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.[6]
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)[8] promote training and support biocuration as a career path.[9][10]
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.[11] With the growth of the field, the
University of Cambridge and the
EMBL-EBI started to jointly offer a Postgraduate Certificate in Biocuration,[12] considered as a step towards recognising biocuration as a discipline on its own.[13] There is a perceived increase in demand of biocuration, and a need for additional biocuration training by
graduate programs.[14]
Organizations that employ biocurators, like
Clinical Genome Resource (ClinGen), often provide specialized materials and training for biocuration.[15]
The role of biocurators is best known among the field of
biological knowledgebases. Such databases, like
UniProt[16] and
PDB[17] rely on professional biocurators to organize information. Among other things, biocurators work to improve the data quality, for example, by merging duplicated entries.[18]
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
The
Unified Medical Language System is one such systems that integrates and distributes millions of terms used in the life sciences domain.[23]
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 [24]
In
genome annotation for example, the identifiers defined by the ontologists and consortia are used to describe parts of the genome. For example, the
gene ontology (GO) curates terms for biological processes, which are used to describe what we know about specific
genes.
Text annotation
As of 2021, life sciences communication is still done primarily via free natural languages, like
English or
German, which hold a degree of ambiguity and make it hard to connect knowledge. So, besides annotating biological sequences, biocurators also annotate texts, linking words to unique identifiers. This aids in disambiguation, clarifying the meaning intended, and making the texts processable by computers. One application of text annotation is to specify the exact gene a scientist is referring to.[25]
Publicly available text annotations make it possible to biologists to take further advantage of biomedical text. The
Europe PMC has an
Application Programming Interface which centralizes text annotations from a variety of sources and make them available in a
Graphic User Interface called SciLite.[26] The PubTator Central also provides annotations, but is fully based on computerized text-mining and does not provide a user interface.[27] There are also programs that allow users to manually annotate the biomedical texts they are interested, such as the ezTag system.[28]
Variant Curation
A type of biocuration within the field of
medical genetics, variant curation is a process for assessment of genetic changes according to the likelihood that they may cause disease.[29] This is an evidence-based process that uses data from a multitude of sources. These sources can include population data, computational data, functional data,
segregation data, de novo data,
allelic data, among others.[30] It is a collaborative process that can be automated, however manual curation is considered to be the gold standard.[31]
There is no single standardised process of variant curation; different researchers and organisations use different variant curation processes.[29] However, a set of internationally-accepted[32] standards and guidelines for the interpretation of genetic variants have been jointly developed by the
American College of Medical Genetics and the
Association for Molecular Pathology.[30] These are known as the ACMG/AMP guidelines. These guidelines provide a framework for classifying genetic variants as “pathogenic”, “likely pathogenic”, “uncertain significance”, “likely benign” or “benign”, in order from most likely to cause disease to least likely to cause disease. The guidelines also list various levels of evidence ranging from very strong, strong, moderate or supporting.[33] The combination of types of evidence found, and the levels in which those pieces of evidence exist, allows for each variant to be classified along the scale from "pathogenic" to "benign".[32]
The
International Society for Biocuration (ISB) is a non-profit organisation "promotes the field of biocuration and provides a forum for information exchange through meetings and workshops." It has grown from the International Biocuration Conferences and founded in early 2009.[4]
The ISB offers the
Biocuration Career Award to biocurators in the community: the Biocurator Career Award (given annually) and the ISB Award for Exceptional Contributions to Biocuration (given biannually).
The official journal of the ISB,
Database, is a venue specialized in articles about databases and biocuration.[34]
Community curation
Traditionally, biocuration has been done by dedicated experts, which integrate data into databases. Community curation has emerged as a promising approach to improve the dissemination of knowledge from published data and provide a cost-effective way to improve the scalability of biocuration. In some cases, community help is leveraged in jamborees that introduce domain experts to curation tasks, carried during the event,[35] while others rely on asynchronous contributions of experts and non-experts.[36]
Biological databases
Several biological databases include author contributions in their functional curation strategy to some extent, which may range from associating gene identifiers with publications or free-text, to more structured and detailed annotation of sequences and functional data, outputting curation to the same standards as professional biocurators. Most community curation at
Model Organism Databases involves annotation by original authors of published research (first-pass annotation) to effectively obtain accurate identifiers for objects to be curated, or identify data-types for detailed curation. For example:
WormBase successfully solicits first-pass annotation from users and has integrated author curation with the micropublication process.[38] WormBase also integrates text-mining to its platform, providing suggestions to community curators.[37]
FlyBase sends email requests to authors of new publications,[39] inviting them to list the genes and data types described via an online tool and has also mobilized the community to write gene summary paragraphs.[40]
Other databases, such as
PomBase, rely on publication authors to submit highly detailed, ontology-based annotations for their publications, and meta-data associated with genome-wide data-sets using controlled vocabularies. A web-based tool
Canto;[41] was developed to facilitate community submissions. Since Canto is freely available, generic and highly configurable, it has been adopted by other projects.[42] Curation is subjected to review by professional curators resulting in high quality in-depth curation of all molecular data-types.[43]
The widely used
UniProt knowledgebase has also a community curation mechanism that allows researchers to add information about proteins.[44]
Wiki-style resources
Bio-wikis rely on their communities to provide content and a series of wiki-style resources are available for biocuration.[45][46]AuthorReward,[47] for example, is an extension to MediaWiki that quantifies researchers' contributions to biology wikis. RiceWiki was an example of a wiki-based database for community curation of rice genes equipped with AuthorReward.[48][49] CAZypedia is another such wiki for community biocuration of information on
carbohydrate-active enzymes (CAZys).[50]
There is some overlap between the work of biocurators and
Wikipedia, with boundaries between scientific
databases and Wikipedia becoming increasingly blurred.[54][46][55] Databases like
Rfam[56][57] and the
Protein Data Bank[58] for example make heavy use of Wikipedia and its editors to curate information.[59][60] However, most databases offer highly structured data that is searchable in complex combinations, which is usually not possible on Wikipedia, although
Wikidata aims at solving this problem to some extent.
The
Gene Wiki project used Wikipedia for collaborative curation of thousands of genes and gene products, such as
titin and
insulin.[61] Several projects also employ Wikipedia as a platform for curation of medical information.[36]
The Wikimedia knowledge base
Wikidata is increasingly being used by the biocuration community as an integrative repository across life sciences.[63] Wikidata is being seen by some as an alternative with better prospects of maintenance and interoperability than smaller independent biological knowledge bases.[64][65]
Wikidata has been used to curate information on
SARS-CoV-2 and the
COVID-19 pandemic[66][67] and by the
Gene Wiki project to curate information about
genes.[68] Data from biocuration on Wikidata is reused on external resources via
SPARQL queries.[69] Some projects use curation via Wikidata as a path to improve life-sciences information on Wikipedia.[70]
Gamified resources
An approach to involve the crowd in biocuration is via gamified platforms that use
game design principles to boost engagement. A few examples are:
Mark2Cure, a gamified platform for community curation of biomedical abstracts[71][72][73]
Cochrane Crowd,[74] a platform by
Cochrane for curation of
clinical trials and to categorize and summarize biomedical literature.[75]
CIViC, a portal for annotation of genomic variants related to
cancer[76] which tracks scores and keeps leaderboards.[77]
APICURON, a database to credit and acknowledge the work of biocurators, that collects and aggregates biocuration events from third party resources and generates achievements and leaderboards.[78]
Computational text mining for curation
Natural-language processing and
text mining technologies can help biocurators to extract of information for manual curation.[80] Text mining can scale curation efforts, supporting the identification of gene names, for example, as well as for partially inferring
ontologies.[81][82] The conversion of unstructured assertions to structured information makes use of techniques like
named entity recognition and
parsing of
dependencies.[83] Text-mining of biomedical concepts faces challenges regarding variations in reporting, and the community is working to increase the machine-readability of articles.[84]
During the
COVID-19 pandemic, biomedical text mining was heavily used to cope with the large amount of published scientific research about the topic (over 50.000 articles).[85]
Among the challenges for text-mining applied to biocuration is the difficulty of accessing full texts of biomedical articles due to pay wall, linking the challenges of biocuration to those of the
open-access movement.[87]
A complementary approach to biocuration via text mining involves applying
optical character recognition to biomedical figures, coupled to automatic annotation algorithms. This has been used to extract gene information from
pathway figures, for example.[88]
Suggestions to improve the written text to facilitate annotations range from using
controlled natural languages[89] to providing clear association of concepts (such as
genes and
proteins) with the particular
species of interest.[89]
While challenges remain, text-mining is already an integral part of the workflow of biocuration in several
biological knowledgebases.[90]
The BioCreAtivE (Critical Assessment of Information Extraction systems in Biology) Challenge is a community-wide effort to develop and evaluate text mining and information extraction systems for the life sciences. The challenge was first launched in 2004 and has since become an important event in the biocuration and bioinformatics communities.[91] The main goal of the challenge is to foster the development of advanced computational tools that can effectively extract information from the vast amount of biological data available.
The BioCreative Challenge is organized into several subtasks that cover various aspects of text mining and information extraction in the life sciences. These subtasks include gene normalization, relation extraction, entity recognition, and document classification. Participants in the challenge are provided with a set of annotated data to develop and test their systems, and their performance is evaluated based on various metrics, such as precision, recall, and F-score.[91]
The BioCreative Challenge has led to the development of many innovative text mining and information extraction systems that have greatly improved the efficiency and accuracy of biocuration efforts. These systems have been integrated into many biocuration pipelines and have helped to speed up the curation process and enhance the quality of curated data.
^Butler D (2008). "Publish in Wikipedia or perish: Journal to require authors to post in the free online encyclopaedia". Nature.
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