Aptamer Base: A collaborative knowledge base to describe aptamers and SELEX experiments, by Cruz-Toledo, Jose; McKeague, Maureen; Zhang, Xueru; Giamberardino, Amanda; McConnell, Erin; Francis, Tariq; DeRosa, Maria; Dumontier, Michel. Presented at the 5th International Biocuration Conference, hosted by PIR in Washington, DC, April 2-4, 2012.

1. Aptamer Base: A collaborative
knowledgebase to describe aptamers and
SELEX experiments
Biocuration 2012
Tuesday April 3rd
Jose Cruz-Toledo
PhD candidate, Carleton University, Canada
1

2. What are aptamers?
• In vitro selected short
nucleic acid polymers
that bind with high
specificity and affinity to
a variety of targets PDBID: 1RAW
– Small molecules, organic
dyes, toxins, proteins
and whole cells
– Binding affinities in the
micro-nano molar range
2

3. Aptamers offer several advantages
over antibodies
• Entirely generated in vitro
• Can be selected to bind to specific targets
• Relatively low production cost
3

4. Aptamers are created using Systematic
Evolution of Ligands by Exponential
Enrichment (SELEX)
Image source: 4
http://bio349.biota.utoronto.ca/20069/bio349jerry1/images/background_fig2.jpg

5. Most of our knowledge about aptamers is still
found only in scientific publications
• There are only a few existing aptamer
databases
– Out of date
– Cannot be updated by users
– Data is not available for download
– Data cannot be queried directly
5

6. Freebase is a community created
knowledge base
• Data in Freebase is
stored as a structured
graph containing over
22 million topics
• Metaweb Query
Language (MQL) is
used for querying
• Topics are organized
into bases
http://www.freebase.com 6

7. The Aptamer Base is a hub for aptamer
knowledge, built on Freebase
• A collection of experimental Type # Instances
details about SELEX based Experimental outcome 1903
experiments
Linear polymer 1629
• Over 5700 topics about Interactor 1582
experimental details of ~250 Nucleic acid 1549
SELEX experiments Aptamer 1239
• Details for over 1200 Interaction 1068
aptamers including RNA 1006
sequences, dissociation Dissociation constant 896
constants and secondary Pairwise interaction 889
structure predictions Experiment 641
7

8. The Aptamer Base facilitates collaborative
data contribution and sharing
8

9. 9

10. SELEX experimental details
10

11. Aptamer & target details
11

12. Aptamer Base data can be accessed in
several ways
aptamer.freebase.com
freebase.com/labs/parallax/
aptamerbase.semanticscience.org 12

13. MQL allows powerful querying over
the Aptamer Base Find all affinity experiments that dispute interactions that have as participant
How many SELEX experiments are described “Sulforhodamine b”
in the Aptamer Base? [{
[{ "mid": null,
"type": "/base/aptamer/selex_experiment", "type": "/base/aptamer/affinity_experiment",
"disputes": [{
"return": "count" "type": "/base/aptamer/interaction",
}]​ "has_participant": [{
Results: http://tinyurl.com/d3ox66m "type": "/base/aptamer/molecule",
"name": "Sulforhodamine b"
Provide a list of all interactions that have as
}]
participants RNA aptamers
}]
[{ }]​
Results: http://tinyurl.com/bmcyfdw
"id": null,
"type": "/base/aptamer/interaction", Find all dissociation constants that have a value that is less than 1E-6 for
interactions involving either L-Arginine or Thrombin
"has_participant": [{ [{
"mid": null,
"id": null, "type": "/base/aptamer/dissociation_constant",
"has_value<": 0.000001,
"a:type": "/base/aptamer/aptamer", "/base/aptamer/dissociation_constant/is_dissociation_constant_of": [{
"b:type": "/base/aptamer/rna" "/base/aptamer/interaction/has_participant": [{
"mid": null,
}] "type": "/base/aptamer/aptamer_target",
"name|=": [
}]​ "L-Arginine",
"Thrombin"
Results: http://tinyurl.com/cckdax7 ]
}]
}] Results: http://tinyurl.com/c8ystcg
}]​
13

14. The Aptamer Base is not just another
Aptamer Database
• The Aptamer Base is the only collaborative
aptamer resource on the web
• Users are not limited to an HTML form for
accessing data
– TSV :
http://download.freebase.com/datadumps/latest/browse/base/aptamer/
– RDF:
http://rdf.freebase.com/rdf/[TOPIC_ID]
– Powerful query language:
http://wiki.freebase.com/wiki/MQL
• The aptamer Base extends over ~2700 pre-
existing topics on Freebase
14

15. Future Work
• Implement a topic entry interface at
http://aptamerbase.semanticscience.org
• Add SELEX based aptamer journal articles
published between 2010 and 2012
• Integrate data with the Bio2RDF network
15

16. Acknowledgements
Supervisors:
Dr. Michel Dumontier and Dr. Maria DeRosa
Collaborators:
Maureen Mckeague, Xueru Zhang, Amanda
Giamberardino, Erin McConnell, Tariq Francis,
Matthew Chan
16

17. Questions?
17