Difference between revisions of "Biological Wikis"
Zhang Zhang (talk | contribs) |
Zhang Zhang (talk | contribs) |
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− | + | {| class="wikitable" | |
− | ==== | + | |- |
− | + | ! scope="col" align="left"| Name | |
− | + | ! scope="col" align="left"| Description | |
− | + | ! scope="col" align="left"| Availability | |
+ | ! scope="col"| MediaWiki-based | ||
+ | ! scope="col"| Reference | ||
+ | |- | ||
+ | |959 Nematode Genomes | ||
+ | |A semantic wiki for coordinating sequencing projects; | ||
+ | |http://www.nematodegenomes.org | ||
+ | |align="center"|Yes | ||
+ | |align="center"|[1] | ||
+ | |- | ||
+ | |ArrayWiki | ||
+ | |A community-maintained system for sharing public microarray data repositories and meta-analyses; | ||
+ | |http://arraywiki.bme.gatech.edu | ||
+ | |align="center"|Yes | ||
+ | |align="center"|[2] | ||
+ | |- | ||
+ | |BOWiki | ||
+ | |An ontology-based wiki for annotation of data and integration of knowledge; | ||
+ | |http://www.bowiki.net | ||
+ | |align="center"|No | ||
+ | |align="center"|[3] | ||
+ | |- | ||
+ | |EcoliWiki | ||
+ | |A wiki-based community resource for Escherichia coli; | ||
+ | |http://ecoliwiki.net | ||
+ | |align="center"|Yes | ||
+ | |align="center"|[4] | ||
+ | |- | ||
+ | |ESND | ||
+ | |A wiki-based English-to-Chinese scientific nomenclature dictionary; | ||
+ | |http://esnd.big.ac.cn | ||
+ | |align="center"|Yes | ||
+ | |align="center"|[5] | ||
+ | |- | ||
+ | |Gene Wiki | ||
+ | |A wiki harnessing community intelligence to the annotation of human gene and protein function; | ||
+ | |http://en.wikipedia.org/wiki/Portal:Gene_Wiki | ||
+ | |align="center"|Yes | ||
+ | |align="center"|[6] | ||
+ | |- | ||
+ | |GONUTS | ||
+ | |A community-based browser and usage guide for Gene Ontology (GO) terms and a community system for general GO annotation of proteins; | ||
+ | |http://gowiki.tamu.edu | ||
+ | |align="center"|Yes | ||
+ | |align="center"|[7] | ||
+ | |- | ||
+ | |MetaBase | ||
+ | |A community-curated database of commonly used biological databases; | ||
+ | |http://www.metadatabase.org | ||
+ | |align="center"|Yes | ||
+ | |align="center"|[8] | ||
+ | |- | ||
+ | |PDBWiki | ||
+ | |A community annotated knowledge base of biological molecular structures; | ||
+ | |http://www.pdbwiki.org | ||
+ | |align="center"|Yes | ||
+ | |align="center"|[9] | ||
+ | |- | ||
+ | |Proteopedia | ||
+ | |A scientific wiki bridging the rift between three-dimensional structure and function of biomacromolecules; | ||
+ | |http://www.proteopedia.org | ||
+ | |align="center"|Yes | ||
+ | |align="center"|[10] | ||
+ | |- | ||
+ | |Rfam | ||
+ | |A community-derived annotation of RNA families; | ||
+ | |http://rfam.sanger.ac.uk | ||
+ | |align="center"|Yes | ||
+ | |align="center"|[11] | ||
+ | |- | ||
+ | |RiceWiki | ||
+ | |A wiki-based, publicly editable and open-content platform for community annotation of rice genes; | ||
+ | |http://ricewiki.big.ac.cn | ||
+ | |align="center"|Yes | ||
+ | |align="center"|Unpublished | ||
+ | |- | ||
+ | |SEQanswers Wiki | ||
+ | |A wiki database of tools for high-throughput sequencing analysis; | ||
+ | |http://wiki.SEQanswers.com | ||
+ | |align="center"|Yes | ||
+ | |align="center"|[12] | ||
+ | |- | ||
+ | |SNPedia | ||
+ | |A wiki supporting personal genome annotation, interpretation and analysis; | ||
+ | |http://www.snpedia.com | ||
+ | |align="center"|Yes | ||
+ | |align="center"|[13] | ||
+ | |- | ||
+ | |SubtiWiki | ||
+ | |A comprehensive community resource for the model organism Bacillus subtilis; | ||
+ | |http://subtiwiki.uni-goettingen.de/wiki/index.php/Main_Page | ||
+ | |align="center"|Yes | ||
+ | |align="center"|[14] | ||
+ | |- | ||
+ | |Transdab Wiki | ||
+ | |A wiki database of transglutaminase substrate proteins; | ||
+ | |http://genomics.dote.hu/wiki | ||
+ | |align="center"|Yes | ||
+ | |align="center"|[15] | ||
+ | |- | ||
+ | |WikiCell | ||
+ | |A unified resource platform for human transcriptomics research; | ||
+ | |http://www.wikicell.org | ||
+ | |align="center"|Yes | ||
+ | |align="center"|[16] | ||
+ | |- | ||
+ | |WikiGenes | ||
+ | |A collaborative knowledge resource for the life sciences; | ||
+ | |http://www.wikigenes.org | ||
+ | |align="center"|No | ||
+ | |align="center"|[17] | ||
+ | |- | ||
+ | |WikiPathways | ||
+ | |An open, public platform dedicated to the curation of biological pathways; | ||
+ | |http://www.wikipathways.org | ||
+ | |align="center"|Yes | ||
+ | |align="center"|[18] | ||
+ | |- | ||
+ | |WikiProteins | ||
+ | |A wiki-based system for community annotation of proteins; | ||
+ | |http://www.wikiprofessional.org | ||
+ | |align="center"|(Not available) | ||
+ | |align="center"|[19] | ||
+ | |} | ||
− | + | ||
− | + | '''References''': | |
− | + | # Kumar S, Schiffer PH, Blaxter M. 959 Nematode Genomes: a semantic wiki for coordinating sequencing projects, Nucleic Acids Res 2012;40:D1295-1300. | |
− | + | # Stokes TH, Torrance JT, Li H et al. ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses, BMC Bioinformatics 2008;9 Suppl 6:S18. | |
− | + | # Hoehndorf R, Bacher J, Backhaus M et al. BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology, BMC Bioinformatics 2009;10 Suppl 5:S5. | |
− | + | # McIntosh BK, Renfro DP, Knapp GS et al. EcoliWiki: a wiki-based community resource for Escherichia coli, Nucleic Acids Res 2012;40:D1270-1277. | |
+ | # Dai L, Xu C, Tian M et al. Community intelligence in knowledge curation: an application to managing scientific nomenclature, PLoS One 2013;8:e56961. | ||
+ | # Good BM, Clarke EL, de Alfaro L et al. The Gene Wiki in 2011: community intelligence applied to human gene annotation, Nucleic Acids Res 2012;40:D1255-1261. | ||
+ | # Renfro DP, McIntosh BK, Venkatraman A et al. GONUTS: the Gene Ontology Normal Usage Tracking System, Nucleic Acids Res 2012;40:D1262-1269. | ||
+ | # Bolser DM, Chibon PY, Palopoli N et al. MetaBase--the wiki-database of biological databases, Nucleic Acids Res 2012;40:D1250-1254. | ||
+ | # Stehr H, Duarte JM, Lappe M et al. PDBWiki: added value through community annotation of the Protein Data Bank, Database (Oxford) 2010;2010:baq009. | ||
+ | # Hodis E, Prilusky J, Martz E et al. Proteopedia - a scientific 'wiki' bridging the rift between three-dimensional structure and function of biomacromolecules, Genome Biol 2008;9:R121. | ||
+ | # Gardner PP, Daub J, Tate J et al. Rfam: Wikipedia, clans and the "decimal" release, Nucleic Acids Res 2011;39:D141-145. | ||
+ | # Li JW, Robison K, Martin M et al. The SEQanswers wiki: a wiki database of tools for high-throughput sequencing analysis, Nucleic Acids Res 2012;40:D1313-1317. | ||
+ | # Cariaso M, Lennon G. SNPedia: a wiki supporting personal genome annotation, interpretation and analysis, Nucleic Acids Res 2012;40:D1308-1312. | ||
+ | # Mader U, Schmeisky AG, Florez LA et al. SubtiWiki--a comprehensive community resource for the model organism Bacillus subtilis, Nucleic Acids Res 2012;40:D1278-1287. | ||
+ | # Csosz E, Mesko B, Fesus L. Transdab wiki: the interactive transglutaminase substrate database on web 2.0 surface, Amino Acids 2009;36:615-617. | ||
+ | # Zhao D, Wu J, Zhou Y et al. WikiCell: a unified resource platform for human transcriptomics research, OMICS 2012;16:357-362. | ||
+ | # Hoffmann R. A wiki for the life sciences where authorship matters, Nat Genet 2008;40:1047-1051. | ||
+ | # Kelder T, van Iersel MP, Hanspers K et al. WikiPathways: building research communities on biological pathways, Nucleic Acids Res 2012;40:D1301-1307. | ||
+ | # Mons B, Ashburner M, Chichester C et al. Calling on a million minds for community annotation in WikiProteins, Genome Biol 2008;9:R89. |
Revision as of 07:27, 15 July 2013
Name | Description | Availability | MediaWiki-based | Reference |
---|---|---|---|---|
959 Nematode Genomes | A semantic wiki for coordinating sequencing projects; | http://www.nematodegenomes.org | Yes | [1] |
ArrayWiki | A community-maintained system for sharing public microarray data repositories and meta-analyses; | http://arraywiki.bme.gatech.edu | Yes | [2] |
BOWiki | An ontology-based wiki for annotation of data and integration of knowledge; | http://www.bowiki.net | No | [3] |
EcoliWiki | A wiki-based community resource for Escherichia coli; | http://ecoliwiki.net | Yes | [4] |
ESND | A wiki-based English-to-Chinese scientific nomenclature dictionary; | http://esnd.big.ac.cn | Yes | [5] |
Gene Wiki | A wiki harnessing community intelligence to the annotation of human gene and protein function; | http://en.wikipedia.org/wiki/Portal:Gene_Wiki | Yes | [6] |
GONUTS | A community-based browser and usage guide for Gene Ontology (GO) terms and a community system for general GO annotation of proteins; | http://gowiki.tamu.edu | Yes | [7] |
MetaBase | A community-curated database of commonly used biological databases; | http://www.metadatabase.org | Yes | [8] |
PDBWiki | A community annotated knowledge base of biological molecular structures; | http://www.pdbwiki.org | Yes | [9] |
Proteopedia | A scientific wiki bridging the rift between three-dimensional structure and function of biomacromolecules; | http://www.proteopedia.org | Yes | [10] |
Rfam | A community-derived annotation of RNA families; | http://rfam.sanger.ac.uk | Yes | [11] |
RiceWiki | A wiki-based, publicly editable and open-content platform for community annotation of rice genes; | http://ricewiki.big.ac.cn | Yes | Unpublished |
SEQanswers Wiki | A wiki database of tools for high-throughput sequencing analysis; | http://wiki.SEQanswers.com | Yes | [12] |
SNPedia | A wiki supporting personal genome annotation, interpretation and analysis; | http://www.snpedia.com | Yes | [13] |
SubtiWiki | A comprehensive community resource for the model organism Bacillus subtilis; | http://subtiwiki.uni-goettingen.de/wiki/index.php/Main_Page | Yes | [14] |
Transdab Wiki | A wiki database of transglutaminase substrate proteins; | http://genomics.dote.hu/wiki | Yes | [15] |
WikiCell | A unified resource platform for human transcriptomics research; | http://www.wikicell.org | Yes | [16] |
WikiGenes | A collaborative knowledge resource for the life sciences; | http://www.wikigenes.org | No | [17] |
WikiPathways | An open, public platform dedicated to the curation of biological pathways; | http://www.wikipathways.org | Yes | [18] |
WikiProteins | A wiki-based system for community annotation of proteins; | http://www.wikiprofessional.org | (Not available) | [19] |
References:
- Kumar S, Schiffer PH, Blaxter M. 959 Nematode Genomes: a semantic wiki for coordinating sequencing projects, Nucleic Acids Res 2012;40:D1295-1300.
- Stokes TH, Torrance JT, Li H et al. ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses, BMC Bioinformatics 2008;9 Suppl 6:S18.
- Hoehndorf R, Bacher J, Backhaus M et al. BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology, BMC Bioinformatics 2009;10 Suppl 5:S5.
- McIntosh BK, Renfro DP, Knapp GS et al. EcoliWiki: a wiki-based community resource for Escherichia coli, Nucleic Acids Res 2012;40:D1270-1277.
- Dai L, Xu C, Tian M et al. Community intelligence in knowledge curation: an application to managing scientific nomenclature, PLoS One 2013;8:e56961.
- Good BM, Clarke EL, de Alfaro L et al. The Gene Wiki in 2011: community intelligence applied to human gene annotation, Nucleic Acids Res 2012;40:D1255-1261.
- Renfro DP, McIntosh BK, Venkatraman A et al. GONUTS: the Gene Ontology Normal Usage Tracking System, Nucleic Acids Res 2012;40:D1262-1269.
- Bolser DM, Chibon PY, Palopoli N et al. MetaBase--the wiki-database of biological databases, Nucleic Acids Res 2012;40:D1250-1254.
- Stehr H, Duarte JM, Lappe M et al. PDBWiki: added value through community annotation of the Protein Data Bank, Database (Oxford) 2010;2010:baq009.
- Hodis E, Prilusky J, Martz E et al. Proteopedia - a scientific 'wiki' bridging the rift between three-dimensional structure and function of biomacromolecules, Genome Biol 2008;9:R121.
- Gardner PP, Daub J, Tate J et al. Rfam: Wikipedia, clans and the "decimal" release, Nucleic Acids Res 2011;39:D141-145.
- Li JW, Robison K, Martin M et al. The SEQanswers wiki: a wiki database of tools for high-throughput sequencing analysis, Nucleic Acids Res 2012;40:D1313-1317.
- Cariaso M, Lennon G. SNPedia: a wiki supporting personal genome annotation, interpretation and analysis, Nucleic Acids Res 2012;40:D1308-1312.
- Mader U, Schmeisky AG, Florez LA et al. SubtiWiki--a comprehensive community resource for the model organism Bacillus subtilis, Nucleic Acids Res 2012;40:D1278-1287.
- Csosz E, Mesko B, Fesus L. Transdab wiki: the interactive transglutaminase substrate database on web 2.0 surface, Amino Acids 2009;36:615-617.
- Zhao D, Wu J, Zhou Y et al. WikiCell: a unified resource platform for human transcriptomics research, OMICS 2012;16:357-362.
- Hoffmann R. A wiki for the life sciences where authorship matters, Nat Genet 2008;40:1047-1051.
- Kelder T, van Iersel MP, Hanspers K et al. WikiPathways: building research communities on biological pathways, Nucleic Acids Res 2012;40:D1301-1307.
- Mons B, Ashburner M, Chichester C et al. Calling on a million minds for community annotation in WikiProteins, Genome Biol 2008;9:R89.