Biocurator: Difference between revisions

Add links
From Wikipedia, the free encyclopedia
Browse history interactively
← Previous editNext edit →
Content deleted Content added
VisualWikitext
Curators of the world unite!
refs and a little on relationship of biocurators with wikipedia
Line 1: Line 1:
A '''biocurator''' is a professional [[scientist]] who collects, annotates, and validates information that is disseminated by [[Biology|biological]] and [[model organism]] [[database]]s.<ref>{{cite doi|10.1093/bioinformatics/btq101}}</ref> The role of a biocurator encompasses quality control of primary biological research data intended for publication, extracting and organizing data from original scientific literature, and describing the data with standard [[annotation]] protocols and vocabularies that enable powerful queries and [[biological database]] inter-operability. Biocurators communicate with researchers to ensure the accuracy of curated information and to foster data exchanges with research laboratories.
A '''biocurator''' is a professional [[scientist]] who [[curator|curates]], collects, annotates, and validates information that is disseminated by [[Biology|biological]] and [[model organism]] [[database]]s.<ref>{{cite doi|10.1093/bioinformatics/btq101}}</ref> The role of a biocurator encompasses quality control of primary biological research data intended for publication, extracting and organizing data from original scientific literature, and describing the data with standard [[annotation]] protocols and vocabularies that enable powerful queries and [[biological database]] inter-operability. Biocurators communicate with researchers to ensure the accuracy of curated information and to foster data exchanges with research laboratories.<ref>{{cite doi|10.1371/journal.pcbi.0020125}}</ref>


Biocurators (also called '''scientific curators''', '''data curators''' or '''annotators''') have been recognized as the "museum catalogers of the Internet age".<ref>{{cite doi|10.1371/journal.pcbi.0020142}}</ref><ref>{{cite doi|10.1093/database/bar059}}</ref>
Biocurators (also called '''scientific curators''', '''data curators''' or '''annotators''') have been recognized as the "museum catalogers of the Internet age".<ref>{{cite doi|10.1371/journal.pcbi.0020142}}</ref><ref>{{cite doi|10.1093/database/bar059}}</ref>


==Curation and annotation==
To annotate data, biocurators commonly employ—and take part in the creation and development of—shared biomedical [[Ontology (computer science)|ontologies]]: structured, [[controlled vocabularies]] that encompass many biological and medical knowledge domains. These domains include [[genomics]] and [[proteomics]], [[anatomy]], animal and plant [[Developmental biology|development]], [[biochemistry]], [[metabolic pathways]], [[Alpha taxonomy|taxonomic classification]], and mutant [[phenotypes]].
In [[genome annotation]] for example, biocurators commonly employ—and take part in the creation and development of—shared biomedical [[Ontology (computer science)|ontologies]]: structured, [[controlled vocabularies]] that encompass many biological and medical knowledge domains, such as the [[Open Biomedical Ontologies]] found in the [[OBO Foundry]]. These domains include [[genomics]] and [[proteomics]], [[anatomy]], animal and plant [[Developmental biology|development]], [[biochemistry]], [[metabolic pathways]], [[Alpha taxonomy|taxonomic classification]], and mutant [[phenotypes]].


Biocurators enforce the consistent use of [[gene nomenclature]] guidelines and participate in the genetic nomenclature committees of various model organisms, often in collaboration with the [[Human Genome Organisation|HUGO]] Gene Nomenclature Committee ([http://www.genenames.org/ HGNC]). They also enforce
Biocurators enforce the consistent use of [[gene nomenclature]] guidelines and participate in the genetic nomenclature committees of various model organisms, often in collaboration with the [[Human Genome Organisation|HUGO]] Gene Nomenclature Committee ([http://www.genenames.org/ HGNC]). They also enforce
other nomenclature guidelines like those provided by the Nomenclature Committee of the [[International Union of Biochemistry and Molecular Biology]] (IUBMB), one example of which is the Enzyme Commission [[Enzyme Commission number|EC number]].
other nomenclature guidelines like those provided by the Nomenclature Committee of the [[International Union of Biochemistry and Molecular Biology]] (IUBMB), one example of which is the Enzyme Commission [[Enzyme Commission number|EC number]].

==International Society for Biocuration (ISB)==


The '''International Society for Biocuration''' (ISB)<ref>http://www.biocurator.org/ International Society for Biocuration (biocurator.org)</ref> was founded in 2008; the non-profit organisation "promotes the field of biocuration and provides a forum for information exchange through meetings and workshops." International Biocurator Conferences have been held in Pacific Grove, California (2005), San José, CA (2007), and Berlin (2009), Chiba, Japan (2010), and a meeting has been scheduled for Washington in 2012.
The '''International Society for Biocuration''' (ISB)<ref>http://www.biocurator.org/ International Society for Biocuration (biocurator.org)</ref> was founded in 2008; the non-profit organisation "promotes the field of biocuration and provides a forum for information exchange through meetings and workshops." International Biocurator Conferences have been held in Pacific Grove, California (2005), San José, CA (2007), and Berlin (2009), Chiba, Japan (2010), and a meeting has been scheduled for Washington in 2012.

==Biocurators and wikipedia==
There is some overlap between the work of biocurators and wikipedia, with boundaries between scientific databases and wikipedia becoming increasingly blurred<ref>{{cite pmid| 22479174}}</ref><ref>{{cite pmid| 22144683}}</ref><ref>{{cite pmid| 21516242}}</ref>. Databases like [[Rfam]]<ref>{{cite pmid|21062808}}</ref> and the [[Protein Data Bank]]<ref>{{cite pmid|17069453}}</ref> for example make heavy use of wikipedia and and its editors to curate information.<ref>{{cite pmid| 20941386}}</ref>




==References==
==References==
{{reflist|2}}
<references/>


==See also==
==See also==
* At the [[Comparative Toxicogenomics Database]], biocurators annotate chemical-gene-disease interactions from the scientific literature.
* At the [[Comparative Toxicogenomics Database]], biocurators annotate chemical-gene-disease interactions from the scientific literature.
*[http://www.xtractor.in/ XTractor] - Discovering Newer Scientific Relations Across [[PubMed]] Abstracts. A tool to obtain manually annotated relationships for Proteins, Diseases, Drugs and Biological Processes as they get published in [[PubMed]].
*[http://www.xtractor.in/ XTractor] - Discovering Newer Scientific Relations Across [[PubMed]] Abstracts. A tool to obtain manually annotated relationships for Proteins, Diseases, Drugs and Biological Processes as they get published in [[PubMed]].
* [[Open Biomedical Ontologies]]
* [[OBO Foundry]]
*[http://ctdbase.org/ Comparative Toxicogenomics Database]
*[http://ctdbase.org/ Comparative Toxicogenomics Database]
* [http://texflame.com TexFlame] - An online tool that renders a single [[PubMed]] abstract as a [[Systems Biology Graphical Notation]] (SBGN)-like graph. Provides biocurators a starting point for creation of pathway maps.
* [http://texflame.com TexFlame] - An online tool that renders a single [[PubMed]] abstract as a [[Systems Biology Graphical Notation]] (SBGN)-like graph. Provides biocurators a starting point for creation of pathway maps.

Revision as of 16:44, 27 July 2012

A biocurator is a professional scientist who curates, collects, annotates, and validates information that is disseminated by biological and model organism databases.[1] The role of a biocurator encompasses quality control of primary biological research data intended for publication, extracting and organizing data from original scientific literature, and describing the data with standard annotation protocols and vocabularies that enable powerful queries and biological database inter-operability. Biocurators communicate with researchers to ensure the accuracy of curated information and to foster data exchanges with research laboratories.[2]

Biocurators (also called scientific curators, data curators or annotators) have been recognized as the "museum catalogers of the Internet age".[3][4]

Curation and annotation

In genome annotation for example, biocurators commonly employ—and take part in the creation and development of—shared biomedical ontologies: structured, controlled vocabularies that encompass many biological and medical knowledge domains, such as the Open Biomedical Ontologies found in the OBO Foundry. These domains include genomics and proteomics, anatomy, animal and plant development, biochemistry, metabolic pathways, taxonomic classification, and mutant phenotypes.

Biocurators enforce the consistent use of gene nomenclature guidelines and participate in the genetic nomenclature committees of various model organisms, often in collaboration with the HUGO Gene Nomenclature Committee (HGNC). They also enforce other nomenclature guidelines like those provided by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB), one example of which is the Enzyme Commission EC number.

International Society for Biocuration (ISB)

The International Society for Biocuration (ISB)[5] was founded in 2008; the non-profit organisation "promotes the field of biocuration and provides a forum for information exchange through meetings and workshops." International Biocurator Conferences have been held in Pacific Grove, California (2005), San José, CA (2007), and Berlin (2009), Chiba, Japan (2010), and a meeting has been scheduled for Washington in 2012.

Biocurators and wikipedia

There is some overlap between the work of biocurators and wikipedia, with boundaries between scientific databases and wikipedia becoming increasingly blurred[6][7][8]. Databases like Rfam[9] and the Protein Data Bank[10] for example make heavy use of wikipedia and and its editors to curate information.[11]


References

  1. ^ Attention: This template ({{cite doi}}) is deprecated. To cite the publication identified by doi:10.1093/bioinformatics/btq101, please use {{cite journal}} (if it was published in a bona fide academic journal, otherwise {{cite report}} with |doi=10.1093/bioinformatics/btq101 instead.
  2. ^ Attention: This template ({{cite doi}}) is deprecated. To cite the publication identified by doi:10.1371/journal.pcbi.0020125, please use {{cite journal}} (if it was published in a bona fide academic journal, otherwise {{cite report}} with |doi=10.1371/journal.pcbi.0020125 instead.
  3. ^ Attention: This template ({{cite doi}}) is deprecated. To cite the publication identified by doi:10.1371/journal.pcbi.0020142, please use {{cite journal}} (if it was published in a bona fide academic journal, otherwise {{cite report}} with |doi=10.1371/journal.pcbi.0020142 instead.
  4. ^ Attention: This template ({{cite doi}}) is deprecated. To cite the publication identified by doi:10.1093/database/bar059, please use {{cite journal}} (if it was published in a bona fide academic journal, otherwise {{cite report}} with |doi=10.1093/database/bar059 instead.
  5. ^ http://www.biocurator.org/ International Society for Biocuration (biocurator.org)
  6. ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 22479174, please use {{cite journal}} with |pmid= 22479174 instead.
  7. ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 22144683, please use {{cite journal}} with |pmid= 22144683 instead.
  8. ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 21516242, please use {{cite journal}} with |pmid= 21516242 instead.
  9. ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 21062808, please use {{cite journal}} with |pmid=21062808 instead.
  10. ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 17069453, please use {{cite journal}} with |pmid=17069453 instead.
  11. ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 20941386, please use {{cite journal}} with |pmid= 20941386 instead.

See also

Retrieved from "https://en.wikipedia.org/w/index.php?title=Biocurator&oldid=504455090"