Biomaterial call 12 december - minutes

[Melanie Courtot]

Hi all,

We went through the next terms in our core list with Bjoern. Below is
the summary of our actions.
Terms 1 and 2 were done last week (added there for comprehensive
summary), we talked about material entity and molecular entities.


* material entity
* organism
* organization
* chemical entities in solution (mixtures)
* environmental matter
* macroscopic part of organism
* molecular entities
* artifact object
* EOO

1. organism
- Homo sapiens alternative term natural person, alt term human person
is subject to confusion, e.g. as a legal term "This is a common
offshore legal term meaning a living breathing person as opposed to an
unnatural person such as a corporation", thus we chose to have natural
person as alternative term
- organism should include dead ones as well

2. organization
- We added an instance organization Affymetrix to serve as model/
template for other branches. For example the instrument branch needs
to represent manufacturers. Instances will be added in a separate file
- Affymetrix has been added in the Biomaterial branch file just as an
example how we proceed. Role branch will add a manufacturer role
Relation branch: there is a relation is_manufactured_by, do we need
the inverse is_manufacturer_of? do we need a more generic one
is_supplier and then use roles?

3. material entity
definition: currently union of 3 types of BFO objects
new proposed definition: material entity def A
"snap:IndependentContinuant" ("independent_continuant") that is
spatially extended, and its identity of is independent of that of
other entities and can be maintained through time.
ex of usage: collection of random bacteria, a chair, dorsal surface
of the body
(examples chosen to cover the 3 cases)

AI: MC to submit to IAO and update the file

4. molecular entities
- instead of adding our own label and preferred term to get rid of
plural form, we should contact external resource and ask for
modification according to OBO Foundry principles. Adding our own form
is not very efficient, and create double display of labels in protege
if both lang tags are set to "en"

Process of adding new subclasses to molecular entities
case of "huge" resources e.g. melanie has a list of 600 fluorochromes
and bjoern a list of 1000 peptides
Proposal is to store these very specific resources in external files
(Bjoern may not want to get 600 fluorochromes when downloading OBI)
AI for BP: contact chebi to ask if update possible, regarding singular
form of molecular entities and refine definition: molecules should be
connected by bonds

- Protein has been moved under molecular entities (but not protein
complex, because they are two chains)
- Recombinant plasmid modfiied to defined class: recombinant plasmid
is a plasmid which is output of process (different from natural
plasmids)
Note: recombinant plasmid should also get classified under artifact
object because is output of a process which is subclass of
"manufacturing-tye"process - this will happen when PA branch updates
their file
- Synthetic polypeptide: defined class polypeptide output of PA
Restriction has_part amino acides should be added on polypeptide
Polypeptide should be a subclass of peptide
BP: keep peptide and not distiguish with polypeptide -polypeptide is
defined as peptide with more than 10 residues, we don't need the
distinction for us.
PRO:protein should be under peptide
AI: MC remove polypeptide from external
AI: MC: move protein PRO_0000000001 under peptides
We moved peptide construct under material entity, removing restriction
derives from protein, modified definition

Please let us know if you have any comment on the above. Special
thanks to Bjoern who did the Protege edits.

Next call should be next Friday, 19th of December. I will be there,
will anybody else be around?

Thanks,
Melanie

[Bjoern Peters]

Thanks for the notes! I will not be able to join any calls until the
second week of January.

--
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