Workshop Data transformation 2007 Nov

Data Transformation Workshop, 5 November, 2007

EMERALD sponsored meeting discussing the data transformation branch of OBI.

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Workshop delegates

Present:

TB Tina Boussard, Stanford

CC Christian Cocos, U. Saarland

MC Melanie Courtot, BCCRC

JM James Malone, EBI

EM Elisabetta Manduchi, UPenn

MM Monnie McGee, Southern Methodist University (SMU, Dallas)

HP Helen Parkinson, EBI

RiS Richard Scheuerman, Texas Southwestern.

DS Daniel Schober, EBI

RoS Robert Stevens,, U Manchester

More abbreviations:

AI Action Item

Links to meeting notes and action items

Summary of Meeting Action Items

Monday 5 November Notes

Tuesday 6 November Notes

Wednesday 7 November Notes

Thursday 8 November Notes

Friday 9 November Notes

Files from workshop and from action items

• Files with terms submitted by communities:
  • Term list submitted to data transformation. This file was reviewed during the workshop and to-dos are now reflected under the workshop action items.
  • Term list submitted and needing review to decide if fit in data transformation branch. This file was discussed during the branch conference calls on September 6 and 13, 2007. Summary of decisions and action items is now in Media:DTvsNonDT.xls.

• Files from TB action items: Media:Defi_TB.doc Media:Defi_and_hierarchy_tb.xls
• Files from RB action items:
• Files from CC action items:
• Files from MC action items:
• Files from JM action items: See subversion OWL file
• Files from EM action items:
  • Action item 1: file with a summary of decisions and consequent action items for the community-submitted terms discussed at conference calls on Sep 6 and 13, 2007: Media:DTvsNonDT.xls.
  • Action items 3, 4, and first half of 5: Media:EM_InsertTerms1new2.xls, DONE JM Media:EM_UpdateDeleteTerms1new.xls DONE JM , Media:EM_Relationships1.xls.
  • Action item 14: Media:EM_UpdateDeleteTerms2.xls DONE JM.
  • Action items 6, 20, and second half of 5: Media:EM_InsertTerms2.xls DONE JM, Media:EM_UpdateDeleteTerms3.xls DONE JM
  • Action item 17: Media:EM_MO2OBI_1.xls
  • Action items 12 and 13: Media:EM_UpdateDeleteTerms4.xls
  • Action item 8: Media:EM_UpdateDeleteTerms5.xls
  • Action item 16: Media:EM_InsertTerms3.xls
• Files from MM action items:: 3, 4, 8, 9 and some of 10 Media:CompletedAI-MM.doc
• Files from HP action items:
• Files from RiS action items: 3, 4 media:RHS_DT_network_analysis_terms.xls

Emerging Design Principles

Qualities describe inherent properties/characteristics in independent continuants, whereas roles are temporary properties that can vary with time.

Avoiding multiple parentage using roles, e.g. descriptive statistics flat list with roles to classify them (moment_calculation, spread_calculation, etc.), and same for normalization and averaging.

Using qualities such as parametric and non parametric tests on classes to infer this hierarchy.

Making general definitions with application specific names and examples, e.g. global_loess_two_channel not global_loess_microarray.

Many of the data transformation terms describe processes that are application specific. We have tried to identify the generic equivalent of the application specific term, to use this term as an upper level node in the hierarchy and them allow the use of the application-specific term as a child/sub-class. This allow the re-use of the generic term in other applications while supporting dataset annotation using the application-specific terms.

Policy related to parallel universes of plan and application of plan. If we create classes in only one of these, do it in plan, not application, as we have qualities that need to inhere in something. According to BFO they inhere in independent continuant, i.e. plan.

Thanks to EMERALD Coordination Action from the EC for workshop funding