Other GO Tools

Agile Protein Interaction Data Analyzer (APID)

Bioinformatics and Functional Genomics Research Group, Cancer Research Center (CiC, CSIC-USAL), Salamanca, Spain
[Publication abstract]

Agile Protein Interaction Data Analyzer (APID) is an interactive bioinformatics web tool developed to integrate and analyze in a unified and comparative platform main currently known information about protein-protein interactions demonstrated by specific small-scale or large-scale experimental methods. At present, the application includes information coming from five main source databases enclosing an unified sever to explore more than 40000 different proteins and close to 150000 different proven interactions. The website includes search tools to query and browse upon the data, allowing selection of the interaction pairs based in calculated parameters that weight and qualify the reliability of each given protein interaction. Parameters for the proteins are connectivity, cluster coefficient, Gene Ontology (GO) functional environment, GO environment enrichment; for the interactions: number of methods, GO overlapping, iPfam domain-domain interaction. APID also includes a graphic interactive tool to visualize selected sub-networks and to navigate on them or along the whole interaction network.

CateGOrizer (was GO Terms Classifications Counter)

U.S. National Animal Genome Research Program (NAGRP)
[abstract]

CateGOrizer takes input of GO term IDs in a list format or unformatted plain text file, allows users to choose one of the available classifications such as GO_slim, GOA, EGAD, MGI_GO_slim or GO-ROOT, performs the count, and returns the results on the web (if it takes too long, it will email the user with the results link). The results include a sorted table of counts, percentages, and a pie chart.

CateGOrizer was previously known as the GO Terms Classifications Counter.

Db for Dummies! (DBD)

Custom Microsystems
No publication

Db for Dummies! (DBD) is a small database that imports the Generic GO Slim. It allows data to be viewed in a tree.

Flash GViewer

Twigger Lab, Medical College of Wisconsin
No publication

Flash GViewer is a customizable Flash movie that can be easily inserted into a web page to display each chromosome in a genome along with the locations of individual features on the chromosomes. It is intended to provide an overview of the genomic locations of a specific set of features - eg. genes associated with a specific ontology term, etc., rather than as a way to view all features on the genome. The features can hyperlink out to a detail page to enable to GViewer to be used as a navigation tool. Genome maps for Rat, Mouse, Human and C. elegans are provided but other genome maps can be easily created. Annotation data can be provided as static text files or produced as XML via server scripts.
This tool is not GO-specific, but was built for the purpose of viewing GO annotation data.

FunSpec

University of Toronto
[Publication abstract]

FunSpec is a web-based tool for statistical evaluation of groups of genes and proteins (e.g. co-regulated genes, protein complexes, genetic interactors) with respect to existing annotations, including GO terms.

FuSSiMeG (Functional Semantic Similarity Measure between Gene Products)

University of Lisbon
No publication

With FuSSiMeG (Functional Semantic Similarity Measure between Gene Products), you can measure the functional similarity between gene products, by comparing the semantic similarity between the GO terms in their annotations. You can also measure the semantic similarity between any GO terms.

Generic GO Term Mapper

Lewis-Sigler Institute for Integrative Genomics at Princeton University
No publication

The Generic GO Term Mapper is a tool for mapping the granular GO annotations for genes in a list to a set of broader, high-level GO parents terms (sometimes referred to as GO Slim terms), allowing you to bin your genes into broad categories.

Genes2Diseases

Bork group at the European Molecular Biology Laboratory
No publication

Genes2Diseases is a database of candidate genes for mapped inherited human diseases. The database is generated using an analysis of relations between phenotypic features and chemical objects, and from chemical objects to Gene Ontology protein function terms, based on the whole MEDLINE and RefSeq databases. Can be used to view all GO terms associated with a particular genetically inherited disease.

GO Slim Mapper

Saccharomyces Genome Database
No publication

The GO Slim Mapper (aka GO Term Mapper) maps the specific, granular GO terms used to annotate a list of budding yeast gene products to corresponding more general parent GO slim terms. Uses the SGD GO Slim sets.

Gene Ontology Browsing Utility (GOBU)

Institute of Information Science, Academia Sinica, Taiwan, ROC
[abstract]

Gene Ontology Browsing Utility (GOBU) is a Java-based software program for integrating biological annotation catalogs under an extendable architecture that uses the Gene Ontology and a user-defined hierarchy as two main atalogs. GOBU has the following features: (1) user-specified hierarchical data as input data, (2) user-defined data types for describing different annotations, and (3) an extendable software architecture for handling user-defined data types.

GOChase

Seoul National University Biomedical Informatics
[Publication abstract]

GOChase is a set of web-based utilities to detect and correct the errors in GO-based annotations.

• GOChase-History resolves the whole modification history of GO IDs.
• GOChase-Correct highlights merged GO IDs and redirects to the correct primary term into which the secondary ID was merged. For obsolete GO terms, the nearest non-discarded parent term is recommended by GOChase. This function may be used by GO browsers such as AmiGO and QuickGO to fix broken hyperlinks.
• A whole database (such as LocusLink) as a flat file can be loaded into GOChase, reporting the annotation errors and GOChase corrections.
• When one inputs a GO ID, GOChase will resolve all gene products annotated with the GO ID across all the major databases.

GOProfiler

AgBase
No publication

GOProfiler provides a summary of the GO annotations available in AgBase. The user provides a species (taxon id) and GOProfiler displays the number of GO associations and the number of annotated proteins for that species. The results are listed by evidence code and a separate list of unannotated proteins is also provided.

GORetriever

AgBase
No publication

GORetriever is used to find all of the GO annotations in AgBase corresponding to a list of user-supplied protein identifiers. Currently supported ID types are Uniprot ID, Uniprot Accession, and GO ID. GORetriever produces a list of proteins and their annotations and a separate list of entries with no GO annotation. The list without GO annotations can be subsequently used as in put for the GOanna tool that finds similar sequences with annotations (where they are available).

GOSlimViewer

AgBase
No publication

GOSlimViewer is used to provide a high level summary of the GO categories for a dataset. It is designed to use output generated by GORetriever. Note that you can add additional annotations that come from GOanna (or other sources) to the GORetriever file. GOSlimViewer currently only supports the listed GOSlim sets.

ProteInOn

XLDB Group, Faculty of Sciences of the University of Lisbon
[Publication abstract]

ProteInOn can be used to find interacting proteins, find assigned GO terms and calculate the functional semantic similarity of proteins and to get the information content and calculate the functional semantic similarity of GO terms.

Additional citations:

1. F. Couto, M. Silva and P. Coutinho. Measuring Semantic Similarity between Gene Ontology Terms. DKE - Data & Knowledge Engineering, Elsevier Science, In press.
2. F. Couto, M. Silva and P. Coutinho. Semantic Similarity over the Gene Ontology: Family Correlation and Selecting Disjunctive Ancestors. ACM CIKM - Conference in Information and Knowledge Management, October 2005.

TXTGate

Bioinformatics group at ESAT/K.U.Leuven (Belgium)
[Publication abstract]

TXTGate is a web-service that combines literature indices of selected public biological resources in a flexible text-mining system designed towards the analysis of groups of genes. By means of tailored vocabularies, selected textual fields and MedLine abstracts of LocusLink and SGD are indexed. Subclustering and links to external resources allow for an in-depth analysis of the resulting term profiles.

Wandora

Grip Studios Interactive, Inc.
No publication

Wandora is a general purpose knowledge extraction, management, and publishing environment based on Topic Maps (ISO 13250). Wandora supports OBO flat file v1.2 format and can convert OBO files, including the Gene Ontology, to a topic map and vice versa. Wandora is well suited to OBO visualizations and knowledge mashups combining OBO, RDF(S), and Topic Map resources for example.

Wandora requires Java v6.

WEGO (Web Gene Ontology Annotation Plot)

Beijing Genomics Institute
No publication

WEGO (Web Gene Ontology Annotation Plot) is a simple but useful tool for plotting Gene Ontology (GO) annotation results. Different from other commercial software for chart creating, WEGO is designed to deal with the directed acyclic graph (DAG) structure of GO to facilitate histogram creation of GO annotation results. WEGO has been widely used in many important biological research projects, such as the rice genome project and the silkworm genome project. It has become one of the useful tools for downstream gene annotation analysis, especially when performing comparative genomics tasks.

Whatizit

Rebholz group at the European Bioinformatics Institute
No publication

Whatizit is a web application which highlights all kinds of "interesting" things in a document. One of its modules marks all GO terms as well as protein and gene names from UniProt and links them to their entries in GO and UniProt respectively.