#745 coordinate assays and observing processes with BCO

[Ramona Walls]

“Observation” has a lot of different meanings, even within the bio-semantics world. In BCO, we have been using the term observing process (http://purl.obolibrary.org/obo/bco_0000003), as distinct from a specimen collection process. We agreed that bco:observing process should be a planned process with a data item as output. The input of an observing process is bco:material target of observation, which is similar to obi:material entity has role obi:evaluant role.

However, we were not certain that bco:observing process is necessarily equivalent to obi:assay. We would like to have a better understanding of the inputs of an assay, of RO's notions of direct and indirect input, and some other issues.

I will be posting more comments here we work on our understanding, and we hope to set up a joint BCO/OBI call sometime in the near future.

[Ramona Walls]

Note that bco:observing process already has subclasses for human observing process and machine observing process, and we need to coordinate those with OBI as well.

[Alan Ruttenberg]

FYI, the BCO purl is broken

It sounds to me that observing process is clearly an assay. Whether it is
equivalent or a subclass depends on the precise definition. Similarly
bco:material
target of observation sounds to me to be in a similar relation with
evaluant role. For example, an example of usage attached to Assay is: "Count
of geese flying over a house.".

On Fri, Mar 20, 2015 at 2:12 PM, Ramona Walls rwalls@users.sf.net wrote:

Note that bco:observing process already has subclasses for human observing
process and machine observing process, and we need to coordinate those with
OBI as well.

---

• [obi-terms:#745] http://sourceforge.net/p/obi/obi-terms/745 coordinate
  assays and observing processes with BCO*

Status: open
Group: plan-and-planned-process
Created: Fri Mar 20, 2015 06:11 PM UTC by Ramona Walls
Last Updated: Fri Mar 20, 2015 06:11 PM UTC
Owner: nobody

“Observation” has a lot of different meanings, even within the
bio-semantics world. In BCO, we have been using the term observing process (
http://purl.obolibrary.org/obo/bco_0000003), as distinct from a specimen
collection process. We agreed that bco:observing process should be a
planned process with a data item as output. The input of an observing
process is bco:material target of observation, which is similar to
obi:material entity has role obi:evaluant role.

However, we were not certain that bco:observing process is necessarily
equivalent to obi:assay. We would like to have a better understanding of
the inputs of an assay, of RO's notions of direct and indirect input, and
some other issues.

I will be posting more comments here we work on our understanding, and we
hope to set up a joint BCO/OBI call sometime in the near future.

---

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[Ramona Walls]

This was discussed at the OBI call on June 6, 2016. The decision was to keep observing process in BCO, make it a subclass of of OBI:assay. Define as per use cases in BCO (where the assay does not sample or physically change the evaluant - i.e. no material processing involved). See also meeting minutes at https://docs.google.com/document/d/1ccc_bYb3EVjVzC6wRxhjleAkQqYCHsO1z4P0Q_UVBgY/edit# and wiki page: http://obi-ontology.org/page/Observational_assays.

[Ramona Walls]

It appears that I don't have the power to close issue in this tracker. Will someone else please close?

[jzheng]

issue solved on OBI dev call 2016-06-06