[Obi-protocol-application-branch] Notes from today

[Bjoern Peters]

We worked on the 'adminstering substance' and children terms, resulting
in the following (some of it done by myself after the call, but
hopefully in the spirit of what was discussed):

- As 'administering' seems to be commonly associated only with
organisms, it will only be used for 'administering in vivo'. The more
general class will be called 'adding material entity into target'. It
will encompass any process in which one material is added into another
one. This includes processes like 'injecting label into organ section',
or 'adding nutrient to cell culture', or 'adding drug into buffer'.
- the corresponding roles for the 'added material' and 'target material'
will be updated by Jennifer.
- metadata for the terms was increased (examples, missing definitions,
editor notes), and definitions updated

In the process, I further cleaned up the file to move all defined
classes under '_defined protocol applications', and removed additional
asserted classes. The one term I could not do that is 'objective driven
process', where the asserted 'process' class seems to have been added in
a different file. Melanie, could you find out where?

- Bjoern

--
Bjoern Peters
Assistant Member
La Jolla Institute for Allergy and Immunology
9420 Athena Circle
La Jolla, CA 92037, USA
Tel: 858/752-6914
Fax: 858/752-6987
http://www.liai.org/pages/faculty-peters

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[Melanie Courtot]

That restriction is in the Role.owl file http://obi.svn.sourceforge.net/viewvc/obi/trunk/src/ontology/branches/Role.owl?revision=1353&view=markup
, at the end (very last lines)
I know that Jennifer is currently editing the Role file so I don't
want to create conflict.

Jennifer - if you can send me an email when you are done editing for
today, I'll make the following modifications:

<rdf:Description rdf:about="http://purl.obofoundry.org/obo/OBI_0000094
">
<IAO_0000115 xml:lang="en">a material_application is
protocol_application which has the objective to
produce output material(s) from input material(s)</IAO_0000115>
</rdf:Description>
=> extra definition for artifact material creation: I will remove it

<rdf:Description rdf:about="http://purl.obofoundry.org/obo/OBI_0200000
">
<IAO_0000115 xml:lang="en">a protocol application which has the
objective to produce output data from input data</IAO_0000115>
</rdf:Description>
=> extra definition for data transformation: I will remove it

<rdf:Description rdf:about="http://purl.obofoundry.org/obo/OBI_0000011
">
<rdfs:subClassOf rdf:resource="http://www.ifomis.org/bfo/1.1/span#Process
"/>
</rdf:Description>
=> assertion of ODP under Process: I will remove it

Bjoern, can you confirm the above changes are ok?

Thanks,
Melanie

---
Mélanie Courtot
TFL- BCCRC
675 West 10th Avenue
Vancouver, BC
V5Z 1L3, Canada