Re: Marmoset atlas and Cross-species query

[anita bandrowski]

Hi Rembrandt,

Great news about the marmoset atlas data. We would love to take it, just send me some spreadsheets and we can get it curated / loaded, especially as the data set is static this will be easy.

Perhaps Stephen can weigh in on the can NeuroLex answer the "which species have this brain region" question. I am not sure that it can.

Yes, NIF will be across the alley from INCF so I will see Daniel there.

We are local so things should be pretty easy this year.

Best,
anita

On Tue, Oct 29, 2013 at 9:08 AM, Rembrandt Bakker <r.ba...@donders.ru.nl> wrote:

Hi Anita,

how are you?
This time some questions from my side relating to NeuroLex,
please redirect where appropriate.

For the INCF demo at SfN I created some new features in the SBA,
in close collaboration with Daniel Wojcik & team.
They managed to arrange the public release of a Marmoset brain
atlas (cortex), and encouraged me to import the data into SBA.
http://scalablebrainatlas.incf.org/PPWRT12

So the first question is whether we can export these data
to NeuroLex as well, I remember Steve Larson used some spreadsheet
import for that.

The next addition to SBA is a cross-template brain region lookup,
which answers for a selected brain region the question
"what templates have it?", whereby the templates currently cover
four species (mouse, marmoset, macaque, human).
http://scalablebrainatlas.incf.org/PPWRT12?plugin=sbaLookup

The lookup occurs both by acronym, alias, and full name.
The second question is whether NeuroLex can provide a similar
service, i.e. answer the question "What species have it".
This I could then add to the NeuroLex plugin, which is now
pretty basic:
http://scalablebrainatlas.incf.org/PHT00?plugin=neurolex

Daniel Wojcik will do the SfN presentation, I will stay
comfortably at home...
Will you be manning the NIF booth?

Looking forward to your response,

Rembrandt

--
Dr. R. Bakker
Radboud University Nijmegen / Forschungszentrum Jülich /
NeuroInformatics.NL / G-Node
+31645774665 (Radboud: 0243652141)

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

[Mihail Bota]

Rembrandt,

Really nice addition! Just curios, how many brain regions are in this atlas?

Mihai

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[Stephen Larson]

On Tue, Oct 29, 2013 at 10:43 AM, anita bandrowski <aband...@ncmir.ucsd.edu> wrote:

The second question is whether NeuroLex can provide a similar
service, i.e. answer the question "What species have it".

Hi all,

   There's some SPARQL query design work that would need to be done, and I'm not sure how much we'd find, but it seems to me that the NeuroLex should have all the elements needed to answer that question.  

The property is called 'Species':

http://neurolex.org/wiki/Property:Species

Best,

  Stephen

[Maryann Martone]

Hi Rembrandt:

Yes, Neurolex would be able to answer the question "which species have it" in theory, because all brain regions are linked to an organism.  In the case of our generic brain structures, they are linked at the level of taxon rank, e.g., mammals.  At the level of individual brain structures that appear in a given paper or atlas, they are linked to the organism in which they are described.  These individual brain structures are then related to the generic brain structures through the "overlaps" relationship. 

That said, I'll have to ask Stephen to weigh in here about whether the query is an easy one to make or requires some tweaking.

Regards,

Maryann

On Tue, Oct 29, 2013 at 10:43 AM, anita bandrowski <aband...@ncmir.ucsd.edu> wrote:

--

[Stephen Larson]

It is a moderately complex query that will take some thought.  I've been helping a student through learning SPARQL queries over here -- perhaps a good next project for him?

Best,

  Stephen