E2 life as_a_scientific_database_curator_(sandra_orchard)


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E2 life as_a_scientific_database_curator_(sandra_orchard)

  1. 1. Life as a scientific database curator Sandra Orchard EBI is an Outstation of the European Molecular Biology Laboratory.
  2. 2. What is a database curator Curator – OED - a keeper of a museum or other collection - from LATIN curare – take care of2/17
  3. 3. What is a database curator The job • Creating a structure for unstructured biological data • Generating order from chaos • Combining literature and automated processes to provide biomolecules with correct sequence/structure, nomenclature, function and contextual information • Give biological context to large experimental datasets The qualification • Need an attention to detail which would annoy even the best of housemates • Passion for reading and understanding literature3/17
  4. 4. What is a database curator The Pros • Read about and gain understanding of all areas of biology The Cons • No specialisation • Persuading biologists that there are benefits to this.4/17
  5. 5. What is a database curator• The International Society for Biocuration (ISB) definition:...integration of information relevant to biology into a database or resource that enables integration of the scientific literature...and large experimental data sets.• Goals are...accurate and comprehensive representation......to facilitate access to data for scientists...as a resource for computational analysis
  6. 6. What does a database curator do?Collects, annotates, and validates information (in adatabase).Extracts & organizes data from literatureDescribes data using standards, protocols andvocabularies (enabling computational queries and dataexchange).Communicates with researchers to ensure the accuracyof curated information and to foster good practice in dataexchange.
  7. 7. What does a database curator do? Takes part in the development of shared biomedical data standards and ontologies and (ideally) enforces their use. Trains users in effectively accessing and using the data in the databases Promotes database usage through talks, conference attendance/posters, publications etc…..7/17
  8. 8. What do I do? • Curate the molecular interaction database8/17
  9. 9. What do I do? Custom curation tools designed by the curation team9/17
  10. 10. What do I do? Controlled vocabulary maintenance10/17
  11. 11. Qualifications for the job • A biology B.Sc./M.Sc./PhD + lab experience or • A bioinformatics M.Sc Plus – an enquiring mind, ability to write good English and the right attitude Training – largely database specific and will be given ‘on- the-job’11/17
  12. 12. Qualifications for the job • Do I need to be able to do programming? • Answer – no. It is often helpful to have some database query ability but it is perfectly possible to do the job without (in most databases)12/17
  13. 13. Career Progression Within the EBI • Progress as a curator – senior curator, curation coordinator • Project management – grant coordinator, project leader Post –EBI • Curation/project leadership positions at many other institutes • Related areas – academic research, research project management, lectureships, journal publishing13/17
  14. 14. Will I still be allowed to publish? Curation The annotation of both human and mouse kinomes in UniProtKB/Swiss-Prot - (MCP) Data Standards The Minimum Information required for reporting a Molecular Interaction Experiment (MIMIx) – (NBT) Data Formats The HUPO PSIs molecular interaction format--a community standard for the representation of protein interaction data. – (NBT)14/17
  15. 15. Will I still be allowed to publish? Tool development Rintact: enabling computational analysis of molecular interaction data from the IntAct repository. (Bioinformatics) Ontologies The use of common ontologies and controlled vocabularies to enable data exchange and deposition for complex proteomic experiments (Pac Symp Biocomput) Training Submit your interaction data the IMEx way - a step by step guide to trouble-free deposition (Proteomics)15/17
  16. 16. Curation as a profession16/17
  17. 17. Curation as a profession • Biocuration conference every 12 months – 2102 in Cambridge, UK • Opportunities for further training – bioinformatic tools, programming, career development/management • Attendance at biological/computational biology conferences encouraged – the EBI often provides speakers17/17
  18. 18. Summary • Curation is not for everyone – it does require a certain mindset • Exposes you to all areas of biology (and chemistry) • Now a recognised profession and our numbers are growing • Many opportunities to be become involved in “extra- curriculum” activities – its not all reading papers18/17