Biocurator
Encyclopedia
A biocurator is a professional scientist
who collects, annotates, and validates information that is disseminated by biological
and model organism
database
s. 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.
Biocurators (also called scientific curators, data curators or annotators) have been recognized as the "museum catalogers of the Internet age".
To annotate data, 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. 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
.
The International Society for Biocuration (ISB) 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.
Scientist
A scientist in a broad sense is one engaging in a systematic activity to acquire knowledge. In a more restricted sense, a scientist is an individual who uses the scientific method. The person may be an expert in one or more areas of science. This article focuses on the more restricted use of the word...
who collects, annotates, and validates information that is disseminated by biological
Biology
Biology is a natural science concerned with the study of life and living organisms, including their structure, function, growth, origin, evolution, distribution, and taxonomy. Biology is a vast subject containing many subdivisions, topics, and disciplines...
and model organism
Model organism
A model organism is a non-human species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the organism model will provide insight into the workings of other organisms. Model organisms are in vivo models and are widely used to...
database
Database
A database is an organized collection of data for one or more purposes, usually in digital form. The data are typically organized to model relevant aspects of reality , in a way that supports processes requiring this information...
s. 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
Annotation
An annotation is a note that is made while reading any form of text. This may be as simple as underlining or highlighting passages.Annotated bibliographies give descriptions about how each source is useful to an author in constructing a paper or argument...
protocols and vocabularies that enable powerful queries and biological database
Biological database
Biological databases are libraries of life sciences information, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analyses. They contain information from research areas including genomics, proteomics, metabolomics, microarray...
inter-operability. Biocurators communicate with researchers to ensure the accuracy of curated information and to foster data exchanges with research laboratories.
Biocurators (also called scientific curators, data curators or annotators) have been recognized as the "museum catalogers of the Internet age".
To annotate data, biocurators commonly employ—and take part in the creation and development of—shared biomedical ontologies
Ontology (computer science)
In computer science and information science, an ontology formally represents knowledge as a set of concepts within a domain, and the relationships between those concepts. It can be used to reason about the entities within that domain and may be used to describe the domain.In theory, an ontology is...
: structured, controlled vocabularies that encompass many biological and medical knowledge domains. These domains include genomics
Genomics
Genomics is a discipline in genetics concerning the study of the genomes of organisms. The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts. The field also includes studies of intragenomic phenomena such as heterosis,...
and proteomics
Proteomics
Proteomics is the large-scale study of proteins, particularly their structures and functions. Proteins are vital parts of living organisms, as they are the main components of the physiological metabolic pathways of cells. The term "proteomics" was first coined in 1997 to make an analogy with...
, anatomy
Anatomy
Anatomy is a branch of biology and medicine that is the consideration of the structure of living things. It is a general term that includes human anatomy, animal anatomy , and plant anatomy...
, animal and plant development
Developmental biology
Developmental biology is the study of the process by which organisms grow and develop. Modern developmental biology studies the genetic control of cell growth, differentiation and "morphogenesis", which is the process that gives rise to tissues, organs and anatomy.- Related fields of study...
, biochemistry
Biochemistry
Biochemistry, sometimes called biological chemistry, is the study of chemical processes in living organisms, including, but not limited to, living matter. Biochemistry governs all living organisms and living processes...
, metabolic pathways, taxonomic classification
Alpha taxonomy
Alpha taxonomy is the discipline concerned with finding, describing and naming species of living or fossil organisms. This field is supported by institutions holding collections of these organisms, with relevant data, carefully curated: such institutes include natural history museums, herbaria and...
, and mutant phenotypes.
Biocurators enforce the consistent use of gene nomenclature
Gene nomenclature
Gene nomenclature is the scientific naming of genes, the units of heredity in living organisms. An international committee published recommendations for genetic symbols and nomenclature in 1957. The need to develop formal guidelines for human gene names and symbols was recognized in the 1960s and...
guidelines and participate in the genetic nomenclature committees of various model organisms, often in collaboration with the HUGO
Human Genome Organisation
The Human Genome Organisation is an organization involved in the Human Genome Project, a project about mapping the human genome. HUGO was established in 1989 as an international organization, primarily to foster collaboration between genome scientists around the world...
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
International Union of Biochemistry and Molecular Biology
The International Union of Biochemistry and Molecular Biology is an international non-governmental organisation concerned with biochemistry and molecular biology...
(IUBMB), one example of which is the Enzyme Commission EC number
EC number
The Enzyme Commission number is a numerical classification scheme for enzymes, based on the chemical reactions they catalyze....
.
The International Society for Biocuration (ISB) 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.
See also
- At the Comparative Toxicogenomics DatabaseComparative Toxicogenomics DatabaseThe Comparative Toxicogenomics Database is a public website and research tool that curates scientific data describing relationships between chemicals, genes, and human diseases....
, biocurators annotate chemical-gene-disease interactions from the scientific literature.
External links
- International Society for Biocuration
- XTractor - Discovering Newer Scientific Relations Across PubMedPubMedPubMed is a free database accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine at the National Institutes of Health maintains the database as part of the Entrez information retrieval system...
Abstracts. A tool to obtain manually annotated relationships for Proteins, Diseases, Drugs and Biological Processes as they get published in PubMedPubMedPubMed is a free database accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine at the National Institutes of Health maintains the database as part of the Entrez information retrieval system...
. - Open Biomedical Ontologies (OBO) Foundry
- Comparative Toxicogenomics Database
- TexFlame - An online tool that renders a single PubMedPubMedPubMed is a free database accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine at the National Institutes of Health maintains the database as part of the Entrez information retrieval system...
abstract as a Systems Biology Graphical NotationSystems Biology Graphical NotationThe Systems Biology Graphical Notation is a standard graphical representation crafted over several years by a community of biochemists, modelers and computer scientists....
(SBGN)-like graph. Provides biocurators a starting point for creation of pathway maps.