Re: CUMBO white matter terms
Maryann Martone
for the partonomies you've established. Swanson has them listed under
"Basic fiber systems", but I don't think that quite captures the
nature of these two types. I'll be interested to hear what Chris
thinks.
On Oct 25, 2011, at 9:10 AM, dmbo...@u.washington.edu wrote:
>
>
> Hi Jyl and Maryann,
>
> You are right there are two different hierarchies for gross neural
> structures (See our Rosetta Stone chapter for more on that.) The
> classical, or cross-sectional, and the functional,or longitudinal,
> hierarchies. They are associated with overlapping nomenclatures.
> Except for the cortical white matter,which hardly exists in the
> rodent, they are pretty much the same in primates and rodents.
>
> The set of structures in the classical hierarchy is available in
> NeuroNames. The set in the functional hierarchy is available as an
> appendix in Swanson's 2004 rat brain atlas. Much of the translation
> between the two representations is in the NeuroNames ancillary
> category, though I haven't checked carefully to be sure that it is
> complete.
>
> I plan to get together with Chris tomorrow (Wednesday) to talk about
> translating NeuroNames into OWL. If and when that happens, perhaps
> you'll find it useful for the classical hierarchy, where primary
> white structures are assigned to the smallest volumetric structure
> that fully contains them. The functional hierarchy from Swanson is at:
> http://braininfo.rprc.washington.edu/OtherModels.aspx?requestID=2868&questID=1320&pTerm=Functional%20CNS%20Model#1320
> ... or may be available in a format more useful to you through BAMS.
>
> Doug
>
>
>
> On Mon, 24 Oct 2011, Maryann Martone wrote:
>
>> I am finding that as I am trying to define the structures in the
>> Neurolex,
>> that I need something along the lines of "White matter structure"
>> or perhaps
>> "predominantly white matter structure", as that is technically more
>> correct
>> (a la Brain Info) to define just gross anatomical structures. Some
>> of these
>> are entire tracts, e.g., the mammillothalamic tract, while others
>> are things
>> like the internal capsule which are divisions that don't delineate
>> entire
>> white matter tracts or pathways. Rather, they contain parts of
>> individual
>> tracts and other pathways. The internal capsule is a segment
>> along a
>> larger "highway", that is, we can define the next part of the
>> highway (the
>> crus cerebri), the pontine white matter, the medullary pyramids.
>> If we can
>> set the CUMBO terms for these two types, we have accomplished a lot.
>> On Oct 24, 2011, at 11:09 AM, Jyl Boline wrote:
>> Hello All,
>> We have been working on some terms to help describe predominantly
>> white matter for CUMBO. The goal is to create explicit and
>> computable
>> representations of basic terms which will serve as the building
>> blocks
>> for defining more complex structures. We probably have more terms
>> than what are needed, with multiple definitions for some of them
>> (sources are FMA, BAMS, Neurolex, and our email discussions), and
>> right now, a pretty flat "hierarchy."
>> We would like to determine what are the fundamental terms, narrow in
>> on a precise definition, identify synonyms, and also determine if
>> there should be a different hierarchy. Please take a look and give
>> us
>> your thoughts. https://docs.google.com/document/d/1YM77LVV4FR-sPU7QBVSIiivF2SNwYke8gjpaHz
>> 41FV4/edit?hl=en_US
>> Thanks much!
>> Best,
>> Jyl
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