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Add representation of compatibility with some PAML actions #28

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rpgoldman opened this issue Apr 7, 2022 · 2 comments
Open

Add representation of compatibility with some PAML actions #28

rpgoldman opened this issue Apr 7, 2022 · 2 comments
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enhancement New feature or request Ontology This item relates to extending the container ontology

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@rpgoldman
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rpgoldman commented Apr 7, 2022

Some questions about requirements:

  • Do we need the ability to represent both necessary and sufficient conditions? Or only one of the two?
  • Do we need negative compatibility? I.e., this container cannot be used in a particular kind of activity (e.g., not the right size for some piece of transfer equipment)?

Please comment with other requirements.

@rpgoldman rpgoldman added enhancement New feature or request Ontology This item relates to extending the container ontology labels Apr 7, 2022
@rpgoldman
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rpgoldman commented Apr 7, 2022

Example from @danbryce:

This container NEST 96 Well Plate Flat is compatible with a primitive of this type TransferByMap if some piece of equipment Opentrons OT2 is used to cherry-pick with a single pipette tip.

I believe that this could be encoded in OWL (translated to English) as:

This container NEST 96 Well Plate Flat is compatible with Class of activities defined as follows:

  • A subclass of uml:CallBehaviorAction
  • It's uml:behavior property has the value paml:TransferByMap
  • Somehow related to the OT2 -- I don't see how this piece of equipment fits into theuml:CallBehaviorAction yet.

@rpgoldman
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rpgoldman commented Apr 8, 2022

A different example, from Jake:

LUDOX example:

  • two provision
  • one empty container
  • 3 select coordinates
  • measure absorbance

Measure absorbance operator takes a sample collection, in this case a sample mask, a boolean mask and a pointer to another sample collection, SC2

SC2 is a sample array, which points to a description of 8 x 12 array of wells.

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Labels
enhancement New feature or request Ontology This item relates to extending the container ontology
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