#812 assay harmonization - processs in assays

[jzheng]

39 out of 175 assays defined what processes take place in an assay.
List of assays with specified outputs (shown in the ‘process’ worksheet):
https://docs.google.com/spreadsheets/d/1wg2Gg2OvnkX84lVeqRO0ie-tSvtEe4Pq0rtnKsveas/edit?usp=sharing

This brings up several questions:
1. Should we add the order of processes in an assay?
There is only one assay, ‘real time reverse-transcription polymerase chain reaction assay’, that specifies chronological order in the logical axiom using the relation immediately preceded by.

1. What are considered as main processes in an assay that we need to specify?
   IEDB specified the detection process in an assay. The assays we are working now have more variations than IEDB ones.
   .
2. What are the start and end points of an assay?
   For example,
   http://purl.obolibrary.org/obo/OBI_0600020 histology
   has part ‘collecting specimen from organism’ in its axiom, which is a ‘specimen collection process.’
   http://purl.obolibrary.org/obo/OBI_0000721 glucose tolerance test
   has part' some ('data transformation' and (has_specified_input some 'measurement datum') and (has_specified_output some graph))

Should 'specimen collection process' and 'data transformation' not be part of assay?

1. Is_a or part_of?
   Sometime an assay has part another assay, is it also a subClass of it?
   For example,
   http://purl.obolibrary.org/obo/OBI_0000716 'ChIP-seq assay'
   has part some 'DNA sequencing' and also a subClassOf 'sequencing assay'. Does it a subClassOf 'DNA sequencing'? ('DNA sequencing' is a subClassOf 'sequencing assay')

http://purl.obolibrary.org/obo/OBI_0001857 RNP (ribonuclear particle) immunoprecipitation high- throughput sequencing assay
has part some 'RNA sequencing'
has part some immunoprecipitation
Should it be a subClassOf 'RNA sequencing' and 'immunoprecipitation assay'?

[bjoernpeters]

Discussed on call 9/19
1) Decided to break up the types of main processes that constitute an assay into material transformations and assays (detection steps) and data transformation (from assay data to the final output).
2) Temporal representation: On the call there was a preference to for now not include a breakdown of the order of steps in the assay, in order to save time. This can be revisited going forward. Also, there might be alternative representations (Kefed modeling via Gully) that can be considered / that migh require more explicit temoporal modeling
3) To determine the start and end of an assay, and thereby the processes that should be included, we should follow the principle that the assay starts with the specified inputs and stops with the generation of the specified outputs that define the assay. Typically assays start with specimens, and should not include sample collection processes. We will have to revisit stepsof sample preparations, to decide if they are part of the assay or not. We should always err on the side of not, to make sure our assay definition is general.

Need to finalize is_a vs. part_of.

[bjoernpeters]

Part_of vs. is_a: Based on the discussion we have had on where an assay starts and where it ends, any sub-class of an assay should have (at least) the same end point. In the example given, A Chip-Seq assay is not over with the generation of DNA sequencing data, and thus is not a subclass of DNA sequencing assay. Rather it has it as a part.

If we want to define grouping terms such as 'sequencing assay', which group assays together by the technology used in terms of 'has_part' a type of process, like we did for immunoprecipitation.