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」

Transcript

1. Research Institute for Information and Systems Database Center for Life Science Tazro Ohta <t.ohta@dbcls.rois.ac.jp> 4FNBOUJD
   8FU
   -BC
   1SPKFDU
   JO
   #JP)BDLBUIPO
   
   1VCMJTIJOH
   3FTFBSDI
   1SPUPDPMT 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