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1
Semantic Network (SN) and Biomedical Ontology
Barry SmithDepartment of Philosophy, University at Buffalo
Institute for Formal Ontology and Medical Information Science
ifomis.org
2
AssumptionSN is designed to support automatic reasoning involving multiple UMLS source terminologies
Conclusion:Relations in SN are very important
3
Inheritance
Body part, Organ or Organ Component location_of Biologic Function
Therefore
Body Part, Organ or Organ Component location_of Disease or Syndrome
Alexa: “We can sometimes infer ... you have to bring some medical knowledge to bear”
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Part_of as a relation between classes is more problematic than is
standardly supposed
testis part_of human being ?
heart part_of human being ?
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Dr Humphreys: SN lists “possible significant relations”
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What we need for automatic inference is uniformly (necessarily)
significant relations
A is_a B
Every instance of A is an instance of B
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What we need for automatic inference is uniformly (necessarily)
significant relations
A is_a B
Every instance of A is an instance of B
We hope all is_a relations are exceptionless in this sense
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Some non-is_a relations are exceptionless in this sense
Fully formed anatomical structure contains body substance
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But most are not
Bacterium causes Experimental Model of Disease
Experimental Model of Disease affects Fungus
Experimental model of disease is_a Pathologic Function
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Bacterium causes Experimental Model of Disease
causes – Brings about a condition or an effect. Implied here is that an agent, such as for example, a pharmacologic substance or an organism, has brought about the effect. This includes induces, effects, evokes, and etiology.
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GALEN: Vomitus contains carrot
Gene Ontology: Menopause part_of Death
HL7: Individual Allele is_a Act of Observation
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Thesis: Biomedical ontology integration
will never be achieved through integration of meanings or concepts in people’s heads
the problem is precisely that different user communities use different concepts
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Promise of evidence-based medicine in the genomics era:
integrating biomedical terminologies with EHR data
need facility for dealing with time and instances (particulars, actual cases)
with this tumor here and now in this breast ...
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Move from associative relations between meanings to strictly
defined relations between the entities themselves
See: Smith, Ceusters, Klagges, Köhler, Kumar, Lomax, Mungall, Neuhaus, Rector, Rosse
“Relations in Biomedical Ontologies”Genome Biology, in press
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Clear instructions
Fewer mistakes
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Key idea
To define ontological relations like SN’s
part_of, contains, adjacent-to
we need also to take account of instances and time
(= link to Electronic Health Record)
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Kinds of relations
<class, class>: is_a, part_of, ...
<instance, class>: this explosion instance_of the class explosion
<instance, instance>: Mary’s heart part_of Mary
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Kinds of relations
<class, class>: is_a, part_of, ...
<instance, class>: this explosion instance_of the class explosion
<instance, instance>: Mary’s heart part_of Mary = instance-level part_of is a primitive (you can’t define everything, on pain of circularity)
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part_of
A part_of B =def.
for all a and all t,
if a is an instance of A at time t,
then there is some instance b of B
such that a is an instance-level part_of b at t
ALL-SOME STRUCTURE
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part_of
A part_of B =def.
for all a and all t,
if a is an instance of A at time t,
then there is some instance b of B
such that a is an instance-level part_of b at t
ALL-SOME STRUCTURE
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testis part_of human being - NO
human testis part_of human being - YES
human ovary part_of human being - YES
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transformation_of
c at t1
C
c at t
C1
time
same instance
mature RNA transformation_of pre-RNA
fetus transformation_of embryo
adult transformation_of child
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transformation_of
C2 transformation_of C1 =def. any instance
of C2 was at some earlier time an instance
of C1
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Note the problem of inverses here
Not every child becomes transformed into an adult
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The Granularity Gulf as an obstacle to reasoning
most existing data-sources are of fixed, single granularity
many (all?) clinical phenomena cross granularities
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C
c at t c at t1
C1
embryological development
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C
c at t c at t1
C1
tumor development
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Advantages of the methodology of enforcing commonly accepted
coherent definitions
promote quality assurance (better coding)
guarantee automatic reasoning across ontologies and across data at different granularities, from molecule to clinic
yields direct connection to times and instances in EHR
29
Automatic reasoning
non-is_a relations are all-some relations A R B =def for all instances a of A there is some instance b
of B such that a r bwhere r is some instance-level relation
If you know A R B, and you know that a is an instance of A, then you know that there is some instance b of B
and inheritance is unrestrained (exceptionless)if you know B R C you can reason with this instance b to
infer that there is some C, and so on
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Conclusions for SN
Remove the merely ‘possibly significant relations’ (these are less than facts)
Reform definitions (remove circularity)
Remove those relations, such as prevents which cannot be given a coherent instance-based all-some definition
Reform treatment of inverses
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preventsDefinition: Stops, hinders or eliminates an
action or condition.Inverse: prevented_by
contraception prevents pregnancy
pregnancy prevented_by contraception
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Better treatment of prevention
contraception
causes
prevention_of_pregnancy
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Reform treatment of inverses
adjacent_to – “Close to, near or abutting another physical unit with no other structure of the same kind intervening. This includes adjoins, abuts, is contiguous to, is juxtaposed, and is close to.”
Inverse: adjacent_to
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Adjacent_to is not its own inverse
nuclear membrane adjacent_to cytoplasm
BUT NOT:
cytoplasm adjacent_to nuclear membrane
ovary adjacent_to parietal pelvic peritoneum
BUT NOT:
parietal pelvic peritoneum adjacent_to ovary
35
Better treatment of inverses
Use preceded_by not precedes as primary relation
preceded_by supports inheritance (supports automatic reasoning)
embryological development precedes birth NOT EXCEPTIONLESS
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If NLM does not reform SN
in something like this way, then someone else will build a competitor to integrate the UMLS for purposes of automatic reasoning and integration across granularities
37http://ifomis.org
The End
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Human-Caused Phenomenon or Process (Environmental Effect of Humans):
Phenomenon and Process put together
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Entity Event
ActivityPhenomenon or
Process
Physical Object
Conceptual Entity
UMLS Semantic Types
40
41
gene part_of cell component
body system conceptual_part_of
fully formed anatomical structure
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conceptual entity
idea or concept
functional concept
body system
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But:
Gene or Genome is defined as: “A specific sequence … of nucleotides along a molecule of DNA or RNA …”
and
nucleotide sequence is_a conceptual entity
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entity
physical conceptual object entity
idea or concept
functional concept
body system
confusion of entity and concept
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Functional Concept:
Body system is_a Functional Concept.
but:
Concepts do not perform functions or have physical parts.
46
This:
is not a concept
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UMLS-SN Semantic Relation
producesDefinition: Brings forth, generates or creates. Inverse: produced_by
artificial insemination produces pregnancy
pregnancy produced by artificial insemination
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Definitions
conceptual_part_of – Conceptually a portion, division, or component of some larger whole.
should not be circular
49
part_of – “Composes, with one or more other physical units, some larger whole. This includes component of, division of, portion of, fragment of, section of, and layer of.” Inverse: has-part
contains – “Holds or is the receptacle for fluids or other substances. This includes is filled with, holds, and is occupied by.” Inverse: contained_in
consists_of – “Is structurally made up of in whole or in part of some material or matter. This includes composed of, made of, and formed of.” Inverse: constitutes
connected_to – “Directly attached to another physical unit as tendons are connected to muscles. This includes attached to and anchored to.” Inverse: connected_to
interconnects – “Serves to link or join together two or more other physical units. This includes joins, links, conjoins, articulates, separates, and bridges.” Inverse: interconnected by
branch_of – “Arises from the division of. For example, the arborization of arteries.” Inverse: has_branch
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tributary_of – “Merges with. For example, the confluence of veins.” Inverse: has_tributary
ingrediant_of – “Is a component of, as in a constituent of a preparation.” Inverse: has_ingredient
physically_related_to – “Related by virtue of some physical attribute or characteristic.” Inverse: physically_related_to
51
connected_to and connects not clearly defined
ingrediant_of doesn’t fit
52
temporally_related_to – (co-occurs_with; precedes): The relevant definitions are as follows:
precedes – “Occurs earlier in time. This includes antedates, comes before, is in advance of, predates, and is prior to.” Inverse: follows
co-occurs_with – “Occurs at the same time as, together with, or jointly. This includes is co-incident with, is concurrent with, is contemporaneous with, accompanies, coexists with, and is concomitant with.” Inverse: co-occurs_with
temporally_related_to – “Related in time by preceding, co-occuring with, or following.” Inverse: temporally_related_to
53
Too unspecific. KIF annotations?
affects – (interacts_with; disrupts; prevents; complicates; manages; treats): The relevant definitions are as follows:
interacts_with – “Acts, functions, or operates together with.” Inverse: interacts_withdisrupts – “Alters or influences an already existing condition, state, or situation. Produces a
negative effect on.” Inverse: disrupted_byprevents – “Stops, hinders or eliminates an action or condition.” Inverse: prevented_bycomplicates – “Causes to become more severe or complex or results in adverse effects.”
Inverse: complicated_bymanages – “Administers, or contributes to the care of an individual or group of individuals.”
Inverse: managed_bytreats – “Applies a remedy with the object of effecting a cure or managing a condition.”
Inverse: treated_byaffects – “Produces a direct effect on. Implied here is the altering or influencing of an existing
condition, state, situation, or entity. This includes has a role in, alters, influences, predisposes, catalyzes, stimulates, regulates, depresses, impedes, enhances, contributes to, leads to, and modifies.” Inverse: affected_by
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interacts_with need not be affects
occurs_in – (process_of): The relevant definitions are as follows:
process_of – “Action, function, or state of.” Inverse: has_process
occurs_in – “Takes place in or happens under given conditions, circumstances, or time periods, or in a given location or population. This includes appears in, transpires, comes about, is present in, and exists in.” Inverse: has_occurrence
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No reason why one is a subclass of the other
brings_about – (produces, causes): The relevant definitions are as follows:
produces – “Brings forth, generates or creates. This includes yields, secretes, emits, biosynthesizes, generates, releases, discharges, and creates.” Inverse: produced_by
causes – “Brings about a condition or an effect. Implied here is that an agent, such as for example, a pharmacologic substance or an organism, has brought about the effect. This includes induces, effects, evokes, and etiology.” Inverse: caused_by
brings_about – “Acts on or influences an entity.” Inverse: brought_about_by
performs – (carries_out, practices, exhibits): The relevant definitions are as follows:
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carries_out – “Executes a function or performs a procedure or activity. This includes transacts, operates on, handles, and executes.” Inverse: carried_out_by
practices – “Performs habitually or customarily.” Inverse: practiced_by
exhibits – “Shows or demonstrates.” Inverse: exhibited_byperforms – “Executes, accomplishes, or achieves an
activity.” Inverse: performed_by
Difference between “performs” and “carries out” unclear
57
functionally_related_to – (manifestation_of; affects; occurs_in; uses; indicates; result_of; brings_about; performs): The relevant definitions are as follows:
manifestation_of – “That part of a phenomenon which is directly observable or concretely or visibly expressed, or which gives evidence to the underlying process. This includes expression of, display of, and exhibition of.” Inverse: has_manifestation
uses – “Employs in the carrying out of some activity. This includes applies, utilizes, employs, and avails.” Inverse: used_by
indicates – “Gives evidence for the presence at some time of an entity or process.” Inverse: indicated_by
result_of – “The condition, product, or state occurring as a consequence, effect, or conclusion of an activity or process. This includes product of, effect of, sequel of, outcome of, culmination of, and completion of.” Inverse: has_result
functionally_related_to – “Related by the carrying out of some function or activity. ” Inverse: functionally_related_to
58
analyzes – (assesses_effect_of): The relevant definitions are as follows:
assesses_effect_of – “Analyzes the influence or consequences of the function or action of.” Inverse: assessed_for_effect_by
analyzes – “Studies or examines using established quantitative or qualitative methods. ” Inverse: analyzed_by
conceptually_related_to – (property_of; conceptual_part_of; evaluation_of; measures; diagnoses; issue_in; derivative_of; developmental_form_of; degree_of; measurement_of; method_of; analyzes): The relevant definitions are as follows:
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property_of – “Characteristic of, or quality of.” Inverse: has_propertyconceptual_part_of – “Conceptually a portion, division, or component of some larger whole.” Inverse:
has_conceptual_partevaluation_of – “Judgment of the value or degree of some attribute or process.” Inverse:
has_evaluationmeasures – “Ascertains or marks the dimensions, quantity, degree, or capacity of.” Inverse:
measured_bydiagnoses – “Distinguishes or identifies the nature or characteristics of.” Inverse: diagnosed_byissue_in – “Is an issue in or a point of discussion, study, debate, or dispute.” Inverse: has_issuederivative_of – “In chemistry, a substance structurally related to another or that can be made from the
other substance. This is used only for structural relationships. This does not include functional relationships such as metabolite of, by product of, nor analog of.” Inverse: has_derivative
developmental_form_of – “An earlier stage in the individual maturation of.” Inverse: has_developmental_form
degree_of – “The relative intensity of a process or the relative intensity or amount of a quality or attribute.” Inverse: has_degree
measurement_of – “The dimension, quantity, or capacity determined by measuring.” Inverse: has_measurement
method_of – “The manner and sequence of events in performing an act or procedure.” Inverse: has_method
conceptually_related_to – “Related by some abstract concept, thought, or idea.” Inverse: conceptually_related_to
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spatially_related_to – (location_of; adjacent_to; surrounds; traverses): The relevant definitions are as follows:location_of – “The position, site, or region of an entity or the site of a process.” Inverse: has_locationadjacent_to – “Close to, near or abutting another physical unit with no other structure of the same kind intervening. This includes adjoins, abuts,
is contiguous to, is juxtaposed, and is close to.” Inverse: adjacent_tosurrounds – “Establishes the boundaries for, or defines the limits of another physical structure. This includes limits, bounds,
confines, encloses, and circumscribes.” Inverse: surrounded_bytraverses – “Crosses or extends across another physical structure or area. This includes crosses over and crosses through.”
Inverse: traversed_byspatially_related_to – “Related by place or region.” Inverse: spatially_related_to
associated_with – (physically_related_to, temporally_related_to, functionally_related_to, conceptually_related_to, spatially_related_to): associated_with is defined as “has a significant or salient relationship to.” Inverse: associated_with
DiscussionThe inclusion of the opposition Chemical Viewed Structurally and Chemical Viewed Functionally raises the suggestion that SN might be better
interpreted as clas‑sifying not entities but rather the concepts we have of such entities. The concepts we use when referring to chemicals can after all be divided quite naturally un‑der these two headings. Then, however, the root nodes of SN should be not: Entity and Event, but rather: Entity Concept and Event Concept, and the latter should themselves be re-assigned to the position of daughters of a new root Concept. A restructuring along these lines would how‑ever in other ways conflict radically with SN’s current architecture. Above all, it would con‑tradict the fact that Idea or Concept is already itself a subnode of Conceptual Entity. It would also contradict explicit statements to the effect that SN is ‘an upper-level ontology … in which all concepts are given a consistent and semantically coherent representation’. [7]
ConclusionA number of proposals have been advanced to increase SN’s effectiveness as a terminology integration platform that can support enhanced
reasoning and information retrieval. Thus [8] argues that UMLS lacks the requisite granularity, semantic types and relationships for comprehensively and consistently representing anatomical concepts in machine readable form. [9] and [10] propose enhancing the efficiency of UMLS-based reasoning systems via a clustering of SN nodes to yield more coarse-grained partitions of the network.
Our proposal is that SN’s power to support terminology-based reasoning can be enhanced through a reclassification along the lines sketched in the above. As an example of how such a reclassification would support inferences currently blocked, consider the way in which SN currently views tissues and cells as physical parts of organs, but views these organs themselves as mere conceptual parts of body systems, which are in turn conceptual parts of fully-formed anatomical structures, which are in turn physical parts of organisms. When we reclassify Body System as a Physical Entity, there is no longer a need for the distinction between conceptual and physical part-of relations. Reasoning systems can thus exploit the full power of mereology, including the rules governing transitivity of part-of.
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