Presentation given at the 2nd DBCLS RDF Summit, discussing Swiss-Prot's RDF representation and why we have one.

1. RDF/SPARQL:
a UniProtKB/Swiss-Prot
practical perspective
Jerven Bolleman
Developer
Swiss-Prot Group

2. Our Goals
• Provide core Bioinformatics resources
– UniProtKB/
–
– …
• Provide services and infrastructure
– Vital-IT : HPC for the life-sciences
– …

3. Genetic Variations and Diseases in
UniProtKB/Swiss-Prot:
The Ins and Outs of Expert Manual Curation
Famiglietti, et al.
We annotate a lot of disease/variants!
http://europepmc.org/abstract/MED/24848695

4. Why provide a public SPARQL endpoint
• A 10 man wet laboratory can not afford:

5. Why provide a public SPARQL endpoint
• A 10 man wet laboratory can not afford:
– to host their own database in house holding
all or even a bit of all life science data.

6. Why provide a public SPARQL endpoint
• A 10 man wet laboratory can not afford:
– to host their own database in house holding
all or even a bit of all life science data.
– not to have access, and use, existing life
science information.

7. ← Not CPU Time...
But Brain Time
↓
The right kind of optimisation

8. Why provide a public SPARQL endpoint
• Classical SQL can be provided on the web
–Is not practical
–No federation
–Poor standards conformance
• Local SQL is expensive
• Local JSON is no better
• Nor is local XML

9. Data Integration Traditional
Pathway.txt
UniProt.txt
Pathway
Parser
UniProt
Parser
Pathway
Schema
UniProt
Schema
Own Lab Data
Data
warehouse
SQL
queries
$
$
$
$
$
$

10. Data Integration RDF/SPARQL
Pathway.rdf
UniProt.rdf
Own Lab Data
Triple Store
SPARQL
Queries
$
$?

11. Why not some other graph database?
Ecosystem
RDF enables sharing and reuse of data at low cost
Identity Precision Standards

12. Why provide a public SPARQL endpoint
• Document centric REST is not enough
–Swiss-Prot available as REST
–(over e-mail !!) since 1986
–expasy.ch since 1993
–www.uniprot.org since 2002
• Most user use a GUI not a CLI
• developers build GUI on a CLI

13. 13
© 2015 SIB

15. 100
10'000
1'000'000
2015-012015-022015-032015-042015-052015-062015-072015-082015-09
queries ask select
construct describe
Queries per month in 2015
peak: 4 million per month

16. Real users
Mix between hard analytics and super specific
Estimate somewhere between:
400 - 1200 real humans per month
We know they are real because they take
holidays ;)

17. Questions?

18. 18
© 2015 SIB
help@uniprot.org