josé cruz toledo - aptamer basebc2012
Post on 19-Oct-2014
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DESCRIPTION
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.TRANSCRIPT
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Aptamer Base: A collaborative knowledgebase to describe aptamers and
SELEX experiments
Biocuration 2012 Tuesday April 3rd
Jose Cruz-Toledo
PhD candidate, Carleton University, Canada
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What are aptamers?
• In vitro selected short nucleic acid polymers that bind with high specificity and affinity to a variety of targets
– Small molecules, organic dyes, toxins, proteins and whole cells
– Binding affinities in the micro-nano molar range
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PDBID: 1RAW
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Aptamers offer several advantages over antibodies
• Entirely generated in vitro
• Can be selected to bind to specific targets
• Relatively low production cost
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Aptamers are created using Systematic Evolution of Ligands by Exponential
Enrichment (SELEX)
4 Image source: http://bio349.biota.utoronto.ca/20069/bio349jerry1/images/background_fig2.jpg
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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– Out of date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
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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
6 http://www.freebase.com
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The Aptamer Base is a hub for aptamer knowledge, built on Freebase
• A collection of experimental details about SELEX based experiments
• Over 5700 topics about experimental details of ~250 SELEX experiments
• Details for over 1200 aptamers including sequences, dissociation constants and secondary structure predictions
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Type # Instances
Experimental outcome 1903
Linear polymer 1629
Interactor 1582
Nucleic acid 1549
Aptamer 1239
Interaction 1068
RNA 1006
Dissociation constant 896
Pairwise interaction 889
Experiment 641
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The Aptamer Base facilitates collaborative data contribution and sharing
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SELEX experimental details
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Aptamer & target details
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Aptamer Base data can be accessed in several ways
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aptamer.freebase.com
freebase.com/labs/parallax/
aptamerbase.semanticscience.org
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MQL allows powerful querying over the Aptamer Base
How many SELEX experiments are described in the Aptamer Base?
[{
"type": "/base/aptamer/selex_experiment",
"return": "count"
}]
Provide a list of all interactions that have as participants RNA aptamers
[{
"id": null,
"type": "/base/aptamer/interaction",
"has_participant": [{
"id": null,
"a:type": "/base/aptamer/aptamer",
"b:type": "/base/aptamer/rna"
}]
}]
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Find all affinity experiments that dispute interactions that have as participant “Sulforhodamine b”
[{
"mid": null,
"type": "/base/aptamer/affinity_experiment",
"disputes": [{
"type": "/base/aptamer/interaction",
"has_participant": [{
"type": "/base/aptamer/molecule",
"name": "Sulforhodamine b"
}]
}]
}]
Find all dissociation constants that have a value that is less than 1E-6 for interactions involving either L-Arginine or Thrombin [{
"mid": null,
"type": "/base/aptamer/dissociation_constant",
"has_value<": 0.000001,
"/base/aptamer/dissociation_constant/is_dissociation_constant_of": [{
"/base/aptamer/interaction/has_participant": [{
"mid": null,
"type": "/base/aptamer/aptamer_target",
"name|=": [
"L-Arginine",
"Thrombin"
]
}]
}]
}]
Results: http://tinyurl.com/d3ox66m
Results: http://tinyurl.com/cckdax7
Results: http://tinyurl.com/bmcyfdw
Results: http://tinyurl.com/c8ystcg
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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
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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
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Acknowledgements
Supervisors:
Dr. Michel Dumontier and Dr. Maria DeRosa
Collaborators:
Maureen Mckeague, Xueru Zhang, Amanda Giamberardino, Erin McConnell, Tariq Francis, Matthew Chan
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Questions?
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