Biocuration is the field of life sciences dedicated to organizing biomedical data, information and knowledge into structured formats, such as spreadsheets, tables and knowledge graphs. The biocuration of biomedical knowledge is made possible by the cooperative work of biocurators, software developers and bioinformaticians and is at the base of the work of biological databases.
Biocuration as a profession
A biocurator is a professional scientist who curates, collects, annotates, and validates information that is disseminated by biological and model organism databases. It is a new profession, with the first mentions in the scientific literature dating of 2006 in the context of the work in databases like the Immune Epitope Database and Analysis Resource. Biocurators usually are PhD-level with a mix of experiences in wet lab and computational representations of knowledge (e.g. via ontologies).
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 interoperability. Biocurators communicate with researchers to ensure the accuracy of curated information and to foster data exchanges with research laboratories.
Biocurators are present in diverse research environments, but may not self-identify as biocurators. Projects such as ELIXIR (the European life-sciences Infrastructure for biological Information) and GOBLET (Global Organization for Bioinformatics Learning, Education and Training) promote training and support biocuration as a career path.
In 2011, biocuration was already recognized as a profession, but there were no formal degree courses to prepare curators for biological data in a targeted fashion. With the growth of the field, the University of Cambridge and the EMBL-EBI started to jointly offer a Postgraduate Certificate in Biocuration, considered as a step towards recognising biocuration as a discipline on its own. There is a perceived increase in demand of biocuration, and a need for additional biocuration training by graduate programs.
Organizations that employ biocurators, like Clinical Genome Resource (ClinGen), often provide specialized materials and training for biocuration.
Biological knowledgebases
The role of biocurators is best known among the field of biological knowledgebases. Such databases, like UniProt and PDB rely on professional biocurators to organize information. Among other things, biocurators work to improve the data quality, for example, by merging duplicated entries.
An important part of those knowledgebases are model organisms databases, which rely on biocurators to curate information regarding organisms of particular kinds. Some notable examples of model organism databases are FlyBase, PomBase, and ZFIN, dedicated to curate information about Drosophila, Schizosaccharomyces pombe and zebrafish respectively.
Curation and annotation
Biocuration is the integration of biological information into on-line databases in a semantically standardized way, using appropriate unique traceable identifiers, and providing necessary metadata including source and provenance.
Ontologies, controlled vocabularies and standard names
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. These domains include genomics and proteomics, anatomy, animal and plant development, biochemistry, metabolic pathways, taxonomic classification, and mutant phenotypes. Given the variety of existing ontologies, there are guidelines that orient researchers on how to choose a suitable one.
The Unified Medical Language System is one such systems that integrates and distributes millions of terms used in the life sciences domain.
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.
More generally, the use of persistent identifiers is praised by the community, so to improve clarity and facilitate knowledge
