology is_a relations. * Web services: Documentation on all Web services and example code is available at: BioPortal Web services.

Proper citation: BioPortal (RRID:SCR_002713) Copy   

•   Source: SciCrunch Registry

http://www.gramene.org

Curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species to facilitate the study of cross-species comparisons using information generated from projects supported by public funds. It currently hosts annotated whole genomes in over two dozen plant species and partial assemblies for almost a dozen wild rice species in the Ensembl browser, genetic and physical maps with genes, ESTs and QTLs locations, genetic diversity data sets, structure-function analysis of proteins, plant pathways databases (BioCyc and Plant Reactome platforms), and descriptions of phenotypic traits and mutations. The web-based displays for phenotypes include the Genes and Quantitative Trait Loci (QTL) modules. Sequence based relationships are displayed in the Genomes module using the genome browser adapted from Ensembl, in the Maps module using the comparative map viewer (CMap) from GMOD, and in the Proteins module displays. BLAST is used to search for similar sequences. Literature supporting all the above data is organized in the Literature database. In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database. Twice a year, Gramene releases a major build of the database and makes interim releases to correct errors or to make important updates to software and/or data. Additionally you can access Gramene through an FTP site.

Proper citation: Gramene (RRID:SCR_002829) Copy   

•   Source: SciCrunch Registry

http://gemdock.life.nctu.edu.tw/3D-Interologs

Database of physical protein-protein interactions across multiple genomes. Based on 3D-domain interolog mapping and a scoring function, protein-protein interactions are inferred by using three-dimensional (3D) structure heterodimers to search the UniProt database. For a query protein, the database utilizes BLAST to identify homologous proteins and the interacting partners from multiple species. Based on the scoring function and structure complexes, it provides the statistic significances, the interacting models (e.g. hydrogen bonds and conserved amino acids), and functional annotations of interacting partners of a query protein. The identification of orthologous proteins of multiple species allows the study of protein-protein evolution, protein functions, and cross-referencing of proteins.

Proper citation: 3D-Interologs (RRID:SCR_003101) Copy   

•   Source: SciCrunch Registry

http://www.bioperl.org

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

Proper citation: BioPerl (RRID:SCR_002989) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/categoryCompare.html

A software package for meta-analysis of high-throughput experiments using feature annotations. It calculates significant annotations (categories) in each of two (or more) feature (i.e. gene) lists, determines the overlap between the annotations, and returns graphical and tabular data about the significant annotations and which combinations of feature lists the annotations were found to be significant. Interactive exploration is facilitated through the use of RCytoscape (heavily suggested).

Proper citation: categoryCompare (RRID:SCR_001223) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/globaltest.html

A software package that tests groups of covariates (or features) for association with a response variable. The package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms.

Proper citation: globaltest (RRID:SCR_001256) Copy   

•   Source: SciCrunch Registry

http://cellfinder.de/about/ontology/

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.

Proper citation: CELDA Ontology (RRID:SCR_001601) Copy   

•   Source: SciCrunch Registry

http://aclame.ulb.ac.be/Classification/mego.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Gene Ontology dedicated to the functions of mobile genetic elements. The terms defined are used to annotate phage and plasmid protein families in ACLAME. Note: The phage ontology PhiGO has now been incorporated in MeGO and can thus be accessed in MeGO version 1.0 and up.

Proper citation: MeGO (RRID:SCR_000110) Copy   

•   Source: SciCrunch Registry

http://mor.nlm.nih.gov/perl/gennav.pl

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. GenNav searches GO terms and annotated gene products, and provides a graphical display of a term's position in the GO DAG.

Proper citation: GenNav (RRID:SCR_000147) Copy   

•   Source: SciCrunch Registry

http://dbserv2.informatik.uni-leipzig.de:8080/onex/

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

Proper citation: OnEx - Ontology Evolution Explorer (RRID:SCR_000602) Copy   

•   Source: SciCrunch Registry

https://bio.tools

Community registry of software tools and data resources for life sciences. Tools and data services registry as community effort to document bioinformatics resources. Registry of software and databases, facilitating researchers from across spectrum of biological and biomedical science. When adding tools to registry, information including URL, contact information, resource function, field its relevant in, and its primary publication are required. Development is supported by ELIXIR - the European Infrastructure for Biological Information.

Proper citation: bio.tools (RRID:SCR_014695) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/GO-EXT

An extension of the Gene Ontology.

Proper citation: Gene Ontology Extension (RRID:SCR_010327) Copy   

•   Source: SciCrunch Registry

http://link.springer.com/article/10.1007%2Fs11357-003-0002-y

A database that stores information on the biomolecules which are modulated during aging and by caloric restriction (CR). To enhance its usefulness, data collected from studies of CR''''s anti-oxidative action on gene expression, oxidative stress, and many chronic age-related diseases are included. AgingDB is organized into two sections A) apoptosis and the various mitochondrial biomolecules that play a role in aging; B) nuclear transcription factors known to be_sensitive to oxidative environment. AgingDB features an imagemap of biomolecular signal pathways and visualized information that includes protein-protein interactions of biomolecules. Authorized users can submit a new biomolecule or edit an existing biomolecule to reflect latest developments.

Proper citation: AgingDB (RRID:SCR_010226) Copy   

•   Source: SciCrunch Registry

http://www.uniprot.org/help/uniprotkb

Central repository for collection of functional information on proteins, with accurate and consistent annotation. In addition to capturing core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible is added. This includes widely accepted biological ontologies, classifications and cross-references, and experimental and computational data. The UniProt Knowledgebase consists of two sections, UniProtKB/Swiss-Prot and UniProtKB/TrEMBL. UniProtKB/Swiss-Prot (reviewed) is a high quality manually annotated and non-redundant protein sequence database which brings together experimental results, computed features, and scientific conclusions. UniProtKB/TrEMBL (unreviewed) contains protein sequences associated with computationally generated annotation and large-scale functional characterization that await full manual annotation. Users may browse by taxonomy, keyword, gene ontology, enzyme class or pathway.

Proper citation: UniProtKB (RRID:SCR_004426) Copy   

•   Source: SciCrunch Registry