Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), Corvallis, Oregon, USA 1 Does the Foundational Model of Anatomy ontology provide a knowledge base for learning and assessment in anatomy education? Melissa D. Clarkson Mark E. Whipple Division of Biomedical Informatics Dept. of Biomedical Informatics and Medical Education Institute for Biomedical Informatics Dept. of Otolaryngology–Head and Neck Surgery University of Kentucky University of Washington Lexington, KY, USA Seattle, WA, USA mclarkson@uky.edu mwhipple@uw.edu Abstract—Throughout the development of the Foundational intended to serve as a knowledge base for diverse applications Model of Anatomy (FMA) ontology, one of the use cases put forth that need a standardized and computable representation of has been anatomy education. In this work, we examine which types human anatomy. of knowledge taught to anatomy students can be supported by the FMA knowledge base. We first categorize types of anatomical The line of research that produced the FMA originated in knowledge, then express these patterns in the form “Given ____, efforts to engineer knowledge-based systems that use the state ____”. Each of the 33 patterns was evaluated for whether this structure of the human body as a basis for organizing spatial and type of knowledge is compatible with the modeling and scope of semantic representations of the body [4,5]. One theme of this the FMA. work was designing systems to be used in anatomy education. Demonstration projects included systems that support browsing Keywords—anatomy; ontology; knowledge representation; of segmented 2D medical images and 3D anatomical models, medical education; nursing education including a web-based atlas of interactive 3D graphics known as the Digital Anatomist [6]. The semantic network underlying this I. INTRODUCTION system was the precursor to the FMA. Knowledge of human anatomy is fundamental to the fields of health sciences. Software applications that support the B. Anatomical education for health science students delivery of healthcare services and training of healthcare The process by which health science students learn anatomy providers often incorporate anatomical knowledge, but rarely in has traditionally consisted of a combination of cadaveric ways that are computable and reusable. As researchers seek to dissection, two-dimensional illustrations or photographs, and make software systems more intelligent, opportunities to draw text-based descriptions of anatomical relationships. Like most upon knowledge bases of anatomy will increase. As part of this areas of modern life, computer-based tools have increasingly research agenda it is important to examine whether the needs of been integrated into anatomy education. These include specific applications can be supported by available knowledge computer-based interactive atlases, such as the Visible Human bases. Project, as well as virtual anatomic models that allow students to rotate and visualize structures and relationships in three This paper categorizes the types of knowledge relevant to dimensions. These types of computer-based 3D visualizations student learning in university-level courses in human anatomy, can successfully augment more traditional methods of and then examines which types are supported by the instruction, resulting in improved understanding and retention of Foundational Model of Anatomy (FMA) ontology. anatomic knowledge [7]. As health science schools move II. BACKGROUND towards more streamlined basic science education with a greater emphasis on student-directed learning, computer-based A. The Foundational Model of Anatomy anatomic teaching tools will play an increasing role in anatomy The FMA is both a theory for representing anatomy and a education [8]. computational artifact [1,2]. It is currently modeled in OWL2 If educational applications for learning anatomy make use of [3]. The majority of the content describes adult human canonical common knowledge bases—instead of relying on application- anatomy, although recent work has incorporated developmental specific catalogues of knowledge—benefits will include greater anatomy. Because the FMA is a reference ontology, it has not standardization of terminologies, less duplication of effort in been developed for a specific type of application; rather, it is constructing knowledge artifacts, and easier implementation of This work was supported in part by the National Library of Medicine of reasoning capabilities. This paper revisits the potential for the the National Institutes of Health under award R21-LM012075. The content is FMA to serve as a knowledge base for education in gross human solely the responsibility of the authors and does not necessarily represent the anatomy, three decades after its conception. official views of the National Institutes of Health. ICBO 2018 August 7-10, 2018 1 Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), Corvallis, Oregon, USA 2 III. METHODS A. High granularity of the FMA A. Identifying knowledge relevant to anatomy education Part relationships within the FMA tend to be much more granular than those taught in anatomy courses. For example, To capture types of knowledge relevant to learning human Figure 1 (top) shows a question about a part of the urinary anatomy in university-level courses, a variety of educational bladder. In the FMA, this information traverses three part resources were reviewed. Particular emphasis was given to relationships. structured information presented as tables in atlases and review guides [9–11], as well as the content of practice questions [12– Implications: This high level of granularity in the FMA is 14]. Content was examined to identify minimal units of appropriate for advanced anatomy courses, but may not be a information and general categories of knowledge. good fit for learners in basic anatomy courses. But just as Consider these examples: advanced learners should be able to understand and reason over high-granularity representations to answer low-granularity • A table describing lymph node groups that provides questions, it is possible that some types of high-granularity information about location, afferent lymphatic structures, representations in the FMA can be converted to low-granularity efferent lymphatic structures, and regions of the body representations. drained (from [11]). • A review question, “The ___ returns blood [to the heart] B. High specificity of the FMA from body regions above the diaphragm” (from [12]). Educational materials may focus on general concepts (“ventral and dorsal roots merge to form a spinal nerve”), while Although these examples describe different anatomical systems, the FMA tends to represent knowledge with greater specificity they are similar in that they both refer to the connectivity and (such as specific ventral and dorsal roots). spatial location of structures. Implications: The class hierarchy may provide an avenue for During the process of identifying units of information and representing knowledge applied to many individual structures. developing categories, a category was created if two or more (For example, “Muscle organ” has regional part “Distal examples of a pattern of knowledge were found within the tendon”.) However, because properties of class are inherited by sampled content. These categories were expressed as assessment all its subclasses, there is a danger that a general anatomical questions using patterns in the form “Given ____, state ____” in principle will not be true for every subclass. order to make explicit the prompt and the knowledge to be recalled. An example of a pattern is “Given a structure, state its C. Formal and explicit representation of the FMA parts”. Educational materials often make use of assumptions and B. Comparing types of assessment questions to the content unwritten knowledge. Making this knowledge explicit, as required by the FMA, can introduce an expected level of and structure of the FMA complexity. As show in Figure 1 (bottom), answering a question Each category of assessment questions was compared with about the passage of air through the nose and into the pharynx the modeling and scope of the FMA. Effort was directed toward using the FMA requires that the nasal cavity is explicitly determining whether the type of knowledge in the assessment recognized as a part of the nose. A medical student has tacit questions could be retrieved from the FMA, not determining knowledge that movement of air through the respiratory system whether the FMA currently contains the content necessary to (at the level of gross anatomy) takes place within tubes and answer specific questions. cavities, and would immedicately recognize that this question refers to air-filled spaces—even if he or she did not conceive of IV. RESULTS “nasal cavity” as an anatomical structure. Five broad categories of anatomical knowledge were identified (see Table 1). Questions were organized into 17 Implications: Directly translating the FMA content into subcategories and expressed through a total of 28 patterns. Table educational contexts is largely inappropriate because it risks 1 also provides examples of specific questions for each pattern directing students’ attention toward modeling details of the and an assessment of whether the FMA could serve as a source FMA, rather than on building upon their existing understanding for each type of knowledge. of anatomy. However, it may be appropriate to use explicit FMA representations as a supplement to less-detailed representations This analysis shows that the FMA is well-suited to as a way to help students construct and deepen their knowledge representing knowledge about synonyms of terms, classification of anatomy. of anatomical structures, parts of structures, and connectivity between structures. As expected, the FMA is not a suitable D. Translating to the language of the FMA knowledge base for questions about the qualities of anatomical As noted in previous work to test the FMA against anatomy structures (such as morphology or variation within the examination questions [15], common English-language population). expressions and terms often need to be translated by someone For the types of knowledge that the FMA can support, familiar with the FMA. An example is shown in Figure 1 (top), several factors may complicate efforts to directly apply the FMA where the phrase “is located in” translates to “is regional part of” to educational applications: and “is constitutional part of”. Implications: The precision of relationships used in the FMA may be helpful in stimulating students to think more deeply ICBO 2018 August 7-10, 2018 2 Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), Corvallis, Oregon, USA 3 TABLE I. CATEGORIES OF ASSESSMENT QUESTIONS FOR ANATOMICAL KNOWLEDGE Category of assessment question Suitable for FMA Category 1: Representations and real anatomy Understanding visual and semantic representations and their relation to real anatomy 1a. Cadaver “pin test” Given a structure marked within a cadaver, state the corresponding anatomical term. No 1b. Translating between visual representations and verbal representations Given a visual representation of a structure, state the corresponding anatomical term. No [And reverse: Given an anatomical term, identify the structure in a visual representation.] 1c. The language of anatomy Given a directional term, state the definition. [And reverse.] No • Superficial: toward the surface • Distal: away from the center Given a plane, state the definition. [And reverse.] No • Median: separates right lateral and left lateral regions at midline • Transverse: separates superior and inferior regions Given an anatomical root word, state the definition. [And reverse.] No • Brachial: of the arm • Orbital: of the eye Given a structure, state a synonym. Yes, synonyms are provided. • Pharyngotympanic tube: Eustachian tube • Nostril: naris Category 2: Classification Understanding how categories are used to describe anatomy, as well as characteristics of members of categories 2a. General vs. specific Given a specific structure, state the type of structure to which it belongs. Yes. Available in the class hierarchy • Elbow joint: synovial joint • Frontal bone: flat bone • Lateral meniscus: cartilage Given a type of structure and a defining characteristic, state the specific structure. No, unless encoded through class hierarchy or • Nerve that innervates the foot and leg: sciatic nerve other relationships. • Fluid in the lymphatic system: lymph • Joint that is the largest and most complex in the body: knee joint 2b. Cardinality Given a type of structure, state how many are present in the (canonical) body. No, although some information may be implied • Permanent teeth: 32 through the class hierarchy. • Major calyces per kidney: 2–3 • Layers of meninges surrounding brain and spinal cord: 3 Category 3: Canonical structure Understanding the location, composition, and demarcation of structures 3a. Whole-part relationships Given a structure, state its parts. Yes. Available in regional and constitutional part • Mandible: left ramus, right ramus, body of mandible hierarchies. • Lymph node: cortex, medulla • Cortex of lymph node: superficial cortex, paracortex Given a region of a structure, state the indicated part of that structure. No, although some information may be available • Lowest portion of the brainstem: medulla oblongata in definitions. • Triangular divisions of the medulla of the kidney: renal pyramids ICBO 2018 August 7-10, 2018 3 Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), Corvallis, Oregon, USA 4 Given a structure, state the types of tissues that compose it. Yes. Available in the constitutional part • Skin: epidermis, dermis hierarchies. • Nasal cartilage: hyaline cartilage 3b. Regional location of structure Given type of structure and region of the body, state the specific structures of that region. [And reverse.] Yes, if a region has been represented. For • Muscles of the neck: longus capitis, longus colli, rectus capitis anterior, … example, classes such as “Musculature of hand” • Foramen of the skull: right/left mental foramen, right/left infraorbital foramen, … have members that are individual muscles. • Lymph node groups of head and neck: submental, submandibular, occipital, … 3c. Spatial relationships among structures Given a structure and a spatial relation, state the associated structure(s). Most, using relationships such as surrounds, • Spinal cord passes through: foramen magnum lateral to, contains. • Femoral triangle contains: femoral vessels, femoral nerve, lymph nodes • Subarachnoid space contains: cerebrospinal fluid • Femoral artery bisects: femoral triangle • Serous pericardium surrounds: heart • Annular ligament surrounds: radial head • Deltopectoral triangle has superior boundary: deltoid • Ribcage is superficial to: lungs Given two structures, state the structure positioned between them. [And reverse.] No • Between the visceral and parietal layers of the peritoneum: peritoneal cavity • Between the lungs, immediately anterior to the heart: thymus • Dividing the right and left sides of the nasal cavity: nasal septum Given a structure (artery, vein, or nerve), state the structures it encounters along its course. No • Internal iliac artery: passes over pelvic brim and descends into pelvic cavity 3d. Connectivity between structures Given a structure and type of connectivity, state the associated structure(s). Yes, using relationships such as articulates with, • Scapula articulates with: clavicle, humerus has origin, has insertion, drains into. • Via the coronal suture, the frontal bone articulates with: right/left parietal bones • Carpometacarpal joint of thumb connects: trapezium and metacarpal of thumb • Anconeus has origin: lateral epicondyle • Anconeus has insertion: lateral side of olecranon, upper ulna • Anconeus has innervation: radial nerve • Right subclavian trunk drains into: right lymphatic duct • Occipital artery has origin (or source): external carotid Given two or more structures, state the structure they join or merge to form. An alternative modeling scheme using branches • Ventral and dorsal roots merge to form: spinal nerves and tributaries (as regional parts) is employed. Given a structure, state the two or more structures it branches, bifurcates, or divides into. An alternative modeling scheme using branches • After exiting the vertebral column, each spinal nerve divides into: dorsal ramus, ventral ramus, and tributaries (as regional parts) is employed. meningeal branch, communicating rami • Trachea bifurcates into: right and left main bronchi 3e. Clinical regions and landmarks (points, lines, borders) Given a region or structure, state the associated clinical regions. Yes, if modeled as regional parts. • Abdomen: epigastrium, umbilical region, suprapubic region, right and left lumbar regions … Given a structure, state the associated landmarks. [And reverse.] Some. For example, the class hierarchy contains • Points of the skull: right and left euryon, right and left coronale, right and left auriculare, … subclasses of “Anatomical point of skull”. Other • T2 (second thoracic vertebra): superior border of scapula landmarks may be captured using the scheme 3D structures are bounded by 2D surfaces, bounded by 1D lines, bounded by 0D points. 3f. Morphology Given a structure, describe its form. No, unless available in definition. • Duodenum: c-shaped part of the small intestine • Vertebral foramen of cervical vertebra: triangular space • Mandibular alveoli: sockets (for teeth) ICBO 2018 August 7-10, 2018 4 Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), Corvallis, Oregon, USA 5 Category 4: Variation in structure Understanding variations in human anatomy 4a. Sexual dimorphism Given a structure, describe the morphological differences between female and male structures. No • Sacrum: female sacra tend to be wider, shorter, and less curved than male sacra • Pelvic inlet: circular in females, heart-shaped in males 4b. Anatomical variation Given a structure, describe common variations. No • Branches from the aortic arch: in the most common variant, the left common carotid artery arises from the brachiocephalic trunk (instead of the aortic arch itself) • Sternalis: a muscle parallel to margin of the sternum, present in less than 10% of population Category 5: Developmental anatomy Understanding structural changes during gestation and early childhood 5a. Development of structures Given a structure, state the structure(s) it develops into or becomes part of. [And reverse.] Some. The relationships derives, matures into, • Urogenital ridge: pronephros, mesonephros, metanephros and transforms into have been used in recent • Neural tube: brain, spinal cord work. 5b. Germ layer origins Given a structure, state the germ layer it developed from. Some. The relationship germ origin has been • Kidney: intermediate mesoderm created. • Epithelium of gastrointestinal track: endoderm 5c. Developmental homologues in males and females Given a (male/female) structure, state the developmentally homologous (female/male) structure. No • Ovary: testis • Cowper’s gland: Bartholin’s gland 5d. Timing of developmental events Given a structure, state the stage (or time interval) at which it is present. [And reverse.] Some. The relationship developmental stage of • Three primary brain vesicles: 4th week has been used in recent work • Implantation: about 7 days about anatomical relationships, but may not be directly relevant [2] C. Rosse, J.L.V. Mejino Jr. “A reference ontology for biomedical to the needs of students in basic anatomy courses. informatics: The Foundational Model of Anatomy,” J Biomed Inform. 2003; 36(6):478–500. V. CONCLUSION [3] L.T. Detwiler, J.L.V. Mejino, J.F. Brinkley. “From frames to OWL2: Converting the Foundational Model of Anatomy,” Artif Intell Med. 2016; This work helps to make explicit ways in which the FMA 69:12–21. knowledge base could (and could not) support learning within a [4] J.F. Brinkley, J.S. Prothero, J.W. Prothero, C. Rosse. “A framework for university-level anatomy course. The work will assist the design of a knowledge-based systems in structural biology.” In: developers of educational applications in identifying types of Proceedings of the 13th Annual Symposium on Computer Application in Medical Care. 1989. p. 61–5. anatomical knowledge, as well as recognizing opportunities for [5] K. Eno, J.W. Sundsten, J.F. Brinkley. “A multimedia Anatomy Browser making use of a knowledge base such as the FMA. incorporating a knowledge base and 3D images.” In: Proceedings of the 15th Annual Annual Symposium on Computer Application in Medical ACKNOWLEDGMENT Care. 1991. p. 727–731. 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ICBO 2018 August 7-10, 2018 5 Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), Corvallis, Oregon, USA 6 Fig. 1. Two examples comparing review questions (from [12]) with content from the FMA. Example 1 (top) contrasts the language of the question ("is located in") with the formal modeling in the FMA. The term “trigone” requires knowledge of the context—it could refer to either the Trigone of urinary bladder or the Trigone of lateral lemniscus (a region of the metencephalon) in the FMA. Example 2 (bottom) makes use of knowledge that the nasal cavity is a constitutional part of the nose (A), the regional parts of the nasal cavity (B), and continuity relationships (C). Dotted blue lines indicate information not currently available in the FMA. [8] R.B. Trelease. “From chalkboard, slides, and paper to e-learning: How [13] R.M. 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