Semantic Wet Lab: Publishing Protocols and Workflow

Semantic Wet Lab: Publishing Protocols and Workflow

BioHackathon2015 #biohack15

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Tazro Inutano Ohta

September 13, 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-BC1VCMJTIJOH1SPUPDPMTBOE8PSLGMPX BioHackathon2015 September 13, 2015
  2. https://github.com/dbcls/bh14/wiki

  3. 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
  4. 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
  5. 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
  6. Semantic Wet Lab Project What we haven’t and this time

    • Tools and Interface for… • Data input/Edit • Read/Browse • Querying • Ideas of modelling for automation • Abstract request to build a study plan? • Order “Get the DEG list from sample A/B” to design a flow of experiments
  7. Semantic Wet Lab Project Possible Collaboration and related projects •

    Other ontologies and framework for biological experiments • SMART Protocol • Data Processing Workflow • Common Workflow Language • Bionode / dat • Data sharing initiatives • researchobject.org
  8. 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
  9. 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 CWL
  10. 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 CWL
  11. Details of Project Design Sampling Primary Data Data Processing &

    Analysis Publication Text, Figs Wet Experiments The future Packaging Whole Research Activities supercool framework CWL
  12. 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 CWL