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GOLEM: an interactive graph-based gene-ontology navigation and analysis tool
BACKGROUND: The Gene Ontology has become an extremely useful tool for the analysis of genomic data and structuring of biological knowledge. Several excellent software tools for navigating the gene ontology have been developed. However, no existing system provides an interactively expandable graph-ba...
Autores principales: | , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2006
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1618863/ https://www.ncbi.nlm.nih.gov/pubmed/17032457 http://dx.doi.org/10.1186/1471-2105-7-443 |
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author | Sealfon, Rachel SG Hibbs, Matthew A Huttenhower, Curtis Myers, Chad L Troyanskaya, Olga G |
author_facet | Sealfon, Rachel SG Hibbs, Matthew A Huttenhower, Curtis Myers, Chad L Troyanskaya, Olga G |
author_sort | Sealfon, Rachel SG |
collection | PubMed |
description | BACKGROUND: The Gene Ontology has become an extremely useful tool for the analysis of genomic data and structuring of biological knowledge. Several excellent software tools for navigating the gene ontology have been developed. However, no existing system provides an interactively expandable graph-based view of the gene ontology hierarchy. Furthermore, most existing tools are web-based or require an Internet connection, will not load local annotations files, and provide either analysis or visualization functionality, but not both. RESULTS: To address the above limitations, we have developed GOLEM (Gene Ontology Local Exploration Map), a visualization and analysis tool for focused exploration of the gene ontology graph. GOLEM allows the user to dynamically expand and focus the local graph structure of the gene ontology hierarchy in the neighborhood of any chosen term. It also supports rapid analysis of an input list of genes to find enriched gene ontology terms. The GOLEM application permits the user either to utilize local gene ontology and annotations files in the absence of an Internet connection, or to access the most recent ontology and annotation information from the gene ontology webpage. GOLEM supports global and organism-specific searches by gene ontology term name, gene ontology id and gene name. CONCLUSION: GOLEM is a useful software tool for biologists interested in visualizing the local directed acyclic graph structure of the gene ontology hierarchy and searching for gene ontology terms enriched in genes of interest. It is freely available both as an application and as an applet at . |
format | Text |
id | pubmed-1618863 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2006 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-16188632006-10-24 GOLEM: an interactive graph-based gene-ontology navigation and analysis tool Sealfon, Rachel SG Hibbs, Matthew A Huttenhower, Curtis Myers, Chad L Troyanskaya, Olga G BMC Bioinformatics Software BACKGROUND: The Gene Ontology has become an extremely useful tool for the analysis of genomic data and structuring of biological knowledge. Several excellent software tools for navigating the gene ontology have been developed. However, no existing system provides an interactively expandable graph-based view of the gene ontology hierarchy. Furthermore, most existing tools are web-based or require an Internet connection, will not load local annotations files, and provide either analysis or visualization functionality, but not both. RESULTS: To address the above limitations, we have developed GOLEM (Gene Ontology Local Exploration Map), a visualization and analysis tool for focused exploration of the gene ontology graph. GOLEM allows the user to dynamically expand and focus the local graph structure of the gene ontology hierarchy in the neighborhood of any chosen term. It also supports rapid analysis of an input list of genes to find enriched gene ontology terms. The GOLEM application permits the user either to utilize local gene ontology and annotations files in the absence of an Internet connection, or to access the most recent ontology and annotation information from the gene ontology webpage. GOLEM supports global and organism-specific searches by gene ontology term name, gene ontology id and gene name. CONCLUSION: GOLEM is a useful software tool for biologists interested in visualizing the local directed acyclic graph structure of the gene ontology hierarchy and searching for gene ontology terms enriched in genes of interest. It is freely available both as an application and as an applet at . BioMed Central 2006-10-10 /pmc/articles/PMC1618863/ /pubmed/17032457 http://dx.doi.org/10.1186/1471-2105-7-443 Text en Copyright © 2006 Sealfon et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Software Sealfon, Rachel SG Hibbs, Matthew A Huttenhower, Curtis Myers, Chad L Troyanskaya, Olga G GOLEM: an interactive graph-based gene-ontology navigation and analysis tool |
title | GOLEM: an interactive graph-based gene-ontology navigation and analysis tool |
title_full | GOLEM: an interactive graph-based gene-ontology navigation and analysis tool |
title_fullStr | GOLEM: an interactive graph-based gene-ontology navigation and analysis tool |
title_full_unstemmed | GOLEM: an interactive graph-based gene-ontology navigation and analysis tool |
title_short | GOLEM: an interactive graph-based gene-ontology navigation and analysis tool |
title_sort | golem: an interactive graph-based gene-ontology navigation and analysis tool |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1618863/ https://www.ncbi.nlm.nih.gov/pubmed/17032457 http://dx.doi.org/10.1186/1471-2105-7-443 |
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