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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



                                                     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:                                                                   4
http://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  – Out of date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 ways
aptamer.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 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
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
Acknowledgements
Supervisors:
Dr. Michel Dumontier and Dr. Maria DeRosa
Collaborators:
Maureen Mckeague, Xueru Zhang, Amanda
Giamberardino, Erin McConnell, Tariq Francis,
Matthew Chan



                                                16
Questions?




             17

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José Cruz Toledo - Aptamer basebc2012

  • 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
  • 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