Biology:Gene Wiki
The Gene Wiki is a project within Wikipedia that aims to describe the relationships and functions of all human genes. It was established to transfer information from scientific resources to Wikipedia stub articles.[1][2][3]
The Gene Wiki project also initiated publication of gene-specific review articles in the journal Gene, together with the editing of the gene-specific pages in Wikipedia.[4]
The Gene Wiki project in collaboration with the journal Gene was terminated in May 2022, ten years after the project's initiation. A report by the project's leaders summarizes the project's achievements.[5]
Project goals and scope
Number of gene articles
The human genome contains an estimated 20,000–25,000 protein-coding genes.[6] The goal of the Gene Wiki project is to create seed articles for every notable human gene, that is, every gene whose function has been assigned in the peer-reviewed scientific literature. Approximately half of human genes have assigned function, therefore the total number of articles seeded by the Gene Wiki project would be expected to be in the range of 10,000–15,000. To date,Template:As of when? approximately 11,000 articles have been created or augmented to include Gene Wiki project content.[citation needed]
Expansion
Once seed articles have been established, the hope and expectation is that these will be annotated and expanded by editors ranging in experience from the lay audience to students to professionals and academics.[1]
Proteins encoded by genes
Only a small portion of the genome actually encodes protein in the human genome. Understanding the function of a gene that codes for a protein generally requires understanding of the function of the corresponding protein. In addition to including basic information about the gene, the project therefore also includes information about the protein encoded by the gene. The function of other portions of the genome, non-coding DNA, also called "junk" DNA in the past because they had no apparent function, actually are thought to have regulatory functions.
Gene Wiki generated content
Stubs for the Gene Wiki project are created by a bot and contain links to the following primary gene/protein databases:
- HUGO Gene Nomenclature Committee – official gene name
- Entrez – Gene database
- OMIM (Mendelian Inheritance in Man) – database that catalogues all the known diseases with a genetic component
- Amigo – Gene Ontology
- HomoloGene – gene homologs in other species
- SymAtlasRNA – gene expression pattern in tissues[7]
- Protein Data Bank – 3D structure of protein encoded by the gene
- UniProt (universal protein resource) – a central repository of protein data
Response
A report found that between 2013 and 2017, the content which Gene Wiki contributed to Wikipedia got crowdsourced development over time.[8]
References
- ↑ 1.0 1.1 "A Gene Wiki for Community Annotation of Gene Function". PLOS Biology 6 (7): e175. July 2008. doi:10.1371/journal.pbio.0060175. PMID 18613750.
- ↑ "SciVee Pubcast: A Gene Wiki for Community Annotation of Gene Function". http://www.scivee.tv/pubcast/18613750.
- ↑ Huss JW; Lindenbaum P; Martone M et al. (January 2010). "The Gene Wiki: community intelligence applied to human gene annotation". Nucleic Acids Research 38 (Database issue): D633–9. doi:10.1093/nar/gkp760. PMID 19755503.
- ↑ "Gene Wiki Reviews-Raising the quality and accessibility of information about the human genome". Gene 592 (2): 235–8. 2 May 2016. doi:10.1016/j.gene.2016.04.053. PMID 27150585.
- ↑ "A retrospective evaluation of a decade of Gene Wiki Reviews and their impact". Gene 830: 146534. July 2022. doi:10.1016/j.gene.2022.146534. PMID 35525475. https://www.science.co.il/hi/pub/Gene-Wiki-Reviews-project.pdf.
- ↑ Clamp M; Fry B; Kamal M; Xie X; Cuff J; Lin MF; Kellis M; Lindblad-Toh K et al. (December 2007). "Distinguishing protein-coding and noncoding genes in the human genome". Proceedings of the National Academy of Sciences USA 104 (49): 19428–33. doi:10.1073/pnas.0709013104. PMID 18040051.
- ↑ "A gene atlas of the mouse and human protein-encoding transcriptomes". Proceedings of the National Academy of Sciences USA 101 (16): 6062–7. April 2004. doi:10.1073/pnas.0400782101. PMID 15075390. Bibcode: 2004PNAS..101.6062S.
- ↑ Zinovyev, Andrei; Czerwinska, Urszula; Cantini, Laura; Barillot, Emmanuel; Frahm, Klaus M.; Shepelyansky, Dima L.; Rzhetsky, Andrey (18 February 2020). "Collective intelligence defines biological functions in Wikipedia as communities in the hidden protein connection network". PLOS Computational Biology 16 (2): e1007652. doi:10.1371/journal.pcbi.1007652. PMID 32069277. Bibcode: 2020PLSCB..16E7652Z.
Further reading
- "Mining the Gene Wiki for functional genomic knowledge". BMC Genomics 12: 603. 2011. doi:10.1186/1471-2164-12-603. PMID 22165947.
- "The Gene Wiki in 2011: community intelligence applied to human gene annotation". Nucleic Acids Research 40 (Database issue): D1255–61. January 2012. doi:10.1093/nar/gkr925. PMID 22075991.
- "Linking genes to diseases with a SNPedia-Gene Wiki mashup". J Biomed Semantics 3 (Suppl 1): S6. 2012. doi:10.1186/2041-1480-3-S1-S6. PMID 22541597.
- "Gene Wiki Reviews: marrying crowdsourcing with traditional peer review". Gene 531 (2): 125. December 2013. doi:10.1016/j.gene.2013.08.093. PMID 24012870.
External links
- Spagat E (2008-07-09). "Edit your DNA: 'Gene wiki' to debut on Wikipedia". The Associated Press (in ABC News. https://abcnews.go.com/Technology/story?id=5353376&page=1.
- McKenney AS (2008-07-08). "Archiving Information About The Human Genome Using Wikipedia". IT / Internet / E-mail News. Medical News Today. http://www.medicalnewstoday.com/articles/113891.php.
- Tay L (2008-07-10). "Wikipedia hosts human gene repository". iTnews Australia. Haymarket Media. http://www.itnews.com.au/News/80128,wikipedia-hosts-human-gene-repository.aspx.
- Mitch Waldrop (3 September 2008). "Big data: Wikiomics". Nature 455 (7209): 22–25. doi:10.1038/455022a. PMID 18769412.
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