Druzinsky, R.E. (2014) An anatomy ontology for oro-pharyngeal muscles and the logical underpinnings of comparative anatomy. In the mini-symposium “Anatomy Ontologies: Bioinformatics in the Anatomical Sciences” at the Annual Meeting of the American Association of Anatomists (FASEB J April 2014 28:338.4), Abstract.

1. An Anatomy Ontology for Oro-Pharyngeal
Muscles and the Logical Underpinnings of
Comparative Anatomy
Robert E. Druzinsky
Dept. of Oral Biology
College of Dentistry
University of Illinois at Chicago

2. People
FEED Investigators
Robert Druzinsky – U. of Illinois, Chicago
Rebecca German – NEOMED
Chris Vinyard - NEOMED
Chris Wall – Duke U.
Susan Williams – Ohio U.
Ontology People
Jim Balhoff - NESCent
Melissa Haendel – Oregon
Health & Science U.
Hilmar Lapp – NESCent
Paula Mabee – U. of South Dakota
Chris Mungall – U. of California, Berkeley
Anatomy People
Alfred “Fuzz” Crompton – Harvard U.
Frits De Vree – U. Antwerp
Anthony Herrel - Museum National
d’Histoire Naturelle, Paris
Sue Herring – U. of Washington, Seattle
David Reed – U. of Illinois, Chicago
Textpresso People
Kimberly Van Auken - WormBase
James Done - WormBase
Hans-Michael Muller – California Institute
of Technology
Paul Sternberg – California Institute of
Technology
Others
Abigail Goben – U. of Illinois, Chicago
Kun Peng – U. of Illinois, Chicago

3. http://www.feedexp.org

4. Druzinsky, Doherty, De Vree, 2011
A Controlled Vocabulary
for oral/pharyngeal
muscles

5. Construction of a vocabulary is not enough.
We need definitions that are general enough to be
true across higher taxa.

6. Construction of these computable definitions
exposes and formalizes the
underlying logic of comparative anatomy
• Why is the masseter called the masseter in each mammal?
• Why does every anatomist know this with no discussion?

7. Muscle attachmentsinnervated_bypart_ofdevelops_fromDefinitionSynonym(s)

8. Oral/Pharyngeal Anatomical Structures

9. Trigeminal muscles as organized in the FEED spreadsheet

10. Ontology of Trigeminal Muscles

11. Ontology of Oral/Pharyngeal Behaviors

12. Ontology of Oral/Pharyngeal Behaviors -Ingestion

13. Hyoglossus definitions
Uberon - Term IRI: http://purl.obolibrary.org/obo/UBERON_0001572 (Gray 1918:1129)
The Hyoglossus, thin and quadrilateral, arises from the side of the body and from the whole length of the greater cornu
of the hyoid bone, and passes almost vertically upward to enter the side of the tongue, between the Styloglossus and
Longitudinalis inferior. The hyoglossus depresses and retracts the tongue makes the dorsum more convex The fibers
arising from the body of the hyoid bone overlap those from the greater cornu. It is important in singing. Structures
passing medially to the hyoglossus muscle are the lingual vein and lingual artery. Laterally, in between the hyoglossus
muscle and the mylohyoid muscle lay several important structures (from superior in inferior): submandibular gland,
submandibular duct, lingual nerve, vena comitans of hypoglossal nerve, and the hypoglossal nerve. Note, posteriorly,
the lingual nerve is superior to the submandibular duct and a portion of the submandibular salivary gland protrudes into
the space between the hyoglossus and mylohyoid muscles.
Morton, Foreman, Albertine 2011 The Big Picture: Gross Anatomy
Hyoglossus muscle. Courses lateral to the genioglossus muscle, with attachments from the hyoid bone to the tongue. The lingual
artery, en route to the tongue, courses between the hyoglossus and genioglossus muscles. In contrast, CN XII and CN V-3 course
from the infratemporal fossa to the tongue, along the external surface of the hyoglossus muscle.
FEED
Textual Definition –
The hyoglossus is a muscle that attaches to the hyoid and tongue and is
innervated by Cranial Nerve XII.
Computable Definition –
('attached to' some 'hyoid bone')
and ('attached to' some tongue)
and ('innervated by' some 'hypoglossal nerve')
and (spatially disjoint with 'intrinsic tongue muscle‘)

14. eh
Protégé – software for construction of ontologies

15. Homology??????
Druzinsky, Doherty,
De Vree, 2011

16. What is the point of this endeavor?
Use cases:

17. Computability

18. Computability

19. IMAGE DEPICTIONS – JIM BALHOFF PLUGIN

20. A Textpresso site to demonstrate the power and usefulness of the FEED ontologies
www.textpresso.org

21. • 1600+ Articles
• FEED Behavior Ontology
• FEED Oro-Pharyngeal Muscle Ontology
• Vertebrate Taxonomy Ontology –
Midford et al. 2013. Journal of biomedical semantics, 4(1), 34.
http://phenoscape.org/wiki/Ontologies#Vertebrate_Taxonomy_Ontology
Textpresso site for FEED

22. Search:
Category 1 – Euarchtoglires (Rodents, Lagomorphs, Primates, Dermopterans)
Category 2 – Muscles innervated by the Trigeminal Nerve
Hits: 606 hits in 101 documents
Search 1
Utilizes VTO and FEED Muscle ontology

23. Search 1: Category 1 – Euarchtoglires, Category 2 – Muscles innervated by the Trigeminal Nerve
Hits: 606 hits in 101 documents

24. Screen clipping taken: 4/18/2014 6:22 PM
Search 1: Category 1 – Euarchtoglires, Category 2 – Muscles innervated by the Trigeminal Nerve
Hits: 606 hits in 101 documents

25. Screen clipping taken: 4/18/2014 6:24 PM
Search 1: Category 1 – Euarchtoglires, Category 2 – Muscles innervated by the Trigeminal Nerve
Hits: 606 hits in 101 documents

26. Search:
Category 1 – Edentata (sloths, anteaters, armadillos)
Category 2 – Behavior (all) – oral/pharyngeal behaviors
Hits: 40 in 3 documents
Search 2
Utilizes VTO and FEED Behavior Ontology

27. Document 1:
Search 2: Category 1 – Edentata, Category 2 – Behavior (all)

28. Search: Category 1 – Edentata, Category 2 – Behavior (all)
Document 2:

29. Search 2: Category 1 – Edentata, Category 2 – Behavior (all)
Document 3:

30. Goals for the FEED Ontologies
• Continue to add anatomical entities to FEED
• Merge into Uberon
• Expand FEED Behavior Ontology

31. Goal for Textpresso for FEED:
To make the site a major resource for students
of vertebrate functional morphology
• Include the bulk of the 20th Century literature on
vertebrate functional morphology
• Increase size of corpus to 10,000 – 20,000
references
• Add other ontologies for searching
• Uberon
• GO

32. The potential of anatomy ontologies –
Queries across databases
• Which genes are active in brachial arch 1 muscles?
• Are there genes in common that are active in muscles that attach to
the mandible?
• Neural crest derivatives?
• “Head somites?”

33. Thanks to:
• Phenotype RCN
• NSF - ABI 1062350
• NSF-ABI-1062333 to Chris Wall
• NSF-EF-0423641 to Chris Wall and the FEED group

34. Gray’s Anatomy (1918)
The Genioglossus (Geniohyoglossus) is a flat triangular muscle close to and parallel with the median
plane, its apex corresponding with its point of origin from the mandible, its base with its insertion into the
tongue and hyoid bone. It arises by a short tendon from the superior mental spine on the inner surface of
the symphysis menti, immediately above the Geniohyoideus, and from this point spreads out in a fan-like
form. The inferior fibers extend downward, to be attached by a thin aponeurosis to the upper part of the
body of the hyoid bone, a few passing between the Hyoglossus and Chondroglossus to blend with the
Constrictores pharyngis; the middle fibers pass backward, and the superior ones upward and forward, to
enter the whole length of the under surface of the tongue, from the root to the apex. The muscles of
opposite sides are separated at their insertions by the median fibrous septum of the tongue; in front,
they are more or less blended owing to the decussation of fasciculi in the median plane.
FEED
Definition - The genioglossus is a muscle that attaches to the mandible and tongue and is innervated by
Cranial Nerve XII.
('attached to' some ‘mandible')
and ('attached to' some tongue)
and ('innervated by' some 'hypoglossal nerve') and
spatially disjoint with 'intrinsic tongue muscle'
Genioglossus