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Literature DB >> 12499308

An extensible application for assembling annotation for genomic data.

Jianhua Zhang¹, Vincent Carey, Robert Gentleman.

Abstract

SUMMARY: AnnBuilder is an R package for assembling genomic annotation data. The system currently provides parsers to process annotation data from LocusLink, Gene Ontology Consortium, and Human Gene Project and can be extended to new data sources via user defined parsers. AnnBuilder differs from other existing systems in that it provides users with unlimited ability to assemble data from user selected sources. The products of AnnBuilder are files in XML format that can be easily used by different systems. AVAILABILITY: (http://www.bioconductor.org). Open source.

Entities: Species

Mesh：

Year: 2003 PMID： 12499308 DOI： 10.1093/bioinformatics/19.1.155

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

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Cited

15 in total

1. ChipInfo: Software for extracting gene annotation and gene ontology information for microarray analysis.

Authors: Sheng Zhong; Cheng Li; Wing Hung Wong
Journal: Nucleic Acids Res Date: 2003-07-01 Impact factor: 16.971

2. Fine mapping of Leishmania major susceptibility Locus lmr2 and evidence of a role for Fli1 in disease and wound healing.

Authors: Anuratha Sakthianandeswaren; Joan M Curtis; Colleen Elso; Beena Kumar; Tracey M Baldwin; Sash Lopaticki; Lukasz Kedzierski; Gordon K Smyth; Simon J Foote; Emanuela Handman
Journal: Infect Immun Date: 2010-04-05 Impact factor: 3.441

3. Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis.

Authors: Henning Redestig; Miyako Kusano; Atsushi Fukushima; Fumio Matsuda; Kazuki Saito; Masanori Arita
Journal: BMC Bioinformatics Date: 2010-04-29 Impact factor: 3.169

4. Bioconductor: open software development for computational biology and bioinformatics.

Authors: Robert C Gentleman; Vincent J Carey; Douglas M Bates; Ben Bolstad; Marcel Dettling; Sandrine Dudoit; Byron Ellis; Laurent Gautier; Yongchao Ge; Jeff Gentry; Kurt Hornik; Torsten Hothorn; Wolfgang Huber; Stefano Iacus; Rafael Irizarry; Friedrich Leisch; Cheng Li; Martin Maechler; Anthony J Rossini; Gunther Sawitzki; Colin Smith; Gordon Smyth; Luke Tierney; Jean Y H Yang; Jianhua Zhang
Journal: Genome Biol Date: 2004-09-15 Impact factor: 13.583

5. Rescue of the mutant CFTR chloride channel by pharmacological correctors and low temperature analyzed by gene expression profiling.

Authors: Elvira Sondo; Valeria Tomati; Emanuela Caci; Alessia Isabella Esposito; Ulrich Pfeffer; Nicoletta Pedemonte; Luis J V Galietta
Journal: Am J Physiol Cell Physiol Date: 2011-07-13 Impact factor: 4.249

An extensible application for assembling annotation for genomic data.

1. ChipInfo: Software for extracting gene annotation and gene ontology information for microarray analysis.

2. Fine mapping of Leishmania major susceptibility Locus lmr2 and evidence of a role for Fli1 in disease and wound healing.

3. Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis.

4. Bioconductor: open software development for computational biology and bioinformatics.

5. Rescue of the mutant CFTR chloride channel by pharmacological correctors and low temperature analyzed by gene expression profiling.

6. ParkDB: a Parkinson's disease gene expression database.

7. IDconverter and IDClight: conversion and annotation of gene and protein IDs.

8. OligoRAP - an Oligo Re-Annotation Pipeline to improve annotation and estimate target specificity.

9. Induction of a chemoattractant transcriptional response by a Campylobacter jejuni boiled cell extract in colonocytes.

10. Microarray expression profiles of 20.000 genes across 23 healthy porcine tissues.