analyte

[obi-bot]

We decided to add a term "analyte" to OBI with definition "The role of a biochemical integral to a biomaterial in a
protocol application with the plan to assay the biomaterials presence
or absence, either relative or absolute."

With comments from the obi-dev list: The "Analyte" definition Bjoern's provides feels very satisfying.
Then a "Hypothesis" can stand by itself regardless of whether it is
actually tested in an "Investigation". A "Hypothesis" that does get
explicitly tested in an "Investigation" would require a corresponding
"Plan" specifically designed to test its assertion about reality
which is executed in a "Protocol application" associated with that
"Investigation". These pieces seem to fit together nicely.

The point in regards to this thread today is, so long as a plan can
stand independent of a hypothesis, then a material can stand
independent of a hypothesis, since it only requires it be defined in
the context of an assay run according to a plan. "

Reported by: mcourtot

Original Ticket: "obi/obi-terms/6":https://sourceforge.net/p/obi/obi-terms/6

[obi-bot]

• assigned_to: nobody --> daniel_schober

Original comment by: alanruttenberg

[obi-bot]

• assigned_to: daniel_schober --> bjoernpeters

Original comment by: alanruttenberg

[obi-bot]

Logged In: YES user_id=1163317 Originator: NO

The remaining issue is to deal with assays in which no analyte is detected. Those are problematic with the definition of role, as there is no bearer for the role. One workshop take on this was to move analyte into the 'objective / specification' realm, i.e. say that the objective of the protocol realized is to detect presence or absence of the analyte. Another is to have the class bear the role. Both approaches are being attempted now.

Original comment by: bpeters42

[obi-bot]

• labels: --> new term

Original comment by: mcourtot

[obi-bot]

I would suggest that an analyte is defined by the following:

An analte is a material entity that has been assayed. That is, a measurement of the properties or characteristic of the material entity which occurred via an assay process. An analyte bears the role analyte_role.

An analyte_role is a role borne by a material entity that is realised in an assay where the measurement of the properties or characteristics has occurred to produce information about that material entity

Original comment by: fgibson_sf

[obi-bot]

• milestone: --> plan-and-planned-process

Original comment by: fgibson_sf

[obi-bot]

Frank: your definition of analyte_role is what we have labeled as 'evaluant_role'. The distinction should be clear from what is now in the OBI files; let me know if not. I am closing this ticket; it was just remaining open to signal that we still need to deal with non-detected analytes. I will create a separate ticket for that.

Original comment by: bpeters42

[obi-bot]

• status: open --> closed

Original comment by: bpeters42