Identify requirements for well layout

[rpgoldman]

What information would a system using PAML -- say a planner or a workflow builder -- need about a multi-well plate?

Without knowing what information is needed, it's hard for me to know what should go into the container ontology.

/cc @jakebeal

[jakebeal]

Based on what I've been putting together so far, things that we definitely need to be able to work with are:

• Well array dimensions and coordinates. For example all 96-well plates are 8x12 with a coordinate system that goes rows A-H and columns 1-12. Coordinates are specified with a row-column swapped Excel notation, e.g., A1:D2 is 4 rows x 2 columns.
• Well depth
• Well volume

Footprint dimensions are abstracted by saying it's a standard 96-well plate. That's likely to hold for other things besides plates as well, though I don't know the standards for them.

[rpgoldman]

@jakebeal I can get you the well dimensions in the form of the properties wellCount rowCount and columnCount. But... as I read ANSI SLAS-4, it does not prescribe the coordinate system, and it's not obvious to me where I would find that information in a catalog.

So I am inclined to think that the three properties above a good enough for now, until we can find a way to identify columnLabels and rowLabels.

I will add those two properties to the ontology, but would like to know what is the right type of their value. Specifically, each should be an owl:FunctionalProperty whose value is a sequence, but represented how? rdf:Seq some more specialized OWL thing (cf. http://ceur-ws.org/Vol-216/submission_12.pdf)? Is there a standard pattern you have used in SBOL?

[jakebeal]

We don't have a standard pattern for sequence representation yet.