wiki:QueriesByProject
Last modified 5 years ago Last modified on 07/31/13 11:50:54

QI Queries By Project

_Table of Contents_

RadLex

Marta's common and granular term comparison queries (modified to handle deprecated RIDs):

Ken's innervation and muscle attachment queries:

  1. For a single RID, retrieve all of its relationships. I would like the preferred name string for each referenced RID to be included in the RDF result.
  1. Given a muscle "supraspinatus muscle", I'd like to get the set of all muscle origins and insertions/attachments. Supraspinatus muscle (RID 1941) has as a direct relation "Has_origin" which should constitute part of the result. But for the distal attachment, it looks like I need to navigate to constitutional part "distal tendon of supraspinatus" (RID 41121) to get its "Attaches_to" relation. So the query result I would like here is the union of all origin / insertion sites associated with the parts of the given muscle.

[Subsequent note from Ken: This query is also already largely doing what I would like, which is that if a higher hierarchical portion of the muscle/tendon is specified (e.g. 1996 for biceps brachii muscle), then all of the lower hierarchical attachments are returned (i.e. three attachments). If, however, I give a more specific part of the muscle (e.g. 1998 for long head of biceps brachii muscle), then only the attachment of that part is returned (i.e. supraglenoid tubercle). Note that there is a granularity issue here. For the biceps brachii, the origin of the short head is RID 40061, "area of origin of short head of biceps brachii" which is a part of RID 40034 "apical part of coracoid process" which is a part of RID 1863 "coracoid process". Clinically, the desired result is "coracoid process" rather than "area of origin of short head of biceps brachii". Perhaps to arrive at the result to be returned, if the specific bony attachment site contains the words "area of" or "part of", then traverse upward in the part hierarchy until the structure name does not contain these phrases? Not sure if this simple rule would work well.]

  1. Given a specific nerve or set of nerves N, what are the muscles innervated by N? N may consist of a single nerve (e.g. musculocutaneous nerve; or anterior ramus of C5 spinal nerve), or a set of nerves (e.g. posterior, medial and lateral cords of the brachial plexus; or anterior rami of the C5, C6 and C7 spinal nerves).
  1. Given a specific muscle or set of muscles M, what are the most distal common innervating nerve segment(s)? There is subtlety and imprecision of this query, but suppose we consider varying cases:

i) In the simplest case, given a single muscle M, what I would like this query to return is the name of the nerve branch which innervates this muscle.

ii) In a second example, given the set supraspinatus muscle and infraspinatus muscle, since both of these are innervated by branches of the suprascapular nerve, this is the desired query result.

iii) In a third example, given a set of muscles supraspinatus, infraspinatus and teres minor, the suprascapular nerve innervates the first two, but the axillary nerve innervates the last of these. It seems that both suprascapular and axillary nerves consist of fibers from C5 and C6, so the desired result would be the set of the anterior rami of the C5 and C6 spinal nerves. However, looking at this, I'm not sure if the ontology might indicate C5, C6 and C7 for the axillary nerve. I'm very curious about this particular point.

[reworded description: For one or more muscles, retrieve the distal-most common innervating nerve segment(s). Any nerve segment N returned by this query should satisfy the following conditions: (a) N innervates all the given muscles, (b) no other segments downstream of N also innervate all of the given muscles. For the set supraspinatus and infraspinatus muscles, return suprascapular nerve. For the set supraspinatus, infraspinatus and levator scapulae muscles, return the ventral ramus of the C5 spinal nerve. For the set supraspinatus, infraspinatus and biceps brachii muscles, return the superior trunk of the brachial plexus. For the set supraspinatus and pectoralis minor muscles, return the empty set.]

  1. Given a bony landmark, retrieve all muscles attaching at this site. As per the granularity issue in (2) above, if I pass in a bony site which has many parts, then return all muscles attaching at any of these parts. For example, if I pass in RID 1863 "coracoid process", then return pectoralis minor, short head of biceps brachii and coracobrachialis muscles.
  1. Given a bony landmark, retrieve all ligaments attaching at this site. Same granularity issue again. If I pass in RID 1863 "coracoid process", then return coracoclavicular, coracoacromial, coracohumeral and superior transverse scapular ligaments.
  1. Anatomical space query. As described by Ken:

What I would like to do is send in the ID for an anatomic space (not the compartment), and I would like the result to contain the preferred name string of ID, as well as the ID/name of any bounding structures, and the ID/name of the parts of the contained structures.

For example, for input RID 42141, I would like the following in the RDF result:

Name - interscalene triangle space
Bounded by: 42584 - posterior surface of scalenus anterior, 42587 - lateral surface of scalenus anterior,etc.
Contains: 7216 - inferior trunk of brachial nerve plexus, 7213 - middle trunk of brachial nerve plexus, etc.

Ideally, rather than "posterior surface of scalenus anterior" and "lateral surface of scalenus anterior", I would really prefer 7496 "anterior scalene muscle", but I don't see a way this can be computed based on current RadLex content.

[Note that the above query produces Contains relationships that are different than those actually present in the ontology. In RadLex, the interscalene triangle space contains the neurovascular bundle of interscalene triangle. The latter has parts such as middle trunk of brachial nerve plexus. In the query output middle trunk of brachial nerve plexus is shown as being directly contained in the space.]

  1. Given a bony landmark, retrieve all myotendinous structures attaching at this site (like query #5 above, but the results are finer grained, but non-ligament, structures).

As further clarified by Ken: By "myotendinous" I mean structures which relate to a muscle-tendon unit. In your sample output you also include ligaments, which I consider different from myotendinous structures. In light of all of this, I wonder if I may request a query which takes in a bony site, and returns all structures (myotendinous or ligamentous) which attach at that site, or at parts of that site. In particular, while this would involve traversal of the part hierarchy of the bony site, it does not involve such traversal of the attaching structures. That is, for coracoid process, the query also retrieves attachments at the regional part apical portion of coracoid process. But whatever those attaching structures are, may simply be returned as is, without traversal of their part hierarchies.

NOTE

Some browsers have a problems with redirected URLs, like PURLs and query fragments (the part of the URL after the '#' symbol). If you experience this problem, try replacing the purl part of the URLs as follows:

For the Query in QI: Replace "http://purl.org/sig/QI" with "http://xiphoid.biostr.washington.edu:8080/QueryManager/QueryManager.html For an example rest call: For URLs containing "TemplateQuery", replace "http://purl.org/sig/QI/TemplateQuery" with "http://xiphoid.biostr.washington.edu:8080/QueryManager/TemplateQueryResults". For URLs containing "ParamQuery", replace "http://purl.org/sig/QI/ParamQuery" with "http://xiphoid.biostr.washington.edu:8080/QueryManager/ParamQueryResults".