ArticleDatabase : the journal of biological databases and curation2010
PDBWiki: added value through community annotation of the Protein Data Bank.
Article in Database : the journal of biological databases and curation, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Understanding the fabric of protein crystals: computational classification of biological interfaces and crystal contacts.Bioinformatics (Oxford, England) · 2016Review
- LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs.Nucleic acids research · 2015Article
- STATdb: a specialised resource for the STATome.PloS one · 2014Article
- miRBase: annotating high confidence microRNAs using deep sequencing data.Nucleic acids research · 2014Article
- RiceWiki: a wiki-based database for community curation of rice genes.Nucleic acids research · 2014Article
- Community intelligence in knowledge curation: an application to managing scientific nomenclature.PloS one · 2013Article
- Structure-based function prediction of uncharacterized protein using binding sites comparison.PLoS computational biology · 2013Article
- Power to the people: a wiki-governance model for biobanks.Genome biology · 2012Article
- Linking genes to diseases with a SNPedia-Gene Wiki mashup.Journal of biomedical semantics · 2012Article
- ProBiS-database: precalculated binding site similarities and local pairwise alignments of PDB structures.Journal of chemical information and modeling · 2012Article
- Enzyme informatics.Current topics in medicinal chemistry · 2012Review
- Making your database available through Wikipedia: the pros and cons.Nucleic acids research · 2012Article
- Tetrahymena Genome Database Wiki: a community-maintained model organism database.Database : the journal of biological databases and curation · 2012Article
- Mining the Gene Wiki for functional genomic knowledge.BMC genomics · 2011Article
- 3DSwap: curated knowledgebase of proteins involved in 3D domain swapping.Database : the journal of biological databases and curation · 2011Article
- TOPSAN: a dynamic web database for structural genomics.Nucleic acids research · 2011Article
- TOPSAN: a collaborative annotation environment for structural genomics.BMC bioinformatics · 2010Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The success of community projects such as Wikipedia has recently prompted a discussion about the applicability of such tools in the life sciences. Currently, there are several such 'science-wikis' that aim to collect specialist knowledge from the community into centralized resources. However, there is no consensus about how to achieve this goal. For example, it is not clear how to best integrate data from established, centralized databases with that provided by 'community annotation'. We created PDBWiki, a scientific wiki for the community annotation of protein structures. The wiki consists of one structured page for each entry in the the Protein Data Bank (PDB) and allows the user to attach categorized comments to the entries. Additionally, each page includes a user editable list of cross-references to external resources. As in a database, it is possible to produce tabular reports and 'structure galleries' based on user-defined queries or lists of entries. PDBWiki runs in parallel to the PDB, separating original database content from user annotations. PDBWiki demonstrates how collaboration features can be integrated with primary data from a biological database. It can be used as a system for better understanding how to capture community knowledge in the biological sciences. For users of the PDB, PDBWiki provides a bug-tracker, discussion forum and community annotation system. To date, user participation has been modest, but is increasing. The user editable cross-references section has proven popular, with the number of linked resources more than doubling from 17 originally to 39 today. Database URL: http://www.pdbwiki.org.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.