Gene Wiki

The Gene Wiki is a project within Wik.ipedia.Pro that aims to describe the relationships and functions of all human genes. It was established to transfer information from scientific resources to Wik.ipedia.Pro 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 Wik.ipedia.Pro.^[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,^{[as of?]} 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 Wik.ipedia.Pro got crowdsourced development over time.^[8]

References

^ ^a ^b Huss JW, Orozco C, Goodale J, Wu C, Batalov S, Vickers TJ, Valafar F, Su AI (July 2008). "A Gene Wiki for Community Annotation of Gene Function". PLOS Biology. 6 (7): e175. doi:10.1371/journal.pbio.0060175. PMC 2443188. PMID 18613750.
^ Huss JW, Orozco C, Goodale J, Wu C, Batalov S, Vickers TJ, Valafar F, Su AI. "SciVee Pubcast: A Gene Wiki for Community Annotation of Gene Function". Archived from the original on 2010-07-24. Retrieved 2008-11-19.
^ 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. PMC 2808918. PMID 19755503.
^ Tsueng G, Good BM, Ping P, Golemis E, Hanukoglu I, van Wijnen AJ, Su AI (2 May 2016). "Gene Wiki Reviews-Raising the quality and accessibility of information about the human genome". Gene. 592 (2): 235–8. doi:10.1016/j.gene.2016.04.053. PMC 5944608. PMID 27150585.
^ van Wijnen AJ, Golemis E, Hanukoglu I, Tsui SK, Hu E, Ul-Hasan S, Joy J, Su AI, Tsueng G (July 2022). "A retrospective evaluation of a decade of Gene Wiki Reviews and their impact" (PDF). Gene. 830: 146534. doi:10.1016/j.gene.2022.146534. PMID 35525475.
^ Clamp M; Fry B; Kamal M; Xie X; Cuff J; Lin MF; Kellis M; Lindblad-Toh K; Lander ES (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. PMC 2148306. PMID 18040051.
^ Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, Cooke MP, Walker JR, Hogenesch JB (April 2004). "A gene atlas of the mouse and human protein-encoding transcriptomes". Proceedings of the National Academy of Sciences USA. 101 (16): 6062–7. Bibcode:2004PNAS..101.6062S. doi:10.1073/pnas.0400782101. PMC 395923. PMID 15075390.
^ 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 Wik.ipedia.Pro as communities in the hidden protein connection network". PLOS Computational Biology. 16 (2): e1007652. Bibcode:2020PLSCB..16E7652Z. doi:10.1371/journal.pcbi.1007652. PMC 7048313. PMID 32069277.

External links

Spagat E (2008-07-09). "Edit your DNA: 'Gene wiki' to debut on Wik.ipedia.Pro". The Associated Press (in ABC News. Retrieved 2011-09-29.
McKenney AS (2008-07-08). "Archiving Information About The Human Genome Using Wik.ipedia.Pro". IT / Internet / E-mail News. Medical News Today. Retrieved 2008-07-19.
Tay L (2008-07-10). "Wik.ipedia.Pro hosts human gene repository". iTnews Australia. Haymarket Media. Archived from the original on 2008-07-13. Retrieved 2008-07-19.
Mitch Waldrop (3 September 2008). "Big data: Wikiomics". Nature. 455 (7209): 22–25. doi:10.1038/455022a. PMID 18769412.

[pmid18613750-1] Huss JW, Orozco C, Goodale J, Wu C, Batalov S, Vickers TJ, Valafar F, Su AI (July 2008). "A Gene Wiki for Community Annotation of Gene Function". PLOS Biology. 6 (7): e175. doi:10.1371/journal.pbio.0060175. PMC 2443188. PMID 18613750.

[SciVee_Pubcast-2] Huss JW, Orozco C, Goodale J, Wu C, Batalov S, Vickers TJ, Valafar F, Su AI. "SciVee Pubcast: A Gene Wiki for Community Annotation of Gene Function". Archived from the original on 2010-07-24. Retrieved 2008-11-19.

[pmid19755503-3] 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. PMC 2808918. PMID 19755503.

[4] Tsueng G, Good BM, Ping P, Golemis E, Hanukoglu I, van Wijnen AJ, Su AI (2 May 2016). "Gene Wiki Reviews-Raising the quality and accessibility of information about the human genome". Gene. 592 (2): 235–8. doi:10.1016/j.gene.2016.04.053. PMC 5944608. PMID 27150585.

[pmid35525475-5] van Wijnen AJ, Golemis E, Hanukoglu I, Tsui SK, Hu E, Ul-Hasan S, Joy J, Su AI, Tsueng G (July 2022). "A retrospective evaluation of a decade of Gene Wiki Reviews and their impact" (PDF). Gene. 830: 146534. doi:10.1016/j.gene.2022.146534. PMID 35525475.

[pmid18040051-6] Clamp M; Fry B; Kamal M; Xie X; Cuff J; Lin MF; Kellis M; Lindblad-Toh K; Lander ES (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. PMC 2148306. PMID 18040051.

[pmid15075390-7] Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, Cooke MP, Walker JR, Hogenesch JB (April 2004). "A gene atlas of the mouse and human protein-encoding transcriptomes". Proceedings of the National Academy of Sciences USA. 101 (16): 6062–7. Bibcode:2004PNAS..101.6062S. doi:10.1073/pnas.0400782101. PMC 395923. PMID 15075390.

[Zinovyev_2020-8] 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 Wik.ipedia.Pro as communities in the hidden protein connection network". PLOS Computational Biology. 16 (2): e1007652. Bibcode:2020PLSCB..16E7652Z. doi:10.1371/journal.pcbi.1007652. PMC 7048313. PMID 32069277.

[1]

[2]

[3]

[4]

[5]

[6]

[7]

[8]