GO Tools: Software Libraries

Bioconductor provides tools for the analysis and comprehension of high-throughput (microarray, sequence, flow, etc.) genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. There are more than core and user-contributed 400 packages. Bioconductor packages the GO ontology into our semi-annual release, with software tools to: query; join with diverse additional gene, microarray, and sequence annotations; incorporate GO into annotation, differential expression, and gene set enrichment work flows; and visualize.

• ontology or annotation browser
• ontology or annotation search engine
• ontology or annotation visualization
• database or data warehouse
• software library
• statistical analysis
• term enrichment
• text mining
• other analysis
• Flexible integration of GO into statistical analysis and comprehension of high-throughput genetic data.

FastSemSim is a package that implements several semantic similarity measures. It is both a library and an end-user application, featuring an intuitive graphical user interface (GUI). It has been implemented with the aim of being fast, expandable, and easy to use. It allows the user to work with the most updated version of GO database and customizable annotation corpora. It provides a set of logically-organized classes that can be easily exploited to both integrate semantic similarity into different analysis pipelines and extend the library with new measures.

• software library
• functional similarity
• semantic similarity
• graphical user interface

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.

• ontology or annotation browser
• ontology or annotation visualization
• software library
• statistical analysis
• term enrichment

GeneMANIA helps you predict the function of your favourite genes and gene sets.
GeneMANIA finds other genes that are related to a set of input genes, using a very large set of functional association data. Association data include protein and genetic interactions, pathways, co-expression, co-localization and protein domain similarity. You can use GeneMANIA to find new members of a pathway or complex, find additional genes you may have missed in your screen or find new genes with a specific function, such as protein kinases. Your question is defined by the set of genes you input.
If members of your gene list make up a protein complex, GeneMANIA will return more potential members of the protein complex. If you enter a gene list, GeneMANIA will return connections between your genes, within the selected datasets.
GeneMANIA also performs Gene Ontology term enrichment of the query list along with the returned gene list.
GeneMANIA is also accessible via a Cytoscape plugin, designed for power users.
GeneMANIA is actively developed at the University of Toronto, in the Donnelly Centre for Cellular and Biomolecular Research, in the labs of Gary Bader and Quaid Morris, with input from an independent scientific advisory board. GeneMANIA development was funded by Genome Canada, through the Ontario Genomics Institute (2007-OGI-TD-05).

• database or data warehouse
• software library
• statistical analysis
• term enrichment
• other analysis
• an interaction browser and GeneMANIA suggests annotations for genes based on Gene Ontology term enrichment of highly interacting genes with the gene of interest., GeneMANIA is also a gene recommendation system

go-db-perl 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.

• database or data warehouse
• software library

go-moose is intended as a replacement for the aging go-perl and go-db-perl Perl libraries. It is written using the object oriented Moose libraries. It can be used for performing a number of analyses on GO data, including the remapping of GO annotations to a selected subset of GO terms.

• software library
• slimmer-type tool
• other analysis

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.

• software library
• slimmer-type tool

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.

• software library

OBO-Edit is best known as a standalone application for editing ontologies. In fact, 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).
org.geneontology.oboedit is used in tools such as the Ontology Lookup Service and Phenote.
See the GO wiki for instructions on downloading the source code.

• software library

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.

• software library

Biomedical Logical Programming (Blip) is a research-oriented deductive database and prolog application library for handling biological and biomedical data. It includes packages for advanced querying of ontologies and annotations.
Blip underpins the Obol tool.

• software library

BioPerl is a set of perl modules for use in bioinformatics. It includes modules written by Sohel Merchant of the GO Consortium for parsing and manipulating OBO ontologies

• software library

LexGrid is the foundation of the National Center for Biomedical Ontology BioPortal interface and web-services. LexGrid can parse OBO format, as well as other formats such as OWL.

• software library

The OWLAPI is a java application programmer interface for OWL-based ontologies. The latest version of the API contains an OBO-Format parser. 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).

• software library