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Enabling Part-Whole Reasoning in Biomedical Terminologies

Enabling Part-Whole Reasoning in Biomedical Terminologies. Stefan Schulz MD Department of Medical Informatics University Hospital Freiburg, Germany. Objectives.

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Enabling Part-Whole Reasoning in Biomedical Terminologies

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  1. Enabling Part-Whole Reasoning in Biomedical Terminologies Stefan Schulz MD Department of Medical InformaticsUniversity Hospital Freiburg, Germany

  2. Objectives • Understand the ontological disctinction between taxonomic (is-a) and partonomic (part-of, has-part) hierarchies in the biomedical domain. • Understand the peculiarities of partonomic reasoning in comparison to taxonomic reasoning • Appreciate a formal ontology engineering approach that emulates partonomic reasoning by classification-based taxonomic reasoning • Discuss these findings in the light of the requirements of knowledge engineering in medicine and biology

  3. Objectives • Understand the ontological disctinction between taxonomic (is-a) and partonomic (part-of, has-part) hierarchies in the biomedical domain. • Understand the peculiarities of partonomic reasoning in comparison to taxonomic reasoning • Appreciate a formal ontology engineering approach that emulates partonomic reasoning by classification-based taxonomic reasoning • Discuss these findings in the light of the requirements of knowledge engineering in medicine and biology

  4. has part has part part of is a is a is a part of Double Hierarchical Structure:Anatomy Taxonomic Order (is a) Mereologic Order (part of, has part) Body Digit part of is a Toe Left Upper Extremity Finger is a is a part of Hallux Index Finger Left Forearm Thumb Left Hand is a is a has part has part part of part of Left Index Finger Left Thumb Left Radius Right Hallux Right Thumb

  5. is a is a is a Double Hierarchical Structure:Biochemistry Taxonomic Order (is a) Partonomic Order (part of, has part) Compound is a Salt Molecule is a is a has part has part Amino Acid N -NH2 Lipid Protein has part H is a -COOH Fat Membrane Protein is a has part Cell Membrane Gly Ala Val

  6. has part is a Double Hierarchical Structure:Events Taxonomic Order (is a) Partonomic Order (part of, has part) Temporal Order(follows) Cell Proliferation part of has part Interphase is a Mitosis Meiosis part of part of has part Differential Mitosis Meiosis I Meiosis II has part part of part of Prophase I Metaphase I

  7. is a is a is a Double Hierarchical Structure:Actions Taxonomic Order (is a) Partonomic Order (part of, has part) Temporal Order(follows) Surgery has part has part Laparoscopic Surgery Digestive Surgery Incision Suture is a is a Laparoscopic Appendectomy OpenAppendectomy has part has part McBurney Incision part of Removal of Appendix

  8. Conclusion • Ubiquity of partonomies in the ordering of biomedically relevant knowledge • Part-of and has-part relation capture notions of • physical parts (components) and wholes • constituents of substances • events and subevents • actions and parts of actions

  9. Partonomies in Medical Terminologies (I) • ICD: only taxonomic structure • Terminologia Anatomica: no explicit hierarchical relations • MeSH: broader/narrower hierarchy regardless of taxonomic or partonomic meaning • Read Codes, SNOMED CT: „Structure“ concepts subsume both an anatomical entity and its parts

  10. Partonomies in Medical Terminologies (II) • Digital anatomist: clear distinction between part-of/has-part and is-a. Recently sub-relations of part-of/has-part • GeneOntology: clear distinction between part-of and is-a. • OpenGalen: clear distinction between part-of and is-a. Formal reasoning across part-of • UMLS: mostly broader/narrower hierarchies, part-of/is-a restricted to anatomy (comes from Digital Anatomist)

  11. Objectives • Understand the ontological disctinction between taxonomic (is-a) and partonomic (part-of, has-part) hierarchies in the biomedical domain. • Understand the peculiarities of partonomic reasoning in comparison to taxonomic reasoning • Appreciate a formal ontology engineering approach that emulates partonomic reasoning by classification-based taxonomic reasoning • Discuss these findings in the light of the requirements of knowledge engineering in medicine and biology

  12. Commonalites ofTaxonomic Reasoning (I) • Classes vs. Instances: • Instances are concrete objects in the world, e.g. my left thumb, Peter‘s cat, Mr X‘s diabetes, ... • Classes denote abstract entities, e.g. all fingers, all cats, all occurrences of diabetes • The assignment of individuals to a class normally obeys defined properties.

  13. Commonalites ofTaxonomic Reasoning (II) • Class subsumption & Inheritance: • One class C1 subsumes an other one C2 if each of the instances of C2 is an instance of C1, too. • All properties of C2are inherited by C1 .Example: Birds can fly  eagles can fly • Multiple inheritance

  14. Commonalites ofTaxonomic Reasoning (III) • Transitivity & Roles: • C1 subsumes C2,, and subsumes C3C1 subsumes C3Example: lymphocyte is a leukocyte is a cell lymphocyte is a cell • Roles: attributes containing links to another concept, e.g. has-location Liver is a role for Liver disease, and is therefore inherited by all subsumees, e.g. Hepatitis, Hepatitis A etc.

  15. Commonalites ofPartonomic reasoning (I) • Mereology: reasoning about individuals, not abstract entities • part-of relation in its broadest sense • transitive: I1part-of I2, I2part-of I3,  I1part-ofI3 • reflexive: I1part-ofI2  I2part-ofI1 • Subrelations of part-of • non-reflexive: proper-part-of (common notion when describing the physical world) • non-transitive: combinations of subrelations (hand part-of musician part-of orchestra)

  16. Commonalites ofPartonomic reasoning (II) • Inverse relation: has-partI1part-ofI2I2has-partI1MyBrain part-ofMyHeadMyHeadhas-partMyBrain • Overlap: I1part-ofI2 , I1part-ofI3 I2 overlaps with I3MyBrain part-ofMyHead, MyBrain part-ofMyCNS MyHead overlapsMyCNS • Disconnected: I2 disconnected from I3 if they do not share any parts MyHead disconnected fromMyFoot, but alsoMyHead disconnected fromX‘s CNS

  17. Taxonomies (is-a)vs. Partonomies (part-of, has-part) • Main difference: • The is-a relation relates concepts (classes of individuals) • part-of and has-part relate individuals(concepts don‘t have parts !) • How to use the part-of relation in conceptual systems ? • Additional semantics needed !

  18. part of has-part Partonomic Relations between Individuals and Concepts • between individuals: My left thumb My left Hand (x,y): x part-of yy has-part x UMLS • between concepts:

  19. „Heart has-part Mitral Valve“ • Possible Meanings: • x,y: Heart(x)  Mitral-Valve(y)  x has-part y“a heart can have a mitral valve” • x:y: Heart(x)  Mitral-Valve(y)  x has-part y“every heart has a mitral valve as part” • x:y: x has-part y  y:x: y part-of x“If for every x there is a part y, then for every y there is an x it is part of

  20. A part-of.B B has-part.A Semantics for Partonomies in Concept Systems (I) hnw • Ahas-necessary-whole B: All instances of a concept A have the role part-of filled by an instance of B (necessary condition) hnp • Bhas-necessary-partA: All instances of a concept B have the role has-part filled by an instance of A (necessary condition) • Ahas-necessary-whole B does not necessarily imply B has-neceesary-part A

  21. Semantics for Partonomies in Concept Systems (II) hpw • Ahas-possible-wholeB: Instances of A and B are in the extension of the relation part-of hpp • Bhas-possible-partA: Instances of A and B are in the extension of the relation has-part . • Ahas-necessary-wholeB implies B has-possible-part A • Ahas-possible-wholeB implies B has-possible-part A • B has-necessary-part A implies Ahas-possible-wholeB • B has-possible-part A implies Ahas-possible-wholeB • A disconnected from B: nothing can be part of both and instance of A and of B

  22. Stipulations for Part/Whole Combinations C A hnw B B hnp A pw(A,B) dc(A,B) B hnw C A hnw C pw(A,B) pw(A,B) pw(A,B) C hnp B pw(A,B) C hnp A pw(A,B) pw(A,B) B pw(B,C) pw(A,B) pw(A,B) pw(A,B) pw(A,B) dc(B,C) dc(A,C) pw(A,B) pw(A,B) pw(A,B) A } hpw = has possible whole hpp = has possible part hnw = has necessary whole hnp = has necessary part pw = can be related by part-whole dc = disconnected (cannot have common parts)

  23. Examples for part-of / has-part Asymmetry • Everythumbis part of a hand, but not everyhandhas a thumb • Every spleen has lymph follicles, but not all lymph follicles are part of a spleen • Every cell nucleus is part of a cell but not every cell has a nucleus • Every amino acid has a -NH2 group, but not every -NH2 group is part of an amino acid • Every meiosis has a prophase, but not every prophase is part of a meiosis • Every defibrillation is part of a CPR, but not in every CPR there is a defibrillation

  24. Azygos Lobe Lung • Congenital Malformations Mitral valve Heart • Pathological Anatomy • Mass concepts Glioblastoma Brain Connective Tissue Liver • „Iatrogenic Anatomy“ • Multiple objects GastricMucosa Appendix Intestine Goblet cell Reasons for part-of / has-part Asymmetry • Anatomical Variations has-necessary-whole has-necessary-part • Unspecific subevents Append-ectomy Suture

  25. x 4 5 3 Role Propagation & Concept Specialization Let R be an arbitrary relation y part-of.z  x  R.y  x r.z Role Propagation: Concept Specialization: y part-of.z  w  R.z  x  R.y  x w z w AnatomicalConcept ("Whole") Concept Related to the "Whole" fracture-of Femur Fracture-of-Femur fracture-of part-of is-a 2 AnatomicalConcept ("Part") Concept Related to the "Part" fracture-of 1 Shaft-of-Femur Fracture-of-Shaft-of-Femur y

  26. inflammation-of inflammation-of inflammation-of Reasoning Anomalies within Partonomies Anatomical Concept Related Anatomical Concept (" Whole ") Concept (" Whole“) to the " Whole " inflammation-of Kidney Kidney Nephritis TRUE ! is -a part - of part-of Anatomical Concept Related Anatomical Concept Related "Part" Concept ("Part") to the "Part" Concept ("Part") to the inflammation-of inflammation-of Glomerulum Glomerulum Glomerulonephritis Glomerulonephritis Anatomical Concept Related Anatomical Concept (" Whole ") Concept (" Whole ") to the " Whole " inflammation-of Enteritis Intestine Intestine FALSE ! is -a part - of part - of Anatomical Concept Related Anatomical Concept Related Concept ("Part") to the "Part" Concept ("Part") to the "Part" inflammation-of Appendicitis Appendicitis Appendix Appendix Concept Related Anatomical Anatomical to the " Whole " Concept (" Whole ") Concept (" Whole ") perforation-of Perforation-of- Intestine Intestine Intestine perforation-of TRUE ! is -a part - of part - of Concept Related Anatomical Concept Related Anatomical to the "Part" Concept ("Part") to the "Part" Concept ("Part") perforation-of perforation-of Perforation-of-Appendix Perforation-of-Appendix Appendix Appendix

  27. Other examples insulin synthetase produce insulin Backbone Fracture fracture-of Backbone Vertebral Fracture fracture-of Vertebra Vertebra part-of Backbone beta cells has-part insulin synthetase  beta cells produce insulin  Vertebral Fracture fracture-of Backbone Langerhans islets has-part beta cells  Langerhans islets produce insulin Spinous Process Fracture fracture-of Vertebra Backbone Fracture fracture-of Backbone Spinous Process part-of Vertebra Vertebra part-of Backbone pancreas has-part Langerhans islets  pancreas produce insulin amputation of toe has-target toe  Spinous Process Fracture fracture-of Backbone toe part-of foot  amputation of toe has-target foot Pancreatectomy removal-of Pancreas Pancreas has-part Beta Cells Vertebra part-of Backbone foot part-of leg  amputation of toe has-target leg  Pancreatectomy removal-of Beta Cells amputation of toe las-location toe toe part-of foot  amputation of toe las-location foot

  28. Analysis of Reasoning Patterns • Propagation „downstream“: „removal-of“, „loss-of“, „death-of“ • Propagation „upstream“: „location-of“ • No propagation: „has-target“ • Uncertain propagation: „inflammation-of“, „fracture-of“, „excision-of“ Important: Most relations have shallow semantics: generalization of propagation behavior is difficult !

  29. Objectives • Understand the ontological disctinction between taxonomic (is-a) and partonomic (part-of, has-part) hierarchies in the biomedical domain. • Understand the peculiarities of partonomic reasoning in comparison to taxonomic reasoning • Appreciate a formal ontology engineering approach that emulates partonomic reasoning by classification-based taxonomic reasoning • Discuss these findings in the light of the requirements of knowledge engineering in medicine and biology

  30. Requirements for a Formal Approach • Retrieve all necessary parts (of necessary parts)* of a concept • Blood has-part ErythrocytesErythrocytes has-part ErythrocyteErythrocyte has-part HemoglobinBlood has-part Hemoglobin • Retrieve all necessary wholes (of necessary wholes)* of a concept • Nucleolus part-of Cell-NucleusCell-Nucleus part-of Eucaryotic-CellNucleolus part-of Eucaryotic-Cell • Control propagation of properties along part/whole hierarchies • Gas-Exchange function-of AlveolusAlveoli has-part AlveolusLung has-part Alveoli .Gas-Exchange function-of Lung . Mitosis function-of Eucaryotic-CellHuman-Body has-part Eucaryotic-CellMitosis function-of Human-Body ???

  31. Proposed Solution • Introduction of "reificator concepts" for each concept and each mereological role • Mereological reasoning via concept subsumption • Parsimonious language: concept subsumption, existential quantification, conjunction

  32. part_of has_part is_a is a part of is a part of is a part of Part-Of Hierarchies as Taxonomies Organism Body Part Left Upper Extremity Finger Left Hand Thumb Left Thumb

  33. part_of has_part is_a is a part of is a part of is a is a Part-Of Hierarchies as Taxonomies Organism Body Part Left Upper Extremity Finger Left Hand_Part Left Hand part of Thumb Left Thumb

  34. part_of has_part is_a is a part of is a is a is a is a Part-Of Hierarchies as Taxonomies Organism Body Part part of Left Upper Extremity_Part Left Upper Extremity Finger Left Hand_Part Left Hand part of Thumb Left Thumb

  35. part_of has_part is_a is a is a is a is a is a is a Part-Of Hierarchies as Taxonomies part of Organism Organism_Part Body Part part of Left Upper Extremity_Part Left Upper Extremity Finger Left Hand_Part Left Hand part of Thumb Left Thumb

  36. part of Part-Of Hierarchies by SEP triplets Schulz et al. AMIA 98; Hahn et al. AAAI 99 P („part“)-node(subsumes conceptshaving “Hand” as a necessary whole ) E („entity“)-node (The conceptHand itself) Hand_Part Hand

  37. part_of has_part is_a is a is a is a is a is a is a Part-Of Hierarchies as Taxonomies part of Organism Organism_Part Body Part part of Left Upper Extremity_Part Left Upper Extremity Finger Left Hand_Part Left Hand part of Thumb Left Thumb

  38. Organism_Structure part of Organism_Part Organism part of SEP-Triplet Finger_Structure is a is a is a is a is a is a is a is a part_of has_part part of Finger_Part Finger is_a Part-Of Reification by SEP triplets Schulz et al. AMIA 98; Hahn et al. AAAI 99 Necessary Whole for Finger and for Hand S ("structure") -node (common subsumer) Hand_Structure Necessary Whole for Finger Hand_Part Hand

  39. SEP Triplets • Emulate part-of-hierarchies by taxonomies • Emulate transitivity of concepts Finger is a Hand_Part, Hand_Partis a Arm_PartFinger is a Arm_Part • Necessary wholes can be inferred by taxonomic subsumption • What about necessary parts ?

  40. part_of has_part is_a is a is a is a Has-Part Hierarchies as Taxonomies Lymphocytes Body Part has-part Lymphatic Tissue Organ has-part Lymph Follicles Lymphatic Organ has-part Spleen

  41. part_of has_part is_a is a is a is a is a Has-Part Hierarchies as Taxonomies Lymphocytes Body Part has-part Lymphatic Tissue Organ has-part Lymph Follicles Lymph-Follicles_Includer has-part Lymphatic Organ Spleen

  42. part_of has_part is_a is a is a is a is a is a Has-Part Hierarchies as Taxonomies Lymphocytes Body Part has-part part of Lymphatic Tissue_Includer Lymphatic Tissue Organ Lymph Follicles Lymph-Follicles_Includer has-part Lymphatic Organ Spleen

  43. part_of has_part is_a is a is a is a is a is a is a Has-Part Hierarchies as Taxonomies Lymphocytes _Includer part of Lymphocytes Body Part part of Lymphatic Tissue_Includer Lymphatic Tissue Organ Lymph Follicles Lymph-Follicles_Includer has-part Lymphatic Organ Spleen

  44. necessary wholes of Cell necessary parts of Cell Organism CellmembraneCytoplasm has-part concepts havingCell as a necessary whole nucleus cell membrane cytoplasm cytoskeleton mitochondria (...) Tissue Organism (...) is a is a is a is a is a is a is a is a part_of concepts havingcell as a necessary part has_part is_a Extended SEP Si-node Sp-node Cell_Structure_I Cell_Structure_P P-node I-node part of Cell_Part Cell Cell_Includer E-node

  45. HSi HSp has-part has-part has-part has-part has-part part-of part-of part-of part-of part-of is-a is-a is-a is-a Hi HP Hand TSi TSp is-a is-a is-a is-a Ti TP Thumb part_of has_part is_a Example 1 BSi BSp is-a is-a is-a is-a Bi BP Bone PPBSi PPBSp is-a is-a is-a is-a PPBi PPBP PPB ofThumb PSi PSp is-a is-a is-a is-a Pi PP Peri-osteum PPB ofThumb Periosteum Bone

  46. HSi HSp has-part has-part has-part has-part has-part has-part has-part part-of part-of part-of part-of part-of part-of is-a is-a is-a is-a Hi HP Hand BSi BSp TSi TSp is-a is-a is-a is-a is-a is-a is-a is-a Bi BP Ti TP Bone Thumb PPBSi PPBSp is-a is-a is-a is-a PPBi PPBP PPB ofThumb PSi PSp is-a is-a is-a is-a Pi PP Peri-osteum part_of has_part is_a Example 1 HP Hand BSi TSi TSp Bone Thumb PPBSi is-a PPBi PPB ofThumb Pi Peri-osteum PPB ofThumb Periosteum Bone

  47. HSi HSp has-part has-part has-part has-part has-part part-of part-of part-of part-of part-of part-of part-of part-of is-a is-a is-a is-a Hi HP Hand BSi BSp TSi TSp is-a is-a is-a is-a is-a is-a is-a is-a Bi BP Ti TP Bone Thumb PPBSi PPBSp is-a is-a is-a is-a PPBi PPBP PPB ofThumb PSi PSp is-a is-a is-a is-a Pi PP Peri-osteum part_of has_part is_a Example 1 HP Hand TSp is-a BP TP Bone Thumb PPBSp PPB ofThumb PSp is-a Peri-osteum PPB ofThumb Periosteum Bone

  48. has-location HSi HSp has-part has-part has-part part-of part-of part-of is-a is-a is-a is-a Hi HP Hand TSi TSp is-a is-a is-a is-a Ti TP Thumb has-location part_of has_part is_a Example 2 (role propagation enabled) HSp Hand Fracture HP TSp TP PPBSi PPBSp PPBSp PPB Fracture is-a is-a is-a is-a PPBi PPBP PPB ofThumb Role Propagation enabled

  49. HSi HSp has-part has-part has-part part-of part-of part-of is-a is-a is-a is-a Hi HP Hand has-target TSi TSp is-a is-a is-a is-a Ti TP Thumb has-target part_of has_part is_a Example 3 (role propagation disabled) Amputation ofHand Amputation ofThumb PPBSi PPBSp is-a is-a is-a is-a PPBi PPBP PPB ofThumb Amputation of a body part targets the body part itself, not a part of it Amputation of Thumb = Amputation has-target.Thumb has-target.Thumb

  50. HSi HSp has-part has-part has-part part-of part-of part-of is-a is-a is-a is-a Hi HP Hand TSi TSp is-a is-a is-a is-a Ti TP Thumb part_of has_part is_a Example 4 (role propagation enabled) Loss ofHand Loss ofThumb Loss ofPPB PPBSi PPBSp is-a is-a is-a is-a PPBi PPBP PPB ofThumb Loss of a body implies the loss of all necessary parts Loss of Thumb = Loss of BodyPart loss-of.ThumbSi  loss-of.ThumbSi

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