Life as a scientific database curator

Transcription

1 Life as a scientific database curator Sandra Orchard EBI is an Outstation of the European Molecular Biology Laboratory.

2 What is a database curator Curator OED - a keeper of a museum or other collection - from LATIN curare take care of 2/17

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 literature 3/17

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 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 What does a database curator do? Collects, annotates, and validates information (in a database). Extracts & organizes data from literature Describes data using standards, protocols and vocabularies (enabling computational queries and data exchange). Communicates with researchers to ensure the accuracy of curated information and to foster good practice in data exchange.

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 What do I do? Curate the molecular interaction database 8/17

9 What do I do? Custom curation tools designed by the curation team 9/17

10 What do I do? Controlled vocabulary maintenance 10/17

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 onthe-job 11/17

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 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 publishing 13/17

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 PSI's molecular interaction format--a community standard for the representation of protein interaction data. (NBT) 14/17

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 16/17 Curation as a profession

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 speakers 17/17

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 extracurriculum activities its not all reading papers 18/17