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
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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
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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.
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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…..
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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
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10. What do I do?
Controlled vocabulary maintenance
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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’
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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)
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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
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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)
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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)
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16. Curation as a profession
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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
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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 papers
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