Beyond the PDF 2        Demo and Supporting             Material                        Daniel Garijo VerdejoOntology Engi...
The TB-DrugomeHave you ever heard about the TB-Drugome?http://funsite.sdsc.edu/drugome/TB/•Workflow presented on the previ...
The Original WorkflowMain Functionality                         3
The Reproduced WorkflowLINK to execution materials                                4
Differences with reproduced results?                                        Connections-                                  ...
Measuring the reproducibility effortTasks                                                       Time (days)Familiarization...
Linked Data PublicationWorkflow executed with the Wings workflow engineProvenance and specification published according th...
Beyond the PDF 2        Demo and Supporting             Material                        Daniel Garijo VerdejoOntology Engi...
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Beyond the PDF demo-presentation

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How difficult is to reproduce an experiment, even when the input results and the outputs are available online? In this work we quantify it.

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Beyond the PDF demo-presentation

  1. 1. Beyond the PDF 2 Demo and Supporting Material Daniel Garijo VerdejoOntology Engineering Group. Laboratorio de Inteligencia Artificial Departamento de Inteligencia Artificial Facultad de Informática Universidad Politécnica de Madrid
  2. 2. The TB-DrugomeHave you ever heard about the TB-Drugome?http://funsite.sdsc.edu/drugome/TB/•Workflow presented on the previous Beyond the PDF Workshop•Constructed to detect whether any approved drug could be a candidate to curethe TB.•All materials used for the experiment are presented in the website.•Can it be reproduced?? How much would it cost?? 2
  3. 3. The Original WorkflowMain Functionality 3
  4. 4. The Reproduced WorkflowLINK to execution materials 4
  5. 5. Differences with reproduced results? Connections- Connection-Drug Name Connections solvedStructures Drug Name Connections SolvedStructures Tretinoin 257 46Alitretinoin 98 14 Levothyroxine 173 36Levothyroxine 63 14 Methotrexate 156 32Methotrexate 48 10 4-Hydroxytamoxifen 115 25Estradiol 38 10 Estradiol 98 20Rifampin 34 6 Amantadine 79 1 Rifampin 78 134-Hydroxytamoxifen 33 10 Raloxifene 75 18Amantadine 32 0 Propofol 54 5 Indinavir 51 14Raloxifene 28 10 Penicillamine 44 10Propofol 24 3 Daunorubicin 44 12Indinavir 23 2 Triclosan 42 5Ritonavir 22 7 Darunavir 40 15Darunavir 22 5 Desoxycorticosterone 39 12Lopinavir 22 4 Diethylstilbestrol 39 7Penicillamine 20 5 Amprenavir 38 14Nelfinavir 20 3 Tadalafil 36 7 Pemetrexed 35 17Original Lopinavir 35 10 Saquinavir 34 13 Indomethacin 34 8 Bepridil 33 14 Testosterone 32 14 2 Bexarotene 32 10 Reproduced Imatinib 32 12 Ritonavir 32 10
  6. 6. Measuring the reproducibility effortTasks Time (days)Familiarization with workflow and running software 20SMAP steps 4SMAP result sorter steps 1Merger steps 0.5Get significant results 0.5FATCAT URL checker 1FATCAT step 0.5Remove significant pairs 0.5Create clip files 1Create ideal ligands 1Ideal ligand checker 1Autodock Vina 2Data visualization steps 2 TOTAL 35 days 6
  7. 7. Linked Data PublicationWorkflow executed with the Wings workflow engineProvenance and specification published according the PROV standard and theOpen Provenance Model. All data is published under the Linked Data Principlesautomatically.The workflow is part of a corpus (LINK) which has been exposed as LinkedData, along with its provenance and specifications. LINK: Querying the LD workflow templatesLINK: Exposing workflows as Wikipages automatically 7
  8. 8. Beyond the PDF 2 Demo and Supporting Material Daniel Garijo VerdejoOntology Engineering Group. Laboratorio de Inteligencia Artificial Departamento de Inteligencia Artificial Facultad de Informática Universidad Politécnica de Madrid

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