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José Cruz  Toledo - Aptamer basebc2012
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José Cruz Toledo - Aptamer basebc2012

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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; ...

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.

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    José Cruz  Toledo - Aptamer basebc2012 José Cruz Toledo - Aptamer basebc2012 Presentation Transcript

    • Aptamer Base: A collaborativeknowledgebase to describe aptamers and SELEX experiments Biocuration 2012 Tuesday April 3rd Jose Cruz-Toledo PhD candidate, Carleton University, Canada 1
    • 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
    • Aptamers offer several advantages over antibodies• Entirely generated in vitro• Can be selected to bind to specific targets• Relatively low production cost 3
    • Aptamers are created using Systematic Evolution of Ligands by Exponential Enrichment (SELEX)Image source: 4http://bio349.biota.utoronto.ca/20069/bio349jerry1/images/background_fig2.jpg
    • 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about aptamers is still found only in scientific publications• There are only a few existing aptamer databases – Out of date – Cannot be updated by users – Data is not available for download – Data cannot be queried directly 5
    • 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
    • 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
    • The Aptamer Base facilitates collaborative data contribution and sharing 8
    • 9
    • SELEX experimental details 10
    • Aptamer & target details 11
    • Aptamer Base data can be accessed in several waysaptamer.freebase.com freebase.com/labs/parallax/ aptamerbase.semanticscience.org 12
    • MQL allows powerful querying over the Aptamer Base Find all affinity experiments that dispute interactions that have as participantHow 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
    • 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
    • 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
    • AcknowledgementsSupervisors:Dr. Michel Dumontier and Dr. Maria DeRosaCollaborators:Maureen Mckeague, Xueru Zhang, AmandaGiamberardino, Erin McConnell, Tariq Francis,Matthew Chan 16
    • Questions? 17