Fwd: NIF Resource Type Hierarchy labels are unclear as they relate to Biobanks

[anita bandrowski]

Hi All,
One of our curators has the following issue with the representation of tissue banks that I think we need some additional brain power to solve.
Essentially tissue banks (brain banks) have two major features that we would like to represent:
1. Who can put in tissue
2. Who can take it out

However these two functions are currently represented under different parts of the ontology: "biomaterial storage repository" and "biomaterial supply".

This seems wrong to us, but we hope to have some feedback from the group to fix it.
Thanks so much in advance for your input,
anita

---------- Forwarded message ----------
From: Andrea Arnaud Stagg <aar...@ucsd.edu>
Date: Mon, Nov 28, 2011 at 1:03 PM
Subject: NIF Resource Type Hierarchy labels are unclear as they relate to Biobanks
To: anita bandrowski <ban...@gmail.com>


Hi Anita,

I have found some issues with the NIF Resource Type Hierarchy as they apply to Biobanks.  We currently have 2 places in the tree where they potentially belong:
* Material resource-->Biomaterial supply resource
* Service resource---> Material storage repository
A problem is that under "Biomaterial supply resource" we have "Cell repository," "Tissue bank" and "Brain bank." Banks and repositories, however, generally imply storage ("Material storage repository"). Additionally, not all Brain banks, for example, supply their brains, they just collect them and use them for their own research.  Additionally, not all Biomaterial suppliers will store samples for people.

To show that 'banks' and 'repositories' are more in line with storage facilities see:
*Tissue bank (MeSH) http://bioportal.bioontology.org/ontologies/1351?p=terms&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMSH%2FD014015
* Bio-repository (Epoch Clinical Trial Ontologies), http://bioportal.bioontology.org/ontologies/1060?p=terms&conceptid=http%3A%2F%2Fepoch.stanford.edu%2FOrganizationOntology.owl%23Bio-Repository

Biomaterial suppliers also need to be represented but our current labels make this somewhat confusing.

Thanks,
Andrea

--
Andrea Stagg
Neuroscience Information Framework
University of California, San Diego
9500 Gilman Drive
La Jolla, CA 92093-0446
http://neuinfo.org/

--
Anita Bandrowski, Ph.D.
NIF Project Lead
UCSD 858-822-3629
http://neuinfo.org
9500 Gillman Dr.#0446
la Jolla, CA 92093-0446

[Jessie Tenenbaum]

Hi Anita-

To clarify, I'm assuming you're referring to NIF's ontology and not eagle-i or BRO?

in BRO there's 

- material resource/biomaterial supply resource

- material resource/facility core/tisue organ facility/biobank facility

fwiw, I would envision "biomaterial storage repository" (equiv of "biobank facility") as both putting it in and taking it out, while "biomaterial supply" would be providing the material, whether produced de novo or pulled from a biobank. not sure if that helps...

-Jessie

[anita bandrowski]

Thanks Jessie,

You are correct, I should have specified that I was talking about NIF's ontology and core facilities are something that we have not aligned.
That seems a little better than the NIF representation, but we still run into the service resource issue with BRO.
It looks like facility core is a subclass of both material and service.
We were trying to avoid multiple parent hierarchy in NIF, but this is a tough case.

anita

[Maryann Martone]

I agree with your representation Jessica.  We discussed this a few weeks ago and have been planning on updating our representation.   We are assuming that unlike a museum, someone can  take a specimen out of a repository, just perhaps not the general public.  So repository and supply should be two different classes.

[Melissa Haendel]

Hi all,

we've been representing these different aspects of services in OBI/eagle-i, and would be happy to work through this with you.

We too are dealing with the biospecimen respositories (and other collections with in/out functionality).

Cheers

melissa

Dr. Melissa Haendel

eagle-i Networking Research Resources

OHSU Library http://www.ohsu.edu/library/

Department of Medical Informatics and Epidemiology
Oregon Health & Science University
hae...@ohsu.edu
skype: melissa.haendel

503-407-5970

[anita bandrowski]

Great, can we put this on the agenda for the next call?
anita

[Trish Whetzel]

Melissa,

Are you handling this via class definitions or are you also adding roles to further specify these tasks?

Trish

[Melissa Haendel]

We can, although our next scheduled call a) I will be away and b) this might be in the weeds modeling. Perhaps we should have a modeling call some other time this month to discuss?

Cheers,

melissa

[Jessie Tenenbaum]

i agree, sounds like a good topic for a Thursday modeling call.

[anita bandrowski]

Fabulous, are you around this Thursday Melissa or should we schedule this for next week?

[Carlo Torniai]

Just a reminder that the modeling call will start in few minutes (1.00pm PST)

Call info:

  1-866-890-3820; 

  passcode 31894534#

We will be using adobe connect for screen sharing:

https://ohsu.adobeconnect.com/eagle-i

Carlo

On Nov 29, 2011, at 9:13 AM, anita bandrowski wrote:

[Carlo Torniai]

Hi all, since just me and Matt showed up we will reschedule the call.

Best,

Carlo

[anita bandrowski]

Hi Sorry Carlo!
I have been up to my eyeballs in crisis mitigation mode all morning with our deployment.
Please let me know when you reschedule.
anita

[Carlo Torniai]

No worries Anita

We will reschedule, probably in two weeks so that Melissa can attend.

Best,

Carlo

--
Carlo

[anita bandrowski]

Thanks! Melissa is probably needed for this discussion.
Again my apologies.
anita