Genome re-annotation: a wiki solution?

The annotation of most genomes becomes outdated over time, owing in part to our ever-improving knowledge of genomes and in part to improvements in bioinformatics software. Unfortunately, annotation is rarely if ever updated and resources to support routine reannotation are scarce. Wiki software, which would allow many scientists to edit each genome's annotation, offers one possible solution.

• Publication year

  2007

• Venue

  Genome Biology

• Publication date

  2007-02-01

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1186/gb-2007-8-1-102PMID 17274839PMCID 1839116
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• National Center for Biotechnology Information

  2008cited by this paper
• The EMBL Nucleotide Sequence Database

  2004cited by this paper
• The sequence of the human genome (abstract only)

  2001cited by this paper
• Initial sequencing and analysis of the human genome

  2001cited by this paper
• The Comprehensive Microbial Resource

  2001cited by this paper
• The EMBL Nucleotide Sequence Database

  2000cited by this paper
• Improved microbial gene identification with GLIMMER.

  1999cited by this paper
• Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1.

  1999cited by this paper
• GeneMark.hmm: new solutions for gene finding.

  1998cited by this paper
• Profile hidden Markov models

  1998cited by this paper
• Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

  1997cited by this paper
• Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.

  1995cited by this paper
• [DNA Data Bank of Japan].

  1986cited by this paper
• Sequence the Human Genome

  1986cited by this paper
• National

  1896cited by this paper

• Annotating genomes at increased scale and resolution.

  2026cites this paper
• The impact of transitive annotation on the training of taxonomic classifiers

  2024cites this paper
• Lineage-specific microbial protein prediction enables large-scale exploration of protein ecology within the human gut

  2024cites this paper
• Experimental investigation of enzyme functional annotations reveals extensive annotation error

  2020cites this paper
• Using conceptual modeling to improve genome data management

  2020cites this paper
• Properties and abundance of overlapping genes in viruses

  2020cites this paper
• Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing

  2020cites this paper
• SILE: A Method for the Efficient Management of Smart Genomic Information

  2019cites this paper
• Human contamination in bacterial genomes has created thousands of spurious proteins

  2019cites this paper
• BDBM 1.0: A Desktop Application for Efficient Retrieval and Processing of High-Quality Sequence Data and Application to the Identification of the Putative Coffea S-Locus

  2019cites this paper
• Blockchain, Wikis, and the Ideal Science Machine: With an Example From Genomics

  2019cites this paper
• Proteome characterizations of microbial systems using MS-based experimental and informatics approaches to examine key metabolic pathways, proteins of unknown function, and phenotypic adaptation

  2018cites this paper
• Second Era of OMICS in Caries Research: Moving Past the Phase of Disillusionment

  2017cites this paper
• An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics

  2017cites this paper
• A framework for developing and validating taxon‐specific primers for specimen identification from environmental DNA

  2017cites this paper
• Nomenclature errors in public 16s rDNA gene databases : strategies to improve the accuracy of sequence annotations

  2017cites this paper
• Mitogenome sequence accuracy using different elucidation methods

  2017cites this paper
• Caracterização de fatores que afetam a detecção de presas através do sequenciamento de alto desempenho do DNA

  2017cites this paper
• IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below.

  2017cites this paper
• Funding knowledgebases: Towards a sustainable funding model for the UniProt use case

  2017cites this paper
• BEACON: automated tool for Bacterial GEnome Annotation ComparisON

  2015cites this paper
• Reconstructing genome-scale metabolic models with merlin

  2015cites this paper
• Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond

  2015cites this paper
• PyPedia: using the wiki paradigm as crowd sourcing environment for bioinformatics protocols

  2015cites this paper
• Prospect, isolation, and characterization of microorganisms for potential use in cases of oil bioremediation along the coast of Trindade Island, Brazil.

  2015cites this paper
• Taking the pseudo out of pseudogenes.

  2015cites this paper
• De Novo Assembly and Characterization of the Invasive Northern Pacific Seastar Transcriptome

  2015cites this paper
• Genomics data curation roles, skills and perception of data quality

  2015cites this paper
• Domain knowledge and data quality perceptions in genome curation work

  2015cites this paper
• Centralization, Fragmentation, and Replication in the Genomic Data Commons

  2015cites this paper
• Computational aspects of presence of drug resistance mechanisms

  2015cites this paper
• BEACON: automated tool for Bacterial

  2015cites this paper
• In Silico Proteomic Functional Re-annotation of Escherichia coli K-12 using Dynamic Biological Data Fusion Strategy

  2014cites this paper
• Introducing a Novel and Robust Technique for Determining Lymph Node Status in Colorectal Cancer

  2014cites this paper
• Recognition of Protein-coding Genes Based on Z-curve Algorithms

  2014cites this paper
• Comparative Genomics and Pathogenicity Islands of Corynebacterium diphtheriae , Corynebacterium ulcerans , and Corynebacterium pseudotuberculosis

  2014cites this paper
• LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs

  2014cites this paper
• The Zebrafish GenomeWiki: a crowdsourcing approach to connect the long tail for zebrafish gene annotation

  2014cites this paper
• PlantSecKB: the Plant Secretome and Subcellular Proteome KnowledgeBase

  2014cites this paper
• In Silico Proteomic Functional Re-annotation of Escherichia coli K-12 using Dynamic Biological Data Fusion Strategy

  2014cites this paper
• PlantSecKB: the Plant Secretome and Subcellular Proteome KnowledgeBase

  2014cites this paper
• Sharing and executing linked data queries in a collaborative environment

  2013cites this paper
• The Evolution of Cooperation: How Patience Matters

  2013cites this paper
• Community Intelligence in Knowledge Curation: An Application to Managing Scientific Nomenclature

  2013cites this paper
• Global transcriptome analysis of Clostridium thermocellum ATCC 27405 during growth on dilute acid pretreated Populus and switchgrass

  2013cites this paper
• Web Apollo: a web-based genomic annotation editing platform

  2013cites this paper
• AuthorReward: increasing community curation in biological knowledge wikis through automated authorship quantification

  2013cites this paper
• RiceWiki: a wiki-based database for community curation of rice genes

  2013cites this paper
• Community annotation and the evolution of cooperation: How patience matters

  2013cites this paper
• Analysis of the Vibrionaceae pan-genome

  2013cites this paper
• Re-Annotation of Protein-Coding Genes in 10 Complete Genomes of Neisseriaceae Family by Combining Similarity-Based and Composition-Based Methods

  2013cites this paper
• Four chromosome replication origins in the archaeon Pyrobaculum calidifontis

  2012cites this paper
• Prioritization of data quality dimensions and skills requirements in genome annotation work

  2012cites this paper
• Theoretical Prediction and Experimental Verification of Protein-Coding Genes in Plant Pathogen Genome Agrobacterium tumefaciens Strain C58

  2012cites this paper
• Picking the high hanging fruit : automated ways to annotate awkward genes

  2012influential citation
• Power to the people: a wiki-governance model for biobanks

  2012cites this paper
• ORCAE: online resource for community annotation of eukaryotes

  2012cites this paper
• Whole genome sequencing of the fish pathogen Francisella noatunensis subsp. orientalis Toba04 gives novel insights into Francisella evolution and pathogenecity

  2012cites this paper
• Wikipedia research and tools: Review and comments

  2012cites this paper
• Reannotation of the Corynebacterium diphtheriae NCTC13129 genome as a new approach to studying gene targets connected to virulence and pathogenicity in diphtheria

  2012cites this paper
• Computational Techniques for the Analysis of Large Scale Biological Systems

  2012cites this paper
• Multiple-omic data analysis of Klebsiella pneumoniae MGH 78578 reveals its transcriptional architecture and regulatory features

  2012cites this paper
• reannotation of the Corynebacterium diphtheriae ncTc13129 genome as a new approach to studying gene targets connected to virulence and pathogenicity in diphtheria

  2012cites this paper
• Comparative Omics-Driven Genome Annotation Refinement: Application across Yersiniae

  2012cites this paper
• Tetrahymena genome database Wiki: a community-maintained model organism database

  2012cites this paper
• On combining collaborative and automated curation for enzyme function prediction

  2012cites this paper
• ONDEX - a data integration framework for the life sciences

  2011cites this paper
• Data Integration in Bioinformatics: Current Efforts and Challenges

  2011cites this paper
• The SEQanswers wiki: a wiki database of tools for high-throughput sequencing analysis

  2011cites this paper
• WikiBuild: A New Online Collaboration Process For Multistakeholder Tool Development and Consensus Building

  2011cites this paper
• What is a Wiki, and How Can it be Used in Resident Education?

  2011cites this paper
• Using IBM Content Manager for genomic data annotation and quality assurance tasks

  2011cites this paper
• Gene Re-annotation in Genome of the Extremophile Pyrobaculum Aerophilum by Using Bioinformatics Methods

  2011cites this paper
• Bioqueries: a social community sharing experiences while querying biological linked data

  2011cites this paper
• BOLD’s role in barcode data management and analysis: a response

  2011cites this paper
• Gene discovery by genome-wide CDS re-prediction and microarray-based transcriptional analysis in phytopathogen Xanthomonas campestris

  2011cites this paper
• Xanthusbase after five years expands to become Openmods

  2011cites this paper
• Identification and isolation of full-length cDNA sequences by sequencing and analysis of expressed sequence tags from guarana (Paullinia cupana).

  2011cites this paper
• An Integrative Method for Identifying the Over-Annotated Protein-Coding Genes in Microbial Genomes

  2011cites this paper
• Exploratory pathway analysis

  2011cites this paper
• Back to Basics: How Technology and the Open Source Movement Can Save Science

  2010cites this paper
• Using comparative genome analysis to identify problems in annotated microbial genomes.

  2010influential citation
• Community annotation in biology

  2010cites this paper
• Merlin : Metabolic Models Reconstruction using Genome-Scale Information ?

  2010cites this paper
• A general framework for optimization of probes for gene expression microarray and its application to the fungus Podospora anserina

  2010cites this paper
• Re-Annotation Is an Essential Step in Systems Biology Modeling of Functional Genomics Data

  2010cites this paper
• Sustainable digital infrastructure

  2010cites this paper
• PDBWiki: added value through community annotation of the Protein Data Bank

  2010cites this paper
• Wiki use in mental health practice: recognizing potential use of collaborative technology.

  2010cites this paper
• Metabolomics for functional genomics, systems biology, and biotechnology.

  2010cites this paper
• Reconstructing genome-scale metabolic models with Merlin

  2010cites this paper
• Merlin: Metabolic Models Reconstruction using Genome-Scale Information*

  2010cites this paper
• Database federation, resource interoperability and digital identity, for management and exploitation of contemporary biological data

  2010cites this paper
• Perception of Quality in Genome Annotation Work

  2010cites this paper
• Detecting distant homologies on protozoans metabolic pathways using scientific workflows

  2010cites this paper
• AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome

  2010cites this paper
• Genome (re‐)annotation and open‐source annotation pipelines

  2010cites this paper
• A proteogenomic update to Yersinia: enhancing genome annotation

  2010cites this paper
• Next generation models for storage and representation of microbial biological annotation

  2010cites this paper
• MicroScope: a platform for microbial genome annotation and comparative genomics

  2009cites this paper