Successfully reported this slideshow.

Beyond the PDF demo-presentation

0

Share

Loading in …3
×
1 of 8
1 of 8

Beyond the PDF demo-presentation

0

Share

Download to read offline

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

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

More Related Content

Related Audiobooks

Free with a 30 day trial from Scribd

See all

Beyond the PDF demo-presentation

  1. 1. Beyond the PDF 2 Demo and Supporting Material Daniel Garijo Verdejo Ontology Engineering Group. Laboratorio de Inteligencia Artificial Departamento de Inteligencia Artificial Facultad de Informática Universidad Politécnica de Madrid
  2. 2. The TB-Drugome Have 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 cure the 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 Workflow Main Functionality 3
  4. 4. The Reproduced Workflow LINK to execution materials 4
  5. 5. Differences with reproduced results? Connections- Connection- Drug Name Connections solvedStructures Drug Name Connections SolvedStructures Tretinoin 257 46 Alitretinoin 98 14 Levothyroxine 173 36 Levothyroxine 63 14 Methotrexate 156 32 Methotrexate 48 10 4-Hydroxytamoxifen 115 25 Estradiol 38 10 Estradiol 98 20 Rifampin 34 6 Amantadine 79 1 Rifampin 78 13 4-Hydroxytamoxifen 33 10 Raloxifene 75 18 Amantadine 32 0 Propofol 54 5 Indinavir 51 14 Raloxifene 28 10 Penicillamine 44 10 Propofol 24 3 Daunorubicin 44 12 Indinavir 23 2 Triclosan 42 5 Ritonavir 22 7 Darunavir 40 15 Darunavir 22 5 Desoxycorticosterone 39 12 Lopinavir 22 4 Diethylstilbestrol 39 7 Penicillamine 20 5 Amprenavir 38 14 Nelfinavir 20 3 Tadalafil 36 7 Pemetrexed 35 17 Original 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 effort Tasks Time (days) Familiarization with workflow and running software 20 SMAP steps 4 SMAP result sorter steps 1 Merger steps 0.5 Get significant results 0.5 FATCAT URL checker 1 FATCAT step 0.5 Remove significant pairs 0.5 Create clip files 1 Create ideal ligands 1 Ideal ligand checker 1 Autodock Vina 2 Data visualization steps 2 TOTAL 35 days 6
  7. 7. Linked Data Publication Workflow executed with the Wings workflow engine Provenance and specification published according the PROV standard and the Open Provenance Model. All data is published under the Linked Data Principles automatically. The workflow is part of a corpus (LINK) which has been exposed as Linked Data, along with its provenance and specifications. LINK: Querying the LD workflow templates LINK: Exposing workflows as Wikipages automatically 7
  8. 8. Beyond the PDF 2 Demo and Supporting Material Daniel Garijo Verdejo Ontology Engineering Group. Laboratorio de Inteligencia Artificial Departamento de Inteligencia Artificial Facultad de Informática Universidad Politécnica de Madrid

×