Semantic Wet Lab Project in BioHackathon - Publishing Research Protocols

Semantic Wet Lab Project in BioHackathon - Publishing Research Protocols

汎用ヒト型ロボット活用研究会ワークショップ 「汎用ヒト型ロボット活用に向けたデータサイエンス」

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Tazro Inutano Ohta

September 05, 2015
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  1. Research Institute for Information and Systems Database Center for Life

    Science Tazro Ohta <t.ohta@dbcls.rois.ac.jp> 4FNBOUJD8FU-BC1SPKFDUJO#JP)BDLBUIPO1VCMJTIJOH3FTFBSDI1SPUPDPMT ൚༻ώτܕϩϘοτ׆༻ݚڀձϫʔΫγϣοϓ ʮ൚༻ώτܕϩϘοτ׆༻ʹ޲͚ͨσʔλαΠΤϯεʯ September 05, 2015
  2. ܦҢ

  3. https://twitter.com/iNut/statuses/5464724109

  4. https://twitter.com/iNut/statuses/2175155823

  5. https://twitter.com/iNut/statuses/5464724109

  6. https://twitter.com/iNut/status/400484536271642625

  7. https://twitter.com/iNut/statuses/12843874913353728

  8. https://www.youtube.com/watch?v=mFUboP4mnN4

  9. https://twitter.com/iNut/statuses/273300528946102272

  10. https://twitter.com/iNut/status/408836006444425216

  11. https://twitter.com/nzmyachie/status/409122793804947456

  12. ͓੠͕͚͍͖ͨͩ͋Γ͕ͱ͏͍͟͝·͢

  13. 1. Semantic Wet Lab Project
 ࣮ݧϓϩτίϧͷػցՄಡͳܗࣜͰͷهड़ - BioHackathon 2014 ʹ͓͚ΔऔΓ૊Έ

    2. Related Topics
 ؔ࿈͢Δ࿩୊ͱ՝୊ 3. The future
 DB͔ΒݟͨࣗಈԽͷະདྷ Agenda
  14. BioHackathon 2014 Working Group: Standardization of RDF data and development

    of tools/ontologies Semantic Wet Lab Project
  15. http://2014.biohackathon.org

  16. https://github.com/dbcls/bh14/wiki

  17. 1. What we’ve done
 ϓϩδΣΫτͷ໨తͱBioHackathon2014Ͱͷ੒Ռ 2. What we haven’t
 ՝୊ͱBioHackathon2015ʹ͓͚Δ໨ඪ

    Semantic Wet Lab Project
  18. Semantic Wet Lab Project • Goal: provide a RDF scheme

    and tool use cases to capture scientific investigations, including: • planning of studies • validation of resources and resource allocation • capture of raw data • insuring data integrity, modelling Plan and Experiments What we’ve done
  19. Users will do; 1. Describe lab specifications for each general

    process model by study plan construction client to generate process model 2. Allocate resources for each process by resource allocation client 3. <execute experiments> 4. Input data to get output Plan and Experiments model
  20. Green: web available (minimum definitions for generic experimental steps,
 generic

    study plans). Blue: lab specifications (additional specifications for experimental steps, SOPs, required
 certifications, … ) Orange: study plan and study itself planned workflow -> signed by study director planned workflow + resources -> signed by facility manager executed workflow + data -> signed by study coordinators -> signed by study director, quality, … (signature using modified trustyURI) RDF Scheme
  21. Semantic Wet Lab Project What we haven’t • Tools and

    Interface for • Data input/Edit • Read/Browse • Querying • Modelling for automation • Abstract request to build a study plan?
  22. Ontologies, Framework, and Initiatives Related Topics

  23. 1. Ontologies 2. Framework 3. Initiatives Related Topics

  24. Related Topics • OBI • http://obi-ontology.org/page/Main_Page • SIO • https://code.google.com/p/semanticscience/

    • EXPO • http://expo.sourceforge.net • EDAM • http://edamontology.org/page • EXACT • http://www.aber.ac.uk/en/cs/research/cb/dss/exact/ Ontologies
  25. http://obi-ontology.org/page/Main_Page

  26. http://www.ontobee.org/browser/rdf.php?o=OBI&iri=http:// purl.obolibrary.org/obo/OBI_0000202 http://www.ontobee.org/browser/rdf.php?o=OBI&iri=http:// purl.obolibrary.org/obo/OBI_0000968

  27. Dumontier, Michel, et al. "The Semanticscience Integrated Ontology (SIO) for

    biomedical research and knowledge discovery." J. Biomedical Semantics 5 (2014): 14.
  28. http://expo.sourceforge.net

  29. http://edamontology.org/page

  30. http://www.aber.ac.uk/en/cs/research/cb/dss/exact/

  31. https://github.com/larisa-soldatova/EXACT/blob/master/EXACT2.pdf

  32. Related Topics • ISA table + model • http://isatab.sourceforge.net/format.html •

    SMART Protocols • http://ceur-ws.org/Vol-1282/lisc2014_submission_2.pdf • Robot Scientist • http://rsif.royalsocietypublishing.org/content/12/104/20141289 • Common Workflow Language • https://github.com/common-workflow-language/common-workflow-language Framework
  33. http://isatab.sourceforge.net/format.html

  34. http://isatab.sourceforge.net/format.html

  35. Giraldo, Olga, Alexander García, and Oscar Corcho. "SMART Protocols: SeMAntic

    RepresenTation for Experimental Protocols." Linked Science: 36.
  36. Williams, Kevin, et al. "Cheaper faster drug development validated by

    the repositioning of drugs against neglected tropical diseases." Journal of The Royal Society Interface 12.104 (2015): 20141289.
  37. Williams, Kevin, et al. "Cheaper faster drug development validated by

    the repositioning of drugs against neglected tropical diseases." Journal of The Royal Society Interface 12.104 (2015): 20141289.
  38. https://github.com/common-workflow-language/common-workflow-language

  39. Related Topics • biosharing.org • https://www.biosharing.org • Reproducibility Initiative, Validation

    by The Science Exchange Network • http://validation.scienceexchange.com/#/ • researchobject.org • http://www.researchobject.org Initiatives
  40. https://www.biosharing.org

  41. https://www.biosharing.org/pages/about/

  42. http://validation.scienceexchange.com/#/reproducibility-initiative

  43. http://validation.scienceexchange.com/#/reproducibility-initiative

  44. http://www.researchobject.org

  45. http://www.researchobject.org/overview/

  46. For the bright one (at least for me) The future

  47. The future Packaging Whole Research Activities • ݚڀϓϩηεʹ͓͚Δશͯͷ࡞ۀΛػցՄಡͳܗࣜͰهड़͢Δ • هड़͞Εͨ΋ͷ͸ͦͷؔ܎ੑΛอͬͨ··σʔλϕʔεʹ֨ೲ͢Δ

    • “Research Package Submission” • ݚڀܭը • αϯϓϦϯάɾ΢Σοτ࣮ݧ • Ұ࣍σʔλ • σʔλॲཧɾσʔλղੳ • ೋ࣍σʔλ • ࿦จ͓Αͼ࿦จͷfig, plot΍tableͳͲͷσʔλ
  48. The future Packaging Whole Research Activities Research Activity Time Course

    Details of 
 Project Design Publication
 Text, Figs Sampling Primary Data Data Processing
 & Analysis Wet Experiments
  49. The future Packaging Whole Research Activities Research Activity Time Course

    Details of 
 Project Design Sampling Primary Data Data Processing
 & Analysis Publication
 Text, Figs Wet Experiments BioProject BioSample Genbank, DRA
  50. The future Packaging Whole Research Activities Research Activity Time Course

    Details of 
 Project Design Sampling Primary Data Data Processing
 & Analysis Publication
 Text, Figs Wet Experiments supercool framework
  51. Details of Project Design Sampling Primary Data Data Processing &

    Analysis Publication Text, Figs Wet Experiments The future Packaging Whole Research Activities supercool framework
  52. Details of Project Design Sampling Primary Data Data Processing &

    Analysis Publication Text, Figs Wet Experiments supercool framework ·΄Ζ Image from: http:// www.aist.go.jp/ Portals/0/ resource_images/ aist_j/aistinfo/ aist_today/vol14_11/ vol14_11_p06.pdf
  53. 1. Introducing semantics (possibly) saves wet labs
 ػցՄಡͳϓϩτίϧ͸࣮ݧΛαϙʔτ͢ΔϙςϯγϟϧΛ͍࣋ͬͯΔ 2. What

    is the benefit?
 هड़ʹඞཁͳࡐྉ͸ἧ͍ͭͭ͋Δ͕ΠϯύΫτΛ·ͩ࢒͍ͤͯͳ͍ 3. DB for Reproducible Research
 σʔλϕʔε͕ݚڀΛ౷߹ࣗ͠ಈԽʹΑͬͯ࠶ݱੑΛ୲อ͢Δ Summary