Biomaterial call 20th March - agenda

[Melanie Courtot]

Hi all,

A reminder for tomorrow's call, at 11h30 EST. (I think that means one
hour earlier than usual for GMT people as they didn't change time yet)
The call will be on centra, and will focus on the EOO/specimen/sample/
x issue.

We have been discussing for a while the terms sample/specimen, and
different communities/persons seem to have different views on what it
covers or not.

Instead of trying to address the higher level class (which causes
trouble as there is always one special case), the proposal is to try
and address a lower level specific use case "material derived from
organism and which is intended to be used in an experiment where it is
representative of the organism/population it originates from".

We will start with this one and try to work our way up.

Talk to you all tomorrow :)
Melanie

[jie zheng]

Hi all,

I left early on last Friday's phone call. I'd like to know whether it
came to any conclusion about EOO/specimen/sample/derives_ from issues.

Can anyone provide the notes of Friday's call? Thanks a lot.

Jie

[Melanie Courtot]

Hi all,

Apologies for the delay in notes - I did take a long week end off :)

You'll find a summary of the discussion below. Just send an email to
the list if you wish to amend anything.

We had some editing issues during the call and consequently - we know
where the trouble is coming from, and will sort out things.

Thanks all for helping out, discussion will resume next week, same
time (11.30 EST), same place (centra).

Melanie





Attending: Jie, Jennifer, Oliver, Alan, Bjoern, James, Melanie

1. start with lower case
"material coming from organism used in study as representative"

issues: derived_from, organism/population, representative role/
quality, link to experiment using is proxy?

[some protege editing issues]


Note: for this call we should try not to use the word specimen or sample
These 2 words have proven problematic, as they mean different things
for different communities. Instead of starting with the label and
trying to write the textual definition, we'll start with simple use
case, and then we'll move forward to assigning label/finding upper
classes.
Plan of action: (not focusing on labels)
We will place tissue sample under material entity, add restrictions
We will place urine sample, blood sample similarly
Then try and see how to organize depending on how things classify


Relation derives_from

derives means some part of new thing was part of old thing

current definition: Derivation as a relation between instances. The
temporal relation of derivation is more complex. Transformation, on
the instance level, is just the relation of identity: each adult is
identical to some child existing at some earlier time. Derivation on
the instance-level is a relation holding between non-identicals. More
precisely, it holds between distinct material continuants when one
succeeds the other across a temporal divide in such a way that at
least a biologically significant portion of the matter of the earlier
continuant is inherited by the later. Thus we will have axioms to the
effect that from c derives_from c1 we can infer that c and c1 are not
identical and that there is some instant of time t such that c1 exists
only prior to and c only subsequent to t. We will also be able to
infer that the spatial region occupied by c as it begins to exist at t
overlaps with the spatial region occupied by c1 as it ceases to exist
in the same instant.

example: blood sample
- accident spiling blood - not a blood sample
- use process output (specified output of extracting part of organism)



issue with derived_from: it would be a mistake if the old thing was
lost (example: when we take a blood sample and say blood sample
derives from blood, we also want to say that the thing it is derived
from, i.e. the blood, doesn't disappear in the process)

Specified input would be organism and part of organism
We want a word describing entity part of organsim (e.g. blood) from
which we will take the sample (blood sample) and the relation
derives_from doesn't fit that case

example: taking_part_of_organism has_specified_input liver that part
of mouse

Note: here there was some discussion about organism/ part of organism/
excretia. We consider the simple use case for now to try and find some
solution. We are doing this case by case for now "cause we've been
thrashing going the other way" ;)

Relations we could use: portion_of, is_extracted, historical_part_of

If we do liver biopsy in mouse: we need to describe organism donor
(mouse), organism part from organism donor (liver) and the liver
tissue is specified output of the taking sample process

[other protege editing problems]

End of calls, with resolutions:

1. remove from core term

2. keep it on biomaterial

3. discuss on biomaterial list

4. BP will update owl file

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