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Biocuration – an introduction Claire O’Donovan odonovan@ebi.ac.uk

My background Team Leader of Protein Function Content team at EMBL-EBI with16 biocurators working on expert and automatic curation for UniProt, Gene Ontology Annotation Project and the Enzyme Portal Hired as an annotator in the Swiss-Prot team at EMBL Heidelberg in 1993 http://www.ebi.ac.uk/about/people/claire-odonovan

Scope of the talk Introduction to the concept of biocuration The different kinds of biocurators and the skill set needed Our community: Biocuration Society and conference The future of biocuration and career paths

Definition and aims of biocuration Biocuration involves the interpretation and integration of information relevant to biology into a database or resource that enables integration of the scientific literature as well as large data sets. Accurate and comprehensive representation of biological knowledge Easy access to this data for working scientists and a basis for computational analysis are primary goals of biocuration.

Definition and aims of biocuration achieved thanks to the convergent endeavors of biocurators, software developers and researchers in bioinformatics. biocurators provide essential resources to the biological community as databases have become an integral part of the tools researchers use on a daily basis for their work.

Definition of a biocurator (Wikipedia) a professional scientist who Curates, collects, annotates and validates information that is disseminated by biological and model organism databases. Role of a biocurator quality control of primary biological research data intended for publication, extracting and organizing data from original scientific literature

Definition of a biocurator (Wikipedia) describes the data with standard annotation protocols and vocabularies that enable powerful queries and biological database inter-operability. communicates with researchers to ensure the accuracy of curated information and to foster data exchanges with research laboratories Otherwise known as scientific curators, data curators, annotators or data wranglers!

Lots of different resources and lots of different curators!

Curation of a UniProtKB/Swiss-Prot entry Sequence UniProtKB/TrEMBL References Sequence variants Literature Annotations Nomenclature Ontologies Sequence features UniProtKB/Swiss-Prot 11.11.2018

The Gene Ontology A way to capture Less specific concepts A way to capture biological knowledge for individual gene products in a written and computable form A set of concepts and their relationships to each other arranged as a hierarchy More specific concepts www.ebi.ac.uk/QuickGO

Collaboration with the biocuration community Gene names Data from structures Additional bibliography GO terms Interactions

http://www.geneontology.org Reactome

Biocuration skill sets (1) Basics of bio-data: introducing the diverse range of data available and the need for harvesting and storing data. Basic curation skills: providing students with a practical foundation in the basic skills required in biocuration. Programming concepts: providing students with a foundation in key programming languages employed for working with bioinformatics tools.

Biocuration skill sets (2) Understanding databases: providing students with a basic working knowledge of database structure and interaction. Ontologies / controlled vocabularies: introducing students to the concept of ontologies and controlled vocabularies, their development and application. Database usability: exploring the issues around database access and use from a user perspective.

Biocuration skill set (3) Data access and management: providing students with an overview of the ethical and legal framework surrounding data acquisition, use and storage. Communication, dissemination and user engagement: introducing students to the importance of communicating to and engaging with stakeholder groups (e.g. users, publishers, funders) to encourage user acceptance of resources.

Biocuration skill set (3) User training: introducing students to basic user training concepts. Data analysis: providing an overview of important concepts in statistics and exploratory data analysis.

International Society for Biocuration Non-profit organisation for biocurators, developers, and researchers with an interest in biocuration Promotes the field of biocuration and provides a forum for information exchange through meeting and workshops Come and explore and contribute www.biocurator.org

Biocuration 2016 Yearly conference – 10-14th of April in Geneva, Switzerland Also celebrating 30th anniversary of Swiss-Prot (part of UniProt since 2002) http://biocuration2015.big.ac.cn/scientific-program https://www.isb-sib.ch/events/biocuration2016/

Biocuration 2016 WS3: Training needs for biocuration Summary: There is currently no recognised qualification in biocuration, either to provide new curators with a route for gaining the requisite skills to work within this field, or as a way for curators working in the field to gain recognition for the varied skill-sets that such a career provides them with. This workshop is intended to stimulate discussion on the training biocurators should have, and the role ISB should have in defining the training needs and gaps, and set of competencies. We will work together to discuss this and other related questions, and propose concrete answers to advance biocuration training.

Future of biocuration A very exciting time  Existing databases and their biocurators continue to evolve in response to big data – new challenges and learning experiences And Recognition of industry and governments for the need for curation of the data flood – big data!

Future of biocuration Centre for Target Validation (CTTV) https://www.targetvalidation.org/ The CTTV platform brings together information on the relationships between potential drug targets and diseases. The core concept is to identify evidence of an association between a target and disease from various data types. Curation of the literature and development of ontologies to tie the research wet lab and the function and consequence predictions with an outcome of a successful drug

Future of biocuration National Research Council (USA) and other agencies http://www.nap.edu/catalog/18590/preparing-the- workforce-for-digital-curation examines the possible career path demands and options for professionals working in digital curation activities, and analyzes the economic benefits and societal importance of digital curation for competitiveness, innovation, and scientific advancement.

Future of biocuration National Health System (NHS), UK and NIH, USA – personalized medicine data – electronic health records Collating, interpreting and relating this data across medical professionals to enable a complete overview of patient including diverse conditions and progression through life An exciting challenge!

Future of biocuration Job in my group  http://www.embl.de/jobs/searchjobs/index.php?ref=EB I_00687&newlang=1 http://www.ebi.ac.uk/about/jobs

Next webinars Ensembl release 84 – Wednesday 16th March at 16:00 GMT Ensembl online training series 2016 – 24th March – 5th May (every Thursday) at 16:00 GMT UniProt website updates 27th April at 16:00 GMT Find out more and register: http://www.ebi.ac.uk/training/webinars