Class Crico-arytenoid muscle - UBERON_0010932

[RDruzinsky]

I request that this class be removed. The posterior cricoarytenoid (UBERON_0008572) and lateral cricoarytenoid (UBERON_0008573) are similar in name only and are not subClasses or part_of a cricoarytenoid muscle.

[cmungall]

Tagged the class as obsoletion candidate. @tfhyamizu should this also be removed from MA?

[cmungall]

Are they not similar in properties?

attaching to arytenoid and cricoid cartilage?

[RDruzinsky]

They are, but they have completely opposite functions and anatomists do not really lump them together.

[tfhayamizu]

Not advocating doing it in this case, but a general issue encountered in data collection is a lack of precision in specifying anatomical structures, which is often why terms like these are created even if they are not proper 'classes' per se. This lack of specificity is quite common in mouse expression literature, where studies are sometimes done by researchers who have more expertise in some areas (other systems, other organisms) than others. Also, the anatomy ontology terms are being used to describe phenotypes, where descriptions are often quite imprecise as well. Is there a way that we might be able to have 'lumping" classes?

[RDruzinsky]

Interesting point, Terry. I actually believe that many problems in comparative biology could be resolved through careful examination of detailed anatomy. However, this particular issue is terminological. I think that if we remove the class, Could we simply remove the super-class cricoarytenoid muscle and refer to it in the text definition, a comment, and as a broad synonym?

[cmungall]

If the class is removed then there is no valid term for gene expression curators to use when faced with lack of specificity. What are the view of other gene expression curators? @ANiknejad?

I think the best compromise is to ensure the class is tagged such that (a) people can build ontology views that exclude it if they don't want it (b) gene expression curators are prompted (but not forced) to use a more specific class.

[RDruzinsky]

In this particular case, I would be very surprised if the class cricoarytenoid muscle is used for anything, but I may be wrong. I guess my concern (clearly based on my ignorance) is what happens (and this concern is with the structure of many, many similar classes in Uberon) when the current logical definition in Uberon is merged with the logical definition from FEED?
For example, the lateral cricoarytenoid (with the current definition from Uberon):

SubClass of 'cricoarytenoid muscle'
SubClass of 'muscles innervated by vagus nerve'

SubClass of (anonymous ancestor) 'muscle organ' and ('innervated by' some 'vagus nerve') and ('develops from' some 'branchial arch 4') and ('develops from' some 'branchial arch 6')

I could load up a slice of Uberon and see, but I don't have it available at this moment.

[tfhayamizu]

Since there are no annotated data, I am perfectly content to remove the term "cricoarytenoid" from the MA, and adding terms for the "posterior" and "lateral" muscles. That said, naming conventions for structures such as muscles, blood vessels and nerves can be quite inconsistent. Similarly named structures can be instances (e.g. left, right), parts of (e.g. ascending, descending), related or even unrelated structures. Furthermore, imprecise use of anatomical descriptors is not just a problem with expression data curation. Anatomical descriptions for phenotypes, disease models and diseases for mouse and for humans often lack great specificity but it nonetheless important to be able to capture the information at the best possible level of granularity.

[cmungall]

Any other opinions here? Is it sufficient to leave the grouping class tagged, or should it be obsoleted?

[RDruzinsky]

If a search or query of 'cricoarytenoid muscle' will hit the lateral and posterior cricoarytenoid muscles, then I vote to obsolete the term. If the group term is required for such functions then I guess that it should be retained.

[cmungall]

We left this hanging, but I was just reminded by this:

• http://phenomena.nationalgeographic.com/2015/02/09/sciencespeak-cricoarytenoideus/

From the article I would guess that this is the lateral cricoarytenoideus?

114 The musculus cricoarytenoideus originates laterally on the cricoid cartilage
115 (Figure 3). It extends to the rostro-lateral aspect of the dorsal branch of the arytenoid and
116 into the soft connective tissue of the vocal folds (Figure 3, L2). Contraction of this
117 cranial aspect of the muscle would pull on the rostral end of the arytenoid arch, causing
118 movement laterad and opening the glottis (vocal fold abduction). There is also a caudal
119 branch of the muscle attaching to the cricoid and to the medial side of the basihyoid
120 (Figure 4). This newly described attachment to the basihyoid confers this muscle’s
121 extrinsic properties. An isolated contraction of the caudal portion would pull the entire
122 larynx caudally, exerting a strain on the vocal folds along their longitudinal (rostro-
123 caudal) axis. This would generate tensile stress, a mechanism most important in
124 facilitating F0 variation, but previously thought to be absent in alligators (Riede et al.
125 2011).

In any case, to summarize where we are:

• The lateral CA and posterior CA are true muscles
• CA is a grouping class (it is tagged as such in Uberon)
  • Is the grouping purely terminological?
    • I would argue the grouping is at least based on shared attachment properties
    • Is the grouping useful?
      • It seems to be of use, given imprecision used by many authors. This is a strong practical reason for maintaining the grouping given curation requirements, but we can still choose to Be Bold and obsolete

Do we think the current tagging in Uberon into the non_informative and grouping_class subsets is sufficient?

Also: I would like to improve on the wikipedia-sourced definitions for the lateral and posterior.

[cewall]

In a mammal at least (not sure about other vertebrates), the part of "cricoarytenoideus" that abducts the vocal cords is the posterior cricoarytenoid and I think this is being described at the beginning of the paragraph. It is distinguished from the lateral cricoarytenoid not just by its attachments, but also by its action of abduction (it is the only laryngeal muscle that can abduct the vocal folds / cords). This action of abduction is important for maintaining the glottis (and thus the airway) in a maximally opened position. The lower part of the paragraph seems to describe a lateral cricoarytenoideus with an additional attachment to the basihyoid (in addition to the "usual" attachments to the cricoid cartilage and the arytenoid cartilage).

Not sure what that means for the grouping.

---

From: Chris Mungall notifications@github.com
Sent: Saturday, February 14, 2015 4:31 PM
To: obophenotype/uberon
Subject: Re: [uberon] Class Crico-arytenoid muscle - UBERON_0010932 (#530)

We left this hanging, but I was just reminded by this:

• http://phenomena.nationalgeographic.com/2015/02/09/sciencespeak-cricoarytenoideus/

From the article I would guess that this is the lateral cricoarytenoideus?

114 The musculus cricoarytenoideus originates laterally on the cricoid cartilage
115 (Figure 3). It extends to the rostro-lateral aspect of the dorsal branch of the arytenoid and
116 into the soft connective tissue of the vocal folds (Figure 3, L2). Contraction of this
117 cranial aspect of the muscle would pull on the rostral end of the arytenoid arch, causing
118 movement laterad and opening the glottis (vocal fold abduction). There is also a caudal
119 branch of the muscle attaching to the cricoid and to the medial side of the basihyoid
120 (Figure 4). This newly described attachment to the basihyoid confers this muscle's
121 extrinsic properties. An isolated contraction of the caudal portion would pull the entire
122 larynx caudally, exerting a strain on the vocal folds along their longitudinal (rostro-
123 caudal) axis. This would generate tensile stress, a mechanism most important in
124 facilitating F0 variation, but previously thought to be absent in alligators (Riede et al.
125 2011).

In any case, to summarize where we are:

• The lateral CA and posterior CA are true muscles
• CA is a grouping class (it is tagged as such in Uberon)
• Is the grouping purely terminological?
  - I would argue the grouping is at least based on shared attachment properties
  - Is the grouping useful?
  • It seems to be of use, given imprecision used by many authors. This is a strong practical reason for maintaining the grouping given curation requirements, but we can still choose to Be Bold and obsolete

Do we think the current tagging in Uberon into the non_informative and grouping_class subsets is sufficient?

Also: I would like to improve on the wikipedia-sourced definitions for the lateral and posterior.

Reply to this email directly or view it on GitHubhttps://github.com//issues/530#issuecomment-74392828.

[gouttegd]

WARNING: This issue has been automatically closed because it has not been updated in more than 3 years. Please re-open it if you still need this to be addressed addressed addressed – we are now getting some resources to deal with such issues.