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superior olivary complex vs superior olive #631

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cmungall opened this Issue Dec 20, 2014 · 5 comments

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cmungall commented Dec 20, 2014

Arose from work on #300, creating separate issue

SOC & SO are treated as distinct by nifstd/nlx, but they are synonymous in sources such as ISBN:0-19-502694-2. FMA also treats as synonyms.

Additionally we have the term Superior Olivary Nucleus (SON here for brevity). In general we often create separate classes for generic nuclei (e.g. nucleus-of-X EquivalentTo nucleus & part_of some X-complex). Butler and Hodos only draw a distinction between SON and SOC if multiple nuclei are present.

http://neurolex.org/wiki/Category:Superior_olive is part_of SOC (undefined). SO is characterized as containing LSO and MSO.

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cmungall commented Dec 20, 2014

Allen:

        po DHBA:12416 ! pontine tegmentum
         po DHBA:12453 ! auditory relay nuclei in pons
          po DHBA:12462 ! superior olivary complex *** 
           po DHBA:12463 ! superior paraolivary nucleus
           po DHBA:12464 ! periolivary nuclei
            po DHBA:12465 ! lateral periolivary nucleus
            po DHBA:12466 ! medial periolivary nucleus
           po DHBA:12467 ! retro-olivary cell group
           po DHBA:12468 ! superior olivary nucleus
            po DHBA:12469 ! lateral superior olivary nucleus
            po DHBA:12470 ! medial superior olive

and

    po HBA:9131 ! pons
     po HBA:9135 ! pontine tegmentum
      po HBA:9177 ! superior olivary complex *** 
       po HBA:9178 ! superior olivary complex, left
        po HBA:265504906 ! superior paraolivary nucleus, left
        po HBA:9179 ! periolivary nucleus, left
        po HBA:9180 ! preolivary nucleus, left
        po HBA:9181 ! retro-olivary cell group, left
        po HBA:9182 ! superior olive, left
         po HBA:9183 ! lateral superior olivary nucleus, left
         po HBA:9184 ! medial superior olivary nucleus, left
        po HBA:9185 ! trapezoid nuclei, left

Here we see a distinction being drawn, consistent with Wikipedia, between the primary SO(N), i.e. LSO(N) and MSO(N), and other (pre,peri,retro).

Compare with FMA:

           is_a FMA:83840 ! Nucleus of brain
            is_a FMA:72246 ! Nucleus of superior olivary complex *** 
             is_a FMA:226217 ! Lateral periolivary nucleus
             is_a FMA:226219 ! Ventral periolivary nucleus
             is_a FMA:72472 ! Lateral superior olivary nucleus [regional_part_of: "Superior olivary complex"]
             is_a FMA:72473 ! Medial superior olivary nucleus [regional_part_of: "Superior olivary complex"]
             is_a FMA:72474 ! Preolivary nucleus [regional_part_of: "Superior olivary complex"]
             is_a FMA:72475 ! Dorsal periolivary nucleus [regional_part_of: "Superior olivary complex"]
             is_a FMA:72476 ! Retro-olivary cell group [regional_part_of: "Superior olivary complex"]
             is_a FMA:72477 ! Ventral nucleus of trapezoid body [regional_part_of: "Superior olivary complex"]
             is_a FMA:75730 ! Lateral nucleus of trapezoid body
             is_a FMA:75732 ! Medial nucleus of trapezoid body
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cmungall commented Dec 20, 2014

Proposed solution is to follow nifga/nlx:

          po NIF_GrossAnatomy:birnlex_1307 ! superior olivary complex *** 
           po NIF_GrossAnatomy:birnlex_745 ! trapezoid nuclear complex
            po NIF_GrossAnatomy:birnlex_2575 ! dorsal nucleus of trapezoid body
            po NIF_GrossAnatomy:birnlex_2576 ! ventral nucleus of trapezoid body
            po NIF_GrossAnatomy:birnlex_2595 ! medial nucleus of trapezoid body
           po NIF_GrossAnatomy:birnlex_804 ! periolivary nucleus
           po NIF_GrossAnatomy:birnlex_814 ! preolivary nucleus
           po NIF_GrossAnatomy:birnlex_900 ! superior olive
            po NIF_GrossAnatomy:birnlex_1675 ! lateral superior olivary nucleus
            po NIF_GrossAnatomy:birnlex_1682 ! medial superior olivary nucleus

To align logically with FMA, we may retain a trivial Nucleus-of-SOC class = nucleus and po some SOC, but this should be labeled appropriately so it is not confused with primary nuclei (what nlx calls SO)

To align logically with MA, we equate their SON with SOC (but we may recommend they relabel to SOC). This is justified as they have periolivary nucleus as a part-child.

To avoid terminological confusion, and to lexically align with sources such as ISBN:0-19-502694-2 we may label what nlx and Allen calls SO as "primary SO"; this is consistent with Wikipedia.

cmungall added a commit that referenced this issue Dec 21, 2014

cmungall added a commit that referenced this issue Dec 21, 2014

@cmungall cmungall closed this in 4abf90c Dec 21, 2014

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cmungall commented Dec 21, 2014

Should this term be merged in to SOC?

[Term]
id: UBERON:0009053
name: dorsal nucleus of trapezoid body
synonym: "dorsal nucleus of trapezoid body" EXACT [NIF_GrossAnatomy:birnlex_2575]
xref: NIF_GrossAnatomy:birnlex_2575 ! Dorsal nucleus of trapezoid body
xref: SCTID:369021001 ! Entire dorsal nucleus of trapezoid body
is_a: UBERON:0007633 ! nucleus of trapezoid body
xref: UMLS:C0228438 {source="NIF_GrossAnatomy:birnlex_2575"}
xref: UMLS:C1289450 {source="NIF_GrossAnatomy:birnlex_2575"}

See:
http://www.medilexicon.com/medicaldictionary.php?t=61428

The SO is located on the dorsal surface of the trapezoid body?

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RDruzinsky commented Dec 22, 2014

These questions are all related to the very interesting and thorny problem
of structures that were identified and named originally as gross anatomical
features and then identified and named again based on microscopic
histological features, and then re-named based on higher resolution of the
histological structure, etc. Then there is the problem of mapping across
species...... Yikes.

Robert E. Druzinsky, Ph.D.
Clinical Associate Professor
Dept. of Oral Biology
College of Dentistry
University of Illinois at Chicago
801 S. Paulina
Chicago, IL 60612
druzinsk@uic.edu

Office: 312-996-0406
Lab: 312-996-0629
Website: www.peerj.com/RobertDruzinsky

On Sat, Dec 20, 2014 at 6:03 PM, Chris Mungall notifications@github.com
wrote:

Should this term be merged in to SOC?

[Term]
id: UBERON:0009053
name: dorsal nucleus of trapezoid body
synonym: "dorsal nucleus of trapezoid body" EXACT [NIF_GrossAnatomy:birnlex_2575]
xref: NIF_GrossAnatomy:birnlex_2575 ! Dorsal nucleus of trapezoid body
xref: SCTID:369021001 ! Entire dorsal nucleus of trapezoid body
is_a: UBERON:0007633 ! nucleus of trapezoid body
xref: UMLS:C0228438 {source="NIF_GrossAnatomy:birnlex_2575"}
xref: UMLS:C1289450 {source="NIF_GrossAnatomy:birnlex_2575"}

See:
http://www.medilexicon.com/medicaldictionary.php?t=61428

The SO is located on the dorsal surface of the trapezoid body?


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cmungall commented Dec 22, 2014

@RDruzinsky it's a fun problem! More to be said here. One approach is that you create some logically perfect but terminologically incomprehensible system that no domain expert understands. Obviously this has it's downsides! There is a tension between retaining familiar terms despite them having accrued semantic drift vs inventing new terminologies... anatomists trained in ontology such as yourself are totally vital to this process!

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