Biomaterial call 13th february - agenda

[Melanie Courtot]

Hi all,

For our call tomorrow I propose to review the branch following the OBI
workshop.
The presentation is available in our newly created Biomaterial
directory: http://obi.svn.sourceforge.net/viewvc/obi/trunk/docs/developer/Biomaterial/

Talk to you then :)

Melanie

[Philippe Rocca-Serra]

Hi Everyone,
Following our call last friday I have made the following changes
(changelog from the commit)

still some work to do on entity of organismal origin and work with
protocol application to reach resolution.

Cheers

Philippe

Changelog:

- material entity:
editor note added to mark the submission to BFO -> term to be imported.

- molecular entities:
AI for BP: log a request to CHEBI to use singular 'molecular entity' ->
term to be imported.

-chemical entities in solution/mixture:
AI for Alan to implement

- anatomical entity (formerly macroscopic part of multicellular organism):
now a defined class: union of (multi-tissue structure, body substance,
portion of tissue_

Label changed to anatomical entity as it was felt that 'macroscopic part
of multicellular organism' introduce an impractical delineation.

editor note added: OBI 'anatomical entity' would essentially correspond
to FMA 'material anatomical entity' rather than FMA 'physical anatomical
entity'. OBI does not include 'immaterial anatomical entity' as it would
clash with the parent class 'material entity'
There is also a documentation note:
DOCUMENTATION NOTE: OBI anatomical entity granularity level excludes
cell and biological molecules.


- environmental matter:
left in place but branch core tag removed.

- entity of organismal origin
label changed to extracted entity of organismal origin during the call.
However I have the following questions:
entity of organismal origin:
Current definition= An entity of organismal origin is a biomaterial
entity which is obtained from an organism.

alter definition to include the following:
An entity of organismal origin is a biomaterial entity which is obtained
from an organism through a protocol application, a collection process

(this would be in agreement with slide 14 (8.EEOO) presented in
'2009-02-BiomaterialCoreTerms-Vancouver.ppt')

Comment #1: Extracted seems to imply that a fraction/portion is
collected from an organism
If we were to use 'derived entity of organismal origin', we might be
able to cover bioengineered organism, should we wish to do. (e.g. we
currently have transgenic organism asserted under EOO.the same entity
asserted under extracted entity of organism origin would be odd).
Comment #2: Necessary and Sufficient conditions may need to be altered
to reflect the changes.

-Organization:
stays where it is for now but feels odd to have it under material entity.
proposition to move if to BFO: possibly as a defined class.
The current editor notes capture the issues very well.