Temporal information is pervasive and crucial in medical records and other clinical text, as it formulates the development process of medical conditions and is vital for clinical decision making. However, providing a holistic knowledge representation and reasoning framework for various time expressions in the clinical text is challenging. In order to capture complex temporal semantics in clinical text, we propose a novel Clinical Time Ontology (CTO) as an extension from OWL framework. More specifically, we identified eight time-related problems in clinical text and created 11 core temporal classes to conceptualize the fuzzy time, cyclic time, irregular time, negations and other complex aspects of clinical time. Then, we extended Allen's and TEO's temporal relations and defined the relation concept description between complex and simple time. Simultaneously, we provided a formulaic and graphical presentation of complex time and complex time relationships. We carried out empirical study on the expressiveness and usability of CTO using real-world healthcare datasets. Finally, experiment results demonstrate that CTO could faithfully represent and reason over 93% of the temporal expressions, and it can cover a wider range of time-related classes in clinical domain.

Time-related information is essential part of in-patient medical records, doctor prescriptions and other clinical text. It describes the sequence of symptoms and treatments received by patients and is crucial in clinical decision-making and medical research [1, 2]. However, natural language expressions about time and temporal relation concepts are diverse and can vary with different contexts and writers. Current research on temporal knowledge representation in text mainly focused on news or open domain [3, 4, 5]. However, due to the distinct features in the medical domain, the research results from the news domain or open domain cannot be applied directly to the medical domain [6].

Temporal knowledge representation is challenging and has been discussed extensively. Generally, OWL-Time [7] can be used to represent instant and interval, and possibly Allen's 13 temporal relations [8]. Reasoning engine CHRONOS [9] can be used for relation inference, inconsistency detection and path consistency check. However, these ontologies do not cover some important features, such as irregular, granular time, and modality. These ontologies designed for general domains are not adequate enough for specific domains such as healthcare [10]. To fill the gap between general tools and the clinical domain, Tao et al. [11] proposed temporal ontology CNTRO. After that, Li et al. [12] extended it and proposed the TEO ontology. They leveraged a Java-based TEO reasoner to realize complex timeline reasoning. We can use it to represent granular time, instant, interval and incomplete time. However, there is also some uncertain and irregular time in the clinical domain, such as “take pills around 6 a.m.,” and “The patient received rehabilitation training twice a day last year, and once every 2 days this year.” The former describes an uncertain time. There is no precise time point for the occurrence of an event, but there is still a rough range. For example, “4 p.m.” is not in the range. The latter one describes an irregular time, and it represents the phased change of the event.

Another challenge is the representation of inference queries with complex time. For example, if we have known that “Patient A had surgery yesterday and was advised by his doctor to do 20 minutes of rehab around 9:00 am every morning,” then for the question, “What should Patient A do at 9:05 am this morning?” Humans can quickly answer it. Nevertheless, all of those ontologies mentioned above cannot get the answer. Based on this, we proposed Clinical Time Ontology (CTO), which aims to represent the complex temporal information in clinical texts.

The contribution of this paper can be summarized as follows:

  1. We defined 11 core time classes, and proposed a robust ontology modeling complex temporal concepts and relations;

  2. We introduced the concept of complex time related classes and the concept of complex temporal relations using the temporal logic language and depicted them in the form of diagrams and formulas;

  3. We invited three annotators to annotate the real data, and evaluated the result by IAA metrics and the coverage ability of the ontology. And The results show that the CTO ontology can cover a wider range of time-related classes and temporal relationships in the medical record data, and it can faithfully represent 93% time-related classes and temporal relationships.

The remainder of this paper is organized as follows: Section 2 discusses the related work; Section 3 summarizes eight types of time-related problems in clinical domain and also introduces 11 core time classes; Section 4 elaborates CTO ontology's design principles; Section 5 presents the definition of complex time classes and complex time relations in terms of semantics; Section 6 depicts data sets, experiments and comparisons with other ontologies about representation; Section 7 summarizes of this paper.

The representation of time information has been discussed extensively in Semantic Web. In this paper, we discuss general purpose of temporal ontologies and medical domain temporal ontologies separately.

2.1 General Domain Temporal Ontologies

Hobbs et al. [13] proposed the DAML ontology of time that integrates first-order predicate calculus for topological temporal relations such as intervals, events, dates and times. Based on which, OWL-Time ontology [7] provides vocabularies for instant and interval, duration, datetime, and Allen's time relations [8] in terms of time ontologies. However, OWL-Time focuses on definitive, accurate timestamp-based time representation and cannot cater to complicated time expressions (e.g., periodic time, fuzzy time, and multi-granularity time representation).

SWRL temporal ontology [14] defined OWL entities to represent interval-based time information in OWL, and provided OWL entities to represent all entities defined by the model. It contains propositions, effective time (instants and interval), granularity and duration, and also contains a set of SWRL built-in functions that can be used to reason about time information. Eleftherios et al. [9] proposed CHRONOS, a system for reasoning about time information in OWL ontologies. CHRONOS provides both qualitative and quantitative information representation, enabling inferring implied relations, detecting inconsistencies, and ensuring path consistency. Vadim et al. [15] proposed PSI-Time Ontology, which can represent concepts of some complex time such as relativist and absolutist duration, periodic time intervals, interval phases, open time, linear time, and the relations, point-to-point, point-to-interval and interval-to-interval. However, they do not cover all time-related aspects in clinical domain, and are difficult to link to structured or unstructured clinical data.

2.2 Clinical Domain Temporal Ontologies

Tao et al. [11] proposed the Clinical Narrative Temporal Relations Ontology (CNTRO), which aims to fill the semantic gap in temporal modeling in the clinical domain. It provides vocabularies such as Event, Time, Duration, Granularity, Precision, and TemporalRelationStatement. Li et al. [12] extended CNTRO to develop a novel Temporal Event Ontology (TEO), which can formally represent and reason about structured and unstructured time information, supporting flexible temporal relationship representation and reasoning. However, TEO is still insufficient in terms of representing and reasoning on fuzzy time, irregular time, and complex relationships.

Representation of complex time (e.g., fuzzy time, irregular collection time, etc.), subjectivity, negation, and complex temporal relationships is significant challenge for temporal ontologies. Based on this, we propose Clinical Time Ontology (CTO), which aims to achieve inference and query complex temporal information problems and mine more relationships between them.

Temporal information is pervasive in clinical data. However, it is nontrivial to capture temporal information in unstructured text from clinical data, which is pivotal to healthcare decision making. For example, a patient's self-description and previous medical history can be obtained from the medical record data. It could take the form of a paragraph in natural language, and healthcare providers need to digest this paragraph to understand the chronological events it implies, so as to make a diagnosis or treatment plan. Formulating a semantic framework for time-related expressions in clinical text is a first step towards automated reasoning and decision support. In this section, we first categorize the time-related expressions in typical clinical text, and then we provide a set of key time concepts.

3.1 Complicated Expressions of Time in Clinical Text

We refer to TIDES [16] for a basic classification of temporal expressions, then we further refine the categorization of temporal expressions in the clinical domain based on our observation over 3.5K anonymized real-world clinical records. We identified different types of time descriptions from the clinical text according to different temporal aspects, including completeness, accuracy, repetition, subjectivity, etc. Regarding to the completeness, there can be complete or incomplete time; to the accuracy, there can be accurate or fuzzy time; to the repetition, there can be cyclic or irregular time. And based on this, we divided time into 5 types (e.g., absolute time, lack information time, fuzzy time, cyclic time, and irregular time). And then, we also obtained three qualitative questions, such as questions of subjectivity (e.g., whether it is worth believing), questions of temporal relationships (e.g., before, after, etc.), and questions of negation temporal relationships (e.g., not before, not after, etc.). In general, we summarized eight problems, which are shown in Table 1.

Table 1.
Classification and examples of time-related problems in clinical texts.
IdTypeExampleAnswer
Absolute Time Problems When was Patient-A hospitalized? July 1, 2021 
Lack Information Time Problems (Relative Time and Incomplete Time) (Patient-A is known that have been hospitalized on July 1, 2021, and developed symptoms 3 days prior to hospitalization.) When did Patient-A present with symptoms? June 28, 2021 
Fuzzy Time Problems (Patient-A is known to have surgery on July 1, 2021, and people usually recover as early as 3 days and as late as 5 days after surgery) When is the earliest Patient-A can be discharged? July 4, 2021 
Cyclic Time Problems When is the following review of Patient-A? July 3, 2021 
Irregular Time Problems When did Patient-A's first course of treatment end? July 1, 2021 
Subjective Problems Is this time subjectively perceived by the patient or objectively recorded? Patient subjectively perceived 
Temporal Relation Problems (Patient-A is known to be hospitalized on July 1, 2021, and Patient-B is known to be hospitalized on July 12, 2021) Who was hospitalized first, Patient A or B? Patient-A 
Negation Problems Whose operation event is not before Patient-A's? Patient-B, Patient-C 
IdTypeExampleAnswer
Absolute Time Problems When was Patient-A hospitalized? July 1, 2021 
Lack Information Time Problems (Relative Time and Incomplete Time) (Patient-A is known that have been hospitalized on July 1, 2021, and developed symptoms 3 days prior to hospitalization.) When did Patient-A present with symptoms? June 28, 2021 
Fuzzy Time Problems (Patient-A is known to have surgery on July 1, 2021, and people usually recover as early as 3 days and as late as 5 days after surgery) When is the earliest Patient-A can be discharged? July 4, 2021 
Cyclic Time Problems When is the following review of Patient-A? July 3, 2021 
Irregular Time Problems When did Patient-A's first course of treatment end? July 1, 2021 
Subjective Problems Is this time subjectively perceived by the patient or objectively recorded? Patient subjectively perceived 
Temporal Relation Problems (Patient-A is known to be hospitalized on July 1, 2021, and Patient-B is known to be hospitalized on July 12, 2021) Who was hospitalized first, Patient A or B? Patient-A 
Negation Problems Whose operation event is not before Patient-A's? Patient-B, Patient-C 

“Absolute time” is a point or duration that can be represented separately on the time axis; “Lack information time” means the sentence which describes the time information about the event is incomplete, and it includes two subcategories, which are “relative time” and “incomplete time.” The former means that we need to find the reference time and get the real time by calculating. The latter is commonly used to describe a time interval but without complete information (e.g., lack start time or end time); “Fuzzy time” indicates that there exist approximate and vague modifiers in sentence, and it may be an instant or an interval; “Cyclic time” means that the event is repeated and the occurrence is regular, and it may be a collection of multiple instants or intervals; “Irregular time” means that the event is repeated, but not regular, and its items may be instants or intervals or collections.

3.2 Time Types

The temporal expressions listed in Table 1 can be addressed using a combination of syntactic forms and/or semantic concepts. Syntactically, all temporal expressions can use 1, 2 or more timestamps to denote the relevant instance, interval or repetitions, additionally, temporal concepts and relations can have modifiers to express beliefs or polarity. Semantically, a temporal concept can be absolute, fuzzy, relative, or periodic, etc. Based on the first five problems in Table 1, we categorized the time. Problems 6 and 8 motivate the subjective and negation modifiers. We analyze the combinations of the above syntactical and semantic axis of temporal concepts and relations and organize them in Table 2 with correlations to the temporal expression types listed in Table 1.

Table 2.
Time types obtained by combinations of the syntactical and semantic axis of temporal concepts and relations.
Syntactic FormsSemantic ConceptsExampleRelated Problems in Table1
Instant Absolute Instant January 1, 2021 10:20:30. Type 1 
 Relative Instant This time yesterday. Type 2 
 Fuzzy Instant About 6:00 this morning. Type 3 
Interval Absolute Interval January 1, 2021, to February 1, 2021. Type 1 
 Relative Interval Yesterday from 9:00 to 10:00. Type 2 
 Fuzzy Interval The patient may have started exercising at 9:00 and finished around 10:00. Type 3 
 Incomplete Interval The patient stopped taking the medication yesterday. Type 2 
Collection Periodic Instant Collection Every morning at 8 am. Type 4 
 Irregular Instant Collection The patient had vomited at 10:00 am, 11:00 am, and 3:00 pm today. Type 5 
 Periodic Interval Collection Once a day, 15 minutes each time. Type 4 
 Irregular Interval Collection The patient started yesterday at 20:00 and exercised for an hour. Today he started at 19:00 and only exercised for half an hour. Type 5 
Modifier Negation Not during this week. Type 8 
 Subjective The time is subjectively described by the patient. Type 6 
Syntactic FormsSemantic ConceptsExampleRelated Problems in Table1
Instant Absolute Instant January 1, 2021 10:20:30. Type 1 
 Relative Instant This time yesterday. Type 2 
 Fuzzy Instant About 6:00 this morning. Type 3 
Interval Absolute Interval January 1, 2021, to February 1, 2021. Type 1 
 Relative Interval Yesterday from 9:00 to 10:00. Type 2 
 Fuzzy Interval The patient may have started exercising at 9:00 and finished around 10:00. Type 3 
 Incomplete Interval The patient stopped taking the medication yesterday. Type 2 
Collection Periodic Instant Collection Every morning at 8 am. Type 4 
 Irregular Instant Collection The patient had vomited at 10:00 am, 11:00 am, and 3:00 pm today. Type 5 
 Periodic Interval Collection Once a day, 15 minutes each time. Type 4 
 Irregular Interval Collection The patient started yesterday at 20:00 and exercised for an hour. Today he started at 19:00 and only exercised for half an hour. Type 5 
Modifier Negation Not during this week. Type 8 
 Subjective The time is subjectively described by the patient. Type 6 

“Absolute Instant” is a point in time, with no fuzzy (e.g., about, server) and relative modifiers (e.g., ago, after); “Relative Instant” is a point in time, but with relative modifiers; “Fuzzy Instant” is a point in time, but with fuzzy modifiers;

“Absolute Interval” is a duration in time, whose start and end time are “Absolute Instant” instances; “Relative Interval” is a duration in time in which at least one of the start or end time is a “Relative Instant” instance; “Fuzzy Interval” is a duration in time, and the condition is satisfied as long as one of its three components (duration quantity, start time and end time) is with a fuzzy modifier, even though its start time may make it like a “Relative Interval” instance; “Incomplete Interval” is a duration in time with only one of the three components, whether or not the component is with a modifier;

“Periodic Instant Collection” is a collection of points in time, which is commonly used to describe the time for the events in cycle, and occurrence time is also a point in time; “Irregular Instant Collection” is a collection of points in time, commonly used to describe the time for events with irregular occurrence time, and the occurrence time is a point in time, and its item can also be some “Periodic Instant Collection” instances; “Periodic Interval Collection” and “Periodic Instant Collection” are more similar, the difference is that the occurrence time of the former is a duration; “Irregular Interval Collection” is similar with “Irregular Instant Collection,” but the occurrence time is a duration, and its item can also be some “Periodic Interval Collection” instances.

We divided the time appearing in the clinical field into the 11 main types mentioned above. And there is no intersection between them. For negation and subjective modifiers, we treat them as a property of temporal instances.

We developed the Clinical Time Ontology (CTO) for semantic representation and reasoning over the temporal aspects discussed in Section 3. In this section, we elaborate on its module design.

4.1 Overview

Temporal concepts cannot be utilized alone, so we need to bind them with the concept of Events. Therefore, we defined the class Event to represent clinical events. It has sub-classes such as HospitalizationEvent, DischargeEvent, etc. We can extend the list of sub-classes upon requirements. According to Table 2, we can obtain 11 classes, such as AbsoluteInstant, RelativeInstant, Fuzzylnstant, Absolutelnterval, etc. They are both the sub-class of Time. Class Event and class Time can be linked by object property hasTime. We refer to the OWL-Time and TEO ontologies when designing our ontology. We have some common and different concepts. For example, class AbsoluteInstant is the same as Instant in OWL-Time, class TimeQuantity is the same as Duration in TEO. However, class IrregularInstanCollection does not exist in their ontologies. Figure 1 shows the taxonomy of CTO and the relationship with OWL-Time and TEO (using sameAs).

Core Taxonomy of Clinical Temporal Ontology.

Figure 1.
Core Taxonomy of Clinical Temporal Ontology.
Figure 1.
Core Taxonomy of Clinical Temporal Ontology.
Close modal

4.2 Module Design

We divided time into four modules, which are Instant, Interval, InstantCollection, and IntervalCollection.Figure 1 illustrates this, and more details can be obtained as followed:

4.2.1 Instant

Class Instant has three subclasses: AbsoluteInstant, Relativelnstant, and Fuzzylnstant, they are respectively designed for absolute instant time, relative instance time, and fuzzy instance time. There exist a number of properties that describe time at a granular level, such as second, minute, hour. Class TimeUnit is designed for representing time's precision, which means the smallest granularity unit of time.

Object property prefixAnchor is designed to give a qualitative representation of the relationship between the moment and its reference moment. Object property relativeQuantity can quantitatively represent the length of difference. For example, “Hospitalized on July 1, 2021, and started showing significant symptoms three days ago.” “Three days ago” is a relative time description, we can set it to <relativeInstantl.> “July 1, 2021” is an AbsoluteInstant instance, and it is the prefixAnchor of <relativeInstantl.> And the relativeQuantity of <relativeInstant1> is “3 days.” Figure 2 illustrates this case.

Relative Time.
Figure 2.
Relative Time.

For fuzzy time, object property leftAnchor can indicate its earliest possible occurrence time, and rightAnchor can indicate the latest one. For example, “Early January” is a fuzzy description, and we can set its leftAnchor to <absoluteInstant1>, which for “1, January,” and set its rightAnchor to <absoluteInstant2>, which for “10, January.” Figure 3 illustrates this case.

Fuzzy Instant.
Figure 3.
Fuzzy Instant.

4.2.2 Interval

Class Interval has four subclasses: AbsoluteInterval, RelativeInterval, FuzzyInterval, and IncompleteInterval. The former two both have object property startTime, endTime, and durationQuantity. The differences between them are that their startTime's and endTime's ranges are not the same class.

Object property minDurationQuantity and object property maxDurationQuantity are designed for fuzzy interval, and they indicate the minimum possible duration and the maximum possible duration respectively. For example, “it started on 1, January, and lasted for about half a month.” Figure 4 illustrates this case.

Fuzzy Interval.
Figure 4.
Fuzzy Interval.
Figure 4.
Fuzzy Interval.
Close modal

Class IncompleteInterval is a special case of Interval, which just has startTime or endTime and does not have durationQuantity.

4.2.3 InstantCollection and IntervalCollection

The temporal description of medication and check-up events in clinical medical texts is cyclical. For example, “From today, review daily at 2:00 pm for five days.” In addition, some irregular time collections still exist in the medical texts, such as ‘The patient received rehabilitation training twice a day last year, and once every 2 days this year.’ Each occurrence may be instant, interval or collection. Therefore, we designed class InstantCollection and class InrevalCollection. Class InstantCollection has two subclasses: PeriodicInstantCollection and IrregularInstantCollection, and class InrevalCollection has two subclasses: PeriodicIntervalCollection and IrregularIntervalCollection.

Object property periodicQuantity can quantitatively represent the cycle, and data property periodicCount can represent the number of cycles. Object property eachTime are designed to represent the time of each occurrence, which range can be class Instant or Interval. And we can use periodicQuantity with a TimeQuantity instance to represent “daily,” and use durationQuantity with a TimeQuantity instance to represent “for five days.” Figure 5 illustrates this case.

Periodic Time.
Figure 5.
Periodic Time.

We can implement the representation of irregular time in two steps as follows: 1) create some Time instances; 2) connect them using object property belongTo or hasSubset and data property itemIndex. The Time instance can be not only Instant or Interval, but also InstantCollection or IntervalCollection. We can set the second sentence mentioned above to <irregularInstantCollection1.> There are two stages, and both of them are cyclic time. They can be represented by two instances of PeriodicInstantCollection: <periodicinstantCollection1> and <periodicInstantCollection2.> And then, use object property hasSubset to connect them. Figure 6 illustrates this case.

Irregular Time.
Figure 6.
Irregular Time.
Figure 6.
Irregular Time.
Close modal

4.2.4 Subjective Time

In clinical texts, it is widespread that patients describe the occurrence time of events by themselves. In this case, the time in the text is subjective and maybe not the real-time of the event. To represent subjectivity, each Time instance can use the data property subjective with True or False value to indicate whether it is a subjective description of the patient or an objective record so that the physician can make some judgments about that time information. Figure 7 illustrates this.

Subjective Time.
Figure 7.
Subjective Time.
Figure 7.
Subjective Time.
Close modal

4.2.5 Temporal Relationship

Besides aforementioned cases, there are also some cases that indicate the temporal relationship between the events, e.g., “receiving treatment B is earlier than taking medicine A.” Allen's 13 temporal relationships can be used to represent partial situations, however, they cannot cover all cases, such as point-to-collection, duration-to-collection, and collection-to-collection situations. Therefore, to fill the gap, we extended them by additions, such as containAll, containNull, and their inverse properties. Figure 8 illustrates a sample.

Temporal Relationship.
Figure 8.
Temporal Relationship.
Figure 8.
Temporal Relationship.
Close modal

4.2.6 Negation

The application of chronological relations sometimes appears with his negation. For example, “taking medicine A is not earlier than the end of treatment B.” In the medical record data, as long as we cannot know or infer that “taking medicine A” before “treatment B,” we can assume that A is not before B. And based on the closed world assumption (CWA), we designed the algorithm not, which can be used to represent the negation of a temporal relationship, such as not before, not after, and not overlap, etc.

This section will introduce class concepts and temporal relationship concepts semantically and graphically. Formally, Baader and Hanschke [17] proposed an extension to ALC, which named ALC(D). We describe the complex time classes and complex temporal relationships in the scheme of this language, and the reasoner can implement inductive reasoning according to the descriptions.

5.1 Complex Time Classes Definition

We defined some new classes for representing complex time, e.g., PeriodicInstantCollection, PeriodicIntervalCollection, etc. Their descriptions are shown below.

The description of concept PeriodicInstantCollection means its instance has start-time (Instant instance), periodic-quantity (Quantity instance), and each-time (Instant instance). And it is worth noting that it may have end-time (Instant instance) or periodic-count (Integer instance). Quantity denotes the quantification distance between one time and another. Pair means the two objects are used to calculate the relationship (One-by-one combinations between all time-related types).

5.2 Complex Temporal Relation Definition

We extended Allen's 13 temporal relationships to cover more comparisons between temporal types, such as startPoint, containAll, etc. We can determine whether the time of two events is completely covered or intersected or unrelated based on whether there is a relationship allDuring, someDuring or nullDuring between the time of the two events. before, after, meet is a special case of nullDuring, but there are more than just these three cases of nullDuring; there is also a case that is similar to overlap, but it may be that each element of the two collections alternates without intersecting each other. These three temporal relationships are mainly for Collection's subclasses. startPoint and finishPoint are mainly for Instant's subclasses, however, start and finish are mainly for Interval's and IntervalCollection's subclasses.

All temporal relationships are shown in Figure 9. We use different colors to distinguish between a, b objects, simple and complex time classes, as well as Allen's, TEO's and the CTO's temporal relationships.

Temporal Relation Semantics in Allen's, TEO and CTO.

Figure 9.
Temporal Relation Semantics in Allen's, TEO and CTO.
Figure 9.
Temporal Relation Semantics in Allen's, TEO and CTO.
Close modal

In Table 3, we used 3 auxiliary functions: AllItems(), CalTime() and StartTime(). The semantics of these functions are provided in  Appendix A.

Table 3.
Description of temporal relation of CTO using ALC(D).
graphic
graphic

5.3 Negation Temporal Relation Definition

If the reasoning machine can infer that there exists a temporal relation r1 between time A and time B, but cannot conclude that there exists temporal relation r2, then according to CWA, there is a negation relation not r2 between the two times. For example, if the reasoner cannot reason out <time1> before <time2>, <time1> not before <time2> can be concluded. All of the temporal relationships can get their negations. Table 4 introduces some examples.

Table 4.
Description of negated temporal relation of CTO using ALC(D).
IdConceptsDescription
not before Pair Π (∄former before latter) 
not equal Pair Π (∄former equal latter) 
10 not meet Pair Π (∄former meet latter) 
IdConceptsDescription
not before Pair Π (∄former before latter) 
not equal Pair Π (∄former equal latter) 
10 not meet Pair Π (∄former meet latter) 

In order to verify the ability of the CTO ontology to express time information in the clinical field, we selected a set of case texts of people with a mental health condition. We used an anonymized realistic dataset from a hospital in China. We randomly selected 300 patients, which contained approximately 3000 Chinese statements. And then, we arranged annotators to annotate the time information and conducted a quantitative analysis using the Inter-Annotator Agreement (IAA) [18] metric. IAA metric is commonly used to evaluate annotation consistency and the difficulty of annotation, usually focusing on the following metrics: Precision, Recall, and F1. At the same time, we analyzed the characteristics of other ontologies. And we also compared and analyzed the expressiveness of CTO with other ontologies in terms of complex time and temporal relations.

6.1 Evaluation Results

For IAA, three annotators were asked to annotate time information in 300 patient cases jointly. The evaluation consists of two parts, (1) evaluation of classes and object properties (without temporal relations), and (2) evaluation of temporal relationships. For evaluation of classes and object properties, they first annotated classes, and the annotation methods were discussed together. After that, they discussed and agreed on the Gold Standard. The annotation of object properties was same, and the base data is the Gold Standard.

The mean value of F1 metric of time-related classes annotation were 77.18% and 83.06% (exact mapping and partial mapping). And the average F1 metric of object properties (without temporal relationship object properties) was 87.34%. Considering that complex time information can be represented in various ways, such as the representation of time interval can use startTime/endTime + durationQuantity or startTime + endTime. If such errors are ignored, the average score is 93.61%.

For evaluation of temporal relations, we asked three annotators to annotate the temporal relations between time entities, using the Gold Standard obtained by previous sub-process. We had developed a reasoning machine for the experiment about evaluating of temporal relations, and regarded the results as Gold Standard for the second evaluation task. Note that we treat pairs of tokens that have the inverse property as true positive as well, such as <time1> before <time2> and <time2> after <time1.> The mean value of Precision, Recall and F1 are 96.98%, 91.97%, 94.39% respectively. We also calculate the three metrics of each temporal relationship to analyze which temporal relations are more difficult to express. The results are shown in Figure 10.

IAA results for CTO temporal relations.

Figure 10.
IAA results for CTO temporal relations.
Figure 10.
IAA results for CTO temporal relations.
Close modal

From Figure 10, it can be seen that it is easy to reach a consensus on the representation of simple relations, such as after, overlap, endBeforeEnd, etc. However, there are difficulties in representing more complex temporal relations, such as containAll, finishPoint, etc. After analysis, it is found that manual annotation will show omissions for this type of data but still maintain a high Fl score, which indicates that the CTO ontology can also achieve better results in the representation of temporal relations.

Concerning the ability of ontologies to cover temporal instances, we found that CTO ontologies are able to cover almost all types of temporal descriptions. As can be seen from the Figure 11 and Figure 12, instances of complex time types (PeriodicInstantCollection, PeriodicIntervalCollection, IrregularInstantCollection, IrregularIntervalCollection) account for approximately 16.77% (594 of 3542) of all time types, and the extended temporal relationships (containAll, containSome, containNull, startPoint, finishPoint) account for 21.19% of all temporal relationships (629 of 2969). We provided 2 sample texts from clinical records as well as their relevant knowledge graphs annotated with CTO in  Appendix B.

Distribution of Time Class.

Figure 11.
Distribution of Time Class.
Figure 11.
Distribution of Time Class.
Close modal

Distribution of temporal relation object properties.

Figure 12.
Distribution of temporal relation object properties.
Figure 12.
Distribution of temporal relation object properties.
Close modal

6.2 Expressiveness Analysis

In this section, OWL-Time, PSI-Time, TEO ontology are compared with the CTO ontology on their ability to represent the eight problems presented in Section 3. Table 5 shows the result, and we use mark ✓ for those ontologies capable of getting problem's results by querying.

Table 5.
Comparison of different temporal ontologies about complex time expressiveness.
Problem/Ontology12345678
OWL-Time ✓      ✓  
PSI-Time ✓ ✓  ✓   ✓  
TEO ✓ ✓  ✓ ✓  ✓  
CTO ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ 
Problem/Ontology12345678
OWL-Time ✓      ✓  
PSI-Time ✓ ✓  ✓   ✓  
TEO ✓ ✓  ✓ ✓  ✓  
CTO ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ 

For Problem-1 (Absolute Time Problems), all of them can be queried to obtain the exact time, even the hour, minute and second.

For Problem-2 (Lack Information Time Problems (Relative Time and Incomplete Time)), OWL-Time mainly focused on absolute instant and interval, and it cannot represent relative quantities and can certainly not represent incomplete time, as TEO said. If we want to obtain the time referred to by “three days before hospitalization,” then we need to implement a representation of relative quantities as well as reference objects, but they do not have this capability and therefore cannot answer questions relating to such times.

For Problem-3 (Fuzzy Time Problems), when we want to compare the temporal relationships between events that occurred more ambiguous times, it is inappropriate to compare their absolute times. For example, the time relationship between time A “at about 8:10 a.m. on November 1, 2021” and time B “at 8 a.m. on November 1, 2021, which lasted about 9 minutes” could be either during, after, or finishPoint. It, of course, is related to the range of fuzzy values. By introducing the maximum and minimum values as left and right anchors, we can compare them in terms of time relationships and obtain a range of values for the end time. OWL-Time and PSI-Time do not consider the concept of fuzzy time and therefore cannot be queried for answers; TEO does take into account fuzzy time, but it only marks time by True and False and does not analyze it quantitatively.

For Problem-4 (Cyclic Time Problems), we can query PSI-Time, TEO and CTO ontologies to obtain the start time, each occurrence and the frequency of the periodic time to answer questions, such as “When is the next check?” “How many times has it been done so far?” etc.

For Problem-5 (Irregular Time Problems), one of the characteristic points of the CTO ontology is that an item of the IrregularCollection can still be a collection. Thus, it is possible to implement a stage-by-stage representation of time, e.g., “once a day for the first session, once a week for the second session,” etc. Not only can we obtain internal time-related calculations such as “How long between the first and second sessions?” and “Which session is now?”, but we can also compare the time relationship with other times.

For Problem-6 (Subjective Problems), we use True or False flag, which is the value of the subjective property, to provide a basis for the user to refer to when reasoning or querying results.

For Problem-7 (Temporal Relation Problems), all of them can get the answer. Both TEO and CTO ontologies extend the temporal relations and CTO ontology defines different temporal relations between multiple types of time.

For Problem-8 (Negation Problems), CTO ontology regards case data as a closed world, and if there does not exist the relation r between the time a and b, then (a, not r, b) is satisfied. Thus, the CTO ontology can answer that question based on the CWA.

Overall, CTO ontology is superior to other time ontologies in terms of answering time-related clinical questions.

In this paper, we identified eight time-related problems in clinical domain, and proposed the CTO ontology with a taxonomy of complicated temporal concepts to solve these problems, which covers the fuzziness, relativity, irregular and cyclic aspects of time expressions in clinical text. In addition, we also marked whether the time is subjective so that we can deal with it in the future. Simultaneously, we defined the concept description of the complex time-related classes, and extended Allen's and TEO's temporal relationship to support temporal relations for complex time. More importantly, we give definitions of the various temporal relationships between all time-related types (Instant, Interval, Collection), both in formulaic and picture form. The experimental results show that complex time classes account for 16.77% of all classes in clinical medical texts and the extended temporal relationships account for 21.19% of all temporal relations, and CTO ontology can represent more than 93% of temporal information and temporal relationships. In summary, we proposed a robust temporal ontology capable of expressing a variety of complex temporal information in clinical texts.

The CTO ontology can be improved or extended in the following aspects: 1) The reasoning about fuzzy time is currently using the way of setting left and right anchor, and the problem of-selecting left and right anchor points is also tricky. In the future, we hope to use probabilistic methods to achieve probability-level representation and reasoning capabilities; 2) Building a patient history knowledge graph using CTO ontology automatically is also on the agenda. By this way, we can further validate and improve its use in realistic scenarios.

This work is supported by the National Natural Science Foundation of China (No. U1836118), the Open Fund of Key Laboratory of Content Organization and Knowledge Services for Rich Media Digital Publishing (ZD2021-11/01), and the Natural Science Foundation of Hubei Province educational Committee (B2019009). Prof. Zhisheng Huang of Vrije Universiteit Amsterdam provided the data for this study.

Danyang Hu (HuDanyang wust@163.com) and Meng Wang (wangmeng@wust.edu.cn) planned and contributed equally to the overall work. Both of them are co-responsible for analyzing case data, the design of the research, the implementation of the approach, and the writing of the manuscript. Feng Gao (feng.gao86@wust.edu.cn) has contributed to the design of the research, the analysis of the results, and the revising of the manuscript. Fangfang Xu (xuff@wust.edu.cn) has contributed to the design of the research and the analysis of the results. Jinguang Gu (simon@wust.edu.cn) has proposed the research problems and contributed to the design of the research.

[1]
Olex
,
A.L.
,
McInnes
,
B.T.
:
Review of temporal reasoning in the clinical domain for timeline extraction: Where we are and where we need to be
.
Journal of Biomedical Informatics
118
,
103784
(
2021
)
[2]
Moharasan
,
G.
,
Ho
,
T.B.
:
Extraction of temporal information from clinical narratives
.
Journal of Healthcare Informatics Research
3
(
2
),
220
244
(
2019
)
[3]
Piskorski
,
J.
,
Zavarella
,
V.
,
Atkinson
,
M.
, et al.:
Timelines: Entity-centric event extraction from online news
. In: Text2Story@ ECIR, pp.
105
114
(
2020
)
[4]
Ding
,
K.
,
Zhou
,
F.
,
Miao
,
J.
, et. al:
Temporal relation recognition method for news events based on cross event theory
.
Computer Engineing
34
(
6
),
6
(
2017
).
[5]
Zhao
,
X.
,
Jin
,
P.
,
Yue
,
L.
:
Discovering topic time from web news
.
Information Processing & Management
51
(
6
),
869
890
(
2015
)
[6]
Zhou
,
X.
,
Zhou
,
Q.
,
Li
H.
:
Automatic annotation of temporal information in Chinese medical narrative records
.
Chinese Journal of Biomedical Engineering
31
(
3
),
434
439
(
2012
)
[7]
Hobbs
,
J.R.
,
Pan
,
F.
:
Time ontology in OWL. W3C working draft 27
. Available at: https://www.w3.org/TR/owl-time/ (
2006
). Accessed on 2021
[8]
Allen
,
J.F.
:
Maintaining knowledge about temporal intervals
.
Communications of the ACM
26
(
1
),
832
843
(
1983
)
[9]
Anagnostopoulos
,
E.
,
Batsakis
,
S.
,
Petrakis
,
E.G.M.
:
CHRONOS: A reasoning engine for qualitative temporal information in OWL
.
Procedia Computer Science
22
,
70
77
(
2013
)
[10]
Madkour
,
M.
,
Benhaddou
,
D.
,
Tao
,
C.
:
Temporal data representation, normalization, extraction, and reasoning: A review from clinical domain
.
Computer Methods and Programs in Biomedicine
128
,
52
68
(
2016
)
[11]
Tao
,
C.
,
Wei
,
W.
,
Solbrig
,
H.R.
, et al.:
CNTRO: a semantic web ontology for temporal relation inferencing in clinical narratives
. In:AMIA annual symposium proceedings. American Medical Informatics Association p.
787
(
2010
)
[12]
Li
,
F.
,
Du
,
J.
,
He
,
Y.
, et al.:
Time event ontology (TEO): to support semantic representation and reasoning of complex temporal relations of clinical events
.
Journal of the American Medical Informatics Association
27
(
7
),
1046
1056
(
2020
)
[13]
Hobbs
,
J.R.
,
Ferguson
,
G.
,
Allen
,
J.
, et al.:
A daml ontology of time
. Available at: http://www.cs.rochester.edu/ (
2002
). Accessed on 2021
[14]
SWRL Temporal Ontology
. Available at: http://protege.cim3.net/cgibin/. Accessed on 2021
[15]
Ermolayev
,
V.
,
Keberle
,
N.
,
Matzke
,
W.E.
:
An ontology of environments, events, and happenings
. In: 2008 32nd Annual IEEE International Computer Software and Applications Conference, pp.
539
546
(
2008
)
[16]
Ferro
,
L.
,
Gerber
,
L.
,
Mani
,
I.
, et al.:
Standard for the annotation of temporal expressions-tides
.
The MITRE Corporation
,
McLean-VG-USA
(
2005
)
[17]
Baader
,
F.
,
Philipp
,
H.
:
A scheme for integrating concrete domains into concept languages
. In: Proceedings of the 12th International Joint Conference on Artificial Intelligence, pp.
446
451
(
1991
)
[18]
Artstein
,
R.
:
Inter-annotator agreement
.
Handbook of linguistic annotation
,
Springer
,
Dordrecht
(
2017
)

APPENDIX A SEMANTICS FOR THE AUXILIARY FUNCTIONS IN TEMPORAL RELATION DEFINITION

AllItems(a.Collection) function can get all the elements in Collection_instance, which is convenient for calculation, especially with cyclic collections, which need to be calculated to get the real time of each occurrence. CalTime(a.Instant, q.Quantity) function can get the calculated real time point of relative time or result of temporal addition. StartTime(a.Time) function provides an interface for obtaining the start time of all time types, which is similar to EndTime(a.Time) function.

APPENDIX B USAGE EXAMPLES FOR TEMPORAL REPRESENTATION AND QUERY

Figure B.13B.16 illustrate the details, in which the words in red italic are manually annotated as events and times. We use lines with arrows to establish a correspondence between statements containing time information and the class to which that time information belongs.

Sample text which Includes Absolute Instant Time, Absolute Interval Time, Relative Time, Fuzzy Time, and Incomplete Time.

Figure B.13.
Sample text which Includes Absolute Instant Time, Absolute Interval Time, Relative Time, Fuzzy Time, and Incomplete Time.
Figure B.13.
Sample text which Includes Absolute Instant Time, Absolute Interval Time, Relative Time, Fuzzy Time, and Incomplete Time.
Close modal

Sample context which includes Cyclic Time, Irregular Time, Subjective Time, and apparent Temporal Relation.

Figure B.14.
Sample context which includes Cyclic Time, Irregular Time, Subjective Time, and apparent Temporal Relation.
Figure B.14.
Sample context which includes Cyclic Time, Irregular Time, Subjective Time, and apparent Temporal Relation.
Close modal

Representation for the text shown in FigureB.13 using CTO.

Figure B.15.
Representation for the text shown in FigureB.13 using CTO.
Figure B.15.
Representation for the text shown in FigureB.13 using CTO.
Close modal

Representation for the text shown in FigureB.14 using CTO.

Figure B.16.
Representation for the text shown in FigureB.14 using CTO.
Figure B.16.
Representation for the text shown in FigureB.14 using CTO.
Close modal

Figure B.13 is an example case data, which contains some events (e.g., hospitalization, discharge, medication, and paroxysm events) and some types of time (e.g., absolute instant time, absolute interval time, relative time, fuzzy time, and incomplete time). Figure B.15 illustrates the representation.

Figure B.13 and Figure B.15 present the time representation for problems 1-3. For problems 4-7, we find some short sentences from the dataset. Figure B.14 shows the corpora, and Figure B.16 illustrates the representation.

Author notes

These authors contributed equally to this work.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. For a full description of the license, please visit https://creativecommons.org/licenses/by/4.0/legalcode.