mibe000256
10.3205/mibe000256
urn:nbn:de:0183-mibe0002565
Research Article
Model-driven execution of phenotype algorithms – introduction of the Terminology- and Ontology-based Phenotyping Framework
Modell-getriebene Ausführung von Phänotyp-Algorithmen – Einführung des Terminology- and Ontology-based Phenotyping Framework
Beger
Beger
Christoph
C
Universität Leipzig, Institut für Medizinische Informatik, Statistik und Epidemiologie, Härtelstraße 16–18, 04107 Leipzig, GermanyInstitute for Medical Informatics, Statistics and Epidemiology, Leipzig University, Leipzig, GermanyGrowth Network CrescNet, Leipzig University, Leipzig, Germany
christoph.beger@imise.uni-leipzig.de
author
Matthies
Matthies
Franz
F
Institute for Medical Informatics, Statistics and Epidemiology, Leipzig University, Leipzig, Germany
author
Schäfermeier
Schäfermeier
Ralph
R
Institute for Medical Informatics, Statistics and Epidemiology, Leipzig University, Leipzig, Germany
author
Uciteli
Uciteli
Alexandr
A
Institute for Medical Informatics, Statistics and Epidemiology, Leipzig University, Leipzig, Germany
author
German Medical Science GMS Publishing House
Düsseldorf
610
phenotype
algorithms
eligibility determination
health information interoperability
terminology as topic
20231120
engl
This is an Open Access article distributed under the terms of the Creative Commons Attribution 4.0 License.
Dieser Artikel ist ein Open-Access-Artikel und steht unter den Lizenzbedingungen der Creative Commons Attribution 4.0 License (Namensnennung).
1860-9171
19
GMS Medizinische Informatik, Biometrie und Epidemiologie
GMS Med Inform Biom Epidemiol
17
Bundesministerium für Bildung und Forschung (BMBF)
Bundesministerium für Bildung und Forschung (BMBF)
Die automatisierte Erkennung von Patienten, die bestimmte klinische Kriterien erfüllen oder unerwünschte Ereignisse aufweisen, spielt eine wichtige Rolle bei der Verbesserung der Patientenversorgung. Regelb<![CDATA[a</PlainText></TextGroup>sierte Systeme sind eine Möglichkeit, die standardisierte Modellierung von Algorithmen zur Erkennung von Patienten mit bestimmten beob<TextGroup><PlainText>a</PlainText></TextGroup>chtbaren Merkmalen (Phänotypen) zu ermöglichen. Ein weiterer wichtiger Aspekt ist der Abruf von Daten aus elektronischen Patientenakten in Krankenhausinformationssystemen und klinischen Forschungsdatenbanksystemen. In dieser Arbeit wird ein neues regelbasiertes System beschrieben, das für Fachleute ohne IT-Hintergrund geeignet ist und die automatische Abfrage von Patientendaten bei der Ausführung ermöglicht, indem Suchanfragen in quellenspezifische Abfragesprachen übersetzt werden.</Pgraph><Pgraph>Als Grundlage für regelbasierte strukturierte Phänotyp-Algorithmen wird ein Modell verwendet, das von der Core Ontology of Phenotypes abgeleitet ist. Das Modell ermöglicht die Definition von Phänotyp-Algorithmen mit Eigenschaften wie Code-System-Beziehungen zur Verbesserung der Interoperabilität. Mit einem relativ einfachen Mapping können IT-Spezialisten eine Spezifikation erstellen, um diese Modelle mit einem lokalen Krankenhausinformationssystem zu verbinden.</Pgraph><Pgraph>Wir haben eine interaktive Webanwendung, das Terminology- and O<TextGroup><PlainText>ntolog</PlainText></TextGroup>y-based Phenotyping Framework, entwickelt, um Fachleute bei der Modellierung und Ausführung von Phänotyp-Algorithmen zu unterstützen. Je nach dem datenhaltenden Quellsystem wird ein geeigneter Adapter verwendet, der die Abfragen in die quellsystemspezifische Sprache übersetzt und ausführt. Das Framework wurde mit einer SQL-Datenbank und einem FHIR-Server getestet, die beide mit zufällig generierten Daten initialisiert wurden. Die generierten Anfragen ergaben identische Ergebnismengen.</Pgraph><Pgraph>Der vorgeschlagene computergestützte Ansatz kann die Erkennung von Krankheiten und die Rekrutierung für klinische Studien verbessern und ermöglicht eine klare Aufgabenteilung zwischen Domänenexperten und IT-Spezialisten.</Pgraph></Abstract>
<Abstract language="en" linked="yes"><Pgraph>Automated detection of patients who meet certain clinical criteria or who experience adverse events plays a key role in improving patient care. Rule-based systems are one approach to enable standardised modelling of algorithms to detect patients with certain observable characteristics (phenotypes). Another important aspect is the retrieval of data from electronic health records in hospital information systems and clinical research database systems. In this work, we propose a new rule-based system, suitable for domain experts without IT background that allows automatic retrieval of patient data on execution by translating search queries into source-specific query languages.</Pgraph><Pgraph>As a basis for rule-based structured phenotype algorithms, we use a model derived from the Core Ontology of Phenotypes. The model allows phenotype algorithms to be defined with properties such as code system relationships to improve interoperability. With a relatively simple mapping, IT specialists can provide a specification to connect these models to a local hospital information system.</Pgraph><Pgraph>We developed an interactive web application, the Terminology- and Ontology-based Phenotyping Framework, to support domain experts in modelling and executing phenotype algorithms. Depending on the data-holding source system, an appropriate adapter is used to translate and execute queries in the source system-specific language. The framework was tested against a SQL database and a FHIR server, both initialised with randomly generated data. Generated queries yielded identical result sets.</Pgraph><Pgraph>The proposed computer-assisted approach can improve disease detection and clinical trial recruitment and enables a clear division of tasks between domain experts and IT specialists.</Pgraph></Abstract>
<TextBlock linked="yes" name="Introduction">
<MainHeadline>Introduction</MainHeadline><Pgraph>In the Medical Informatics Initiative (MII) innovative IT solutions are developed to support medical research and enhance patient care. An important aspect of this is the automatic detection of diseases, risks for the same and adverse events of medications. For the implementation of such detection, patient data must be extracted from electronic health records (EHR) or research databases and evaluated. This may involve machine-interpretable phenotype algorithms, which use structured filter criteria and rules to detect individuals with specific properties (phenotypes) and derive further properties. With this, computer-assisted algorithms can, among other things, improve clinical trial recruitment <TextLink reference="1"></TextLink>. The National Portal for Medical Research Data (FDPG) was recently developed in the MII <TextLink reference="2"></TextLink>. It provides scientists with federated access to 31 German university hospitals, enabling them to perform feasibility queries and submit data use proposals. The query interface allows relatively simple matching criteria to be defined.</Pgraph><Pgraph>In this work, we want to focus on a more general approach of defining shareable models that can be used to perform complex queries and calculations in order to find matching individuals and infer additional characteristics. For this, we distinguish between three core notions: <Mark2>phenotype</Mark2>, <Mark2>phenotype model</Mark2> and<Mark2> phenotype algorithm</Mark2>.</Pgraph><Pgraph>We use the definition of ‘<Mark2>phenotype</Mark2>‘ as a ‘(combination of) bodily feature(s) of an organism determined by the interaction of its genetic make-up and environment’ by Scheuermann et al. <TextLink reference="3"></TextLink>. And in a broader sense, we also consider all observable human characteristics to be phenotypes.</Pgraph><Pgraph>A <Mark2>phenotype model</Mark2> is a formal representation of phenotypic knowledge. We hereby distinguish between general and specific phenotype models <TextLink reference="4"></TextLink>. The general model provides a basic classification of phenotypes, the required attributes of phenotype classes (e.g., labels, data types, codes, units of measurement, derivation rules/formulas etc.), relation types and rules (axioms), which must be used/followed by developing specific models. A specific phenotype model represents phenotypic knowledge by defining specific phenotype classes (such as ‘weight’, ‘height’, ‘BMI’, ‘obesity’, etc.) according to the general model. This means, all required attributes of the classes (e.g., including the formula for calculating BMI from weight and height, as well as the ranges to classify the BMI value in categories from underweight to obesity) and relations between the classes (e.g., weight and height values are required for calculating BMI) are specified.</Pgraph><Pgraph>A <Mark2>phenotype algorithm</Mark2> is generally understood as an algorithm designed to identify or classify phenotypic traits <TextLink reference="5"></TextLink>, <TextLink reference="6"></TextLink>. Specifically, we consider a phenotype algorithm to be a sequence of instructions to</Pgraph><Pgraph><OrderedList><ListItem level="1" levelPosition="1" numString="1.">query data representing phenotypes,</ListItem><ListItem level="1" levelPosition="2" numString="2.">derive additional properties (derived/composite phenotypes) from other phenotypes,</ListItem><ListItem level="1" levelPosition="3" numString="3.">classify phenotypes into phenotype classes, and</ListItem><ListItem level="1" levelPosition="4" numString="4.">provide results in a machine- and human-readable format.</ListItem></OrderedList></Pgraph><Pgraph>A <Mark2>generic</Mark2> <Mark2>phenotype algorithm</Mark2> is model-driven (i.e., it can be configured by a phenotype model). This means, the algorithm always performs the same (generic) steps (see above) and uses the specific phenotype definitions specified in a phenotype model (e.g., identifying obese patients based on weight and height or identifying patients with acute kidney injury based on creatinine).</Pgraph><Pgraph>The effort required to design algorithms can be very high depending on the complexity <TextLink reference="7"></TextLink> and typically requires a close collaboration between domain and IT experts. To support domain experts in creating phenotype models and executing phenotype algorithms, we developed a framework, the Terminology- and Ontology-based Phenotyping (TOP) Framework, which will be presented in this work. The goal was for the framework to allow domain experts to define phenotypes with respective filters and roles on their own, and to be embeddable by IT experts into the hospital’s information system, thus allowing the execution of algorithms on patient data from routine patient care and medical research.</Pgraph></TextBlock>
<TextBlock linked="yes" name="Methods">
<MainHeadline>Methods</MainHeadline><Pgraph>We use the Core Ontology of Phenotypes (COP) <TextLink reference="8"></TextLink> as the generic phenotype model and as a basis for developing specific models. COP specifies that all phenotypes of organisms are instances of one or more phenotype classes. These classes are distinguished into single and composite phenotype classes. Single phenotypes (e.g., height or weight of a person) are atomic and can be components/parts of composite phenotypes (e.g., BMI). The two described class types can further be subdivided into unrestricted and restricted phenotype classes. A restricted class (e.g., ‘height above 150 cm’) is always a subclass of an unrestricted class (‘height’) and possess a value restriction so that only a subset of the corresponding unrestricted class instances belongs to the restricted class. For example, the phenotype ‘height’ with value 18<TextGroup><PlainText>0 c</PlainText></TextGroup>m of the individual John Doe is an instance of the unrestricted single phenotype class ‘height’ and, at the same time, of the restricted single phenotype class ‘height above 150 cm’.</Pgraph><Pgraph>Single phenotype classes must be annotatable with terms of standard terminologies like Logical Observation Identifiers Names and Codes (LOINC) or Systematized Nomenclature of Medicine and Clinical Terms (SNOMED CT). These annotations are used to assign the phenotype classes with corresponding data from the source systems. For instance, the phenotype ‘height’ is annotated with code ‘LOINC:3137-7’. With this annotation in place, a mapping can be provided to assign all height values from electronic health records to the phenotype ‘height’, which makes them available for classifications and calculations.</Pgraph><Pgraph>As composite phenotypes result from calculations and compositions of single phenotypes, constants and other composite phenotypes, we developed a generic specification to express these cases. According to the specification, all composite phenotype classes have exactly one expression representing either a phenotype, a constant, or exactly one function with a set of arguments. Expressions can be nested because arguments are also expressions. Functions convert argument sets into a single expression (usually a value), though they are not limited to mathem<TextGroup><PlainText>at</PlainText></TextGroup>ical functions and the available set of functions is exte<TextGroup><PlainText>ns</PlainText></TextGroup>ible. For instance, the expression of the phenotype ‘Body Mass Index’ can be expressed as follows: ‘quotient(weight, power(height, 2))’.</Pgraph><Pgraph>The TOP Framework implements a generic phenotype algorithm, which can be executed by selecting a desired phenotype model and defining (single or composite) phenotype classes as in- or exclusion criteria. Composite phenotypes can be traced back to singles from which they are derived. This results in a set of single phenotypes, which all have terminology annotations. For each of them, queries can be inferred that are translated to the respective query language of the source system and executed on the system. We assume that relevant data elements are available in structured form and are retrievable from data-holding systems (source system) with respective query languages. In the MII, Fast Healthcare Interoperability Resources (FHIR, <Hyperlink href="https://www.hl7.org/fhir">https://www.hl7.org/fhir</Hyperlink>), by the standardisation organisation Health Level 7, is used to make patient data from electronic health records accessible. And also, many research data management systems are using databases based on the Structured Query Language (SQL). We therefore focused on SQL database management systems and FHIR servers with FHIR Search (<Hyperlink href="https://www.hl7.org/fhir/search.html">https://www.hl7.org/fhir/search.html</Hyperlink>) support. The inference is done by generic or source system-specific adapters. For SQL and FHIR, we provide generic Java-based adapters based on <TextLink reference="4"></TextLink>, which are configurable by a mapping file. The query results are subsequently used to evaluate expressions of composite phenotypes.</Pgraph><Pgraph>The whole process of modelling phenotypes and executing phenotype algorithms is depicted in Figure 1 <ImgLink imgNo="1" imgType="figure"/> and can be carried out by domain experts. Only adapters and an optional source system mapping must be provided by IT specialists. The mapping associates the terminology codes of the phenotype classes in the phenotype model with the corresponding data elements contained in the source system, e.g. FHIR resource types like ‘Observation’ and ‘Condition’ or SQL database tables and columns. In addition, value ranges contained in the phenotype algorithm can be modified. This is especially helpful to customise an algorithm to facility-specific norm values like laboratory thresholds. If the terminology codes and also value ranges in the phenotype model and in the source system are identical, the mapping can be omitted.</Pgraph></TextBlock>
<TextBlock linked="yes" name="Results">
<MainHeadline>Results</MainHeadline><Pgraph>Based on the described methodological blueprint, we have developed an interactive web application, the TOP Framework (see Figure 2 <ImgLink imgNo="2" imgType="figure"/>). The framework is used by domain experts to develop phenotype models and execute phenotype algorithms. It consists of a JavaScript-based frontend, a Java Spring Backend, and a vendor-independent database. The framework can optionally be connected to an Ontology Lookup Service (version 3) <TextLink reference="9"></TextLink>. The main functions provided by the corresponding user interface elements or API are the following:</Pgraph><Pgraph><OrderedList><ListItem level="1" levelPosition="1" numString="1.">Developing phenotype models: Phenotype classes, attributes, relations, ranges, and expressions/formulas can be structurally defined.</ListItem><ListItem level="1" levelPosition="2" numString="2.">Storing and exporting phenotype models: Phenotype models are stored in a relational database and can be exported in different formats (e.g., Ontology Web Language, CSV or Decision Model and Notation).</ListItem><ListItem level="1" levelPosition="3" numString="3.">Execution of phenotype algorithms: Phenotype algorithms can be initiated by selecting a phenotype model (in-/exclusion criteria) and a source system. Depending on the selected source system, a suitable adapter is used to translate and execute queries in source system-specific language.</ListItem><ListItem level="1" levelPosition="4" numString="4.">Providing results: The number of patients/probands who fulfil all criteria of the phenotype model or also the corresponding data are provided in a machine and human readable format (e.g., CSV).</ListItem></OrderedList></Pgraph><Pgraph>Furthermore, the framework allows search in existing phenotype models and supports, among other things, the creation of expressions for composite phenotypes and thus ensures syntactic correctness. Frontend and backend communicate over an API (the API’s OpenAPI specification is available in <TextLink reference="10"></TextLink>), which can also be used to integrate backend functionalities into other software applications. </Pgraph><Pgraph>The framework was tested with randomly generated test data consisting of 10,000 patients with about 50,000 visits. We provided the data both in an SQL database and via a FHIR server and created corresponding mapping configurations. Queries to both source systems yielded identical result sets.</Pgraph></TextBlock>
<TextBlock linked="yes" name="Discussion">
<MainHeadline>Discussion</MainHeadline><Pgraph>Typically, bioinformaticians, statisticians and comparable groups of people are tasked with implementing algorithms to detect individuals with specific traits. Since domain experts (i.e., medical staff) must provide the knowledge to implement such algorithms, very close collaboration between both groups is required <TextLink reference="11"></TextLink>. Algorithms are often written in programming languages such as R, Python, Clinical Quality Language, which are more powerful and expressive than the TOP Framework but are not familiar to domain experts. As a result, there is no clear separation between modelling and implementation tasks. In addition, access to the source data must be implemented separately, e.g. using libraries such as FHIRcrackr <TextLink reference="12"></TextLink> or FHIR-PYrate <TextLink reference="13"></TextLink>. The TOP Framework can solve these issues by the described separation between phenotype models and phenotype algorithms. Consider phenotype models as different configurations applied to the generic phenotype algorithm described earlier. The framework provides a user interface suitable for domain experts to create such models and use them to compute or infer complex phenotypes for a given set of patient data, and to query patient data management systems for individuals with matching characteristics. Query results can be numbers of individuals or data sets containing selected patient characteristics for further statistical analysis. The approach of separating modelling and implementation tasks has been used previously by Uciteli et al. <TextLink reference="14"></TextLink>, <TextLink reference="15"></TextLink>, where ontological models built by domain experts were used to search text corpora and to identify perioperative risks.</Pgraph><Pgraph>The expressions used in the TOP Framework for modelling composite phenotypes are generic and thus suitable for mapping a large part, but not all, of the calculations and rules that occur in practice in algorithms. Some phenotypes can only be assessed using complex computations (e.g., Python and R scripts) or trained models (e.g., from machine learning). They are therefore not yet supported by the framework. In the future, we would like to integrate such complex calculations into the TOP Framework as external services.</Pgraph><Pgraph>The TOP Framework is a platform for easy definition of reusable phenotype models. All models can be accessed and referenced via URLs. However, the model is only partially standards compliant and introduces a proprietary format. To overcome this, we plan to extend the model with additional audit and metadata, and to enable automated transformation into community standard formats such as RDF with common annotations. This is in line with our commitment to the FAIR data principles <TextLink reference="16"></TextLink>.</Pgraph><Pgraph>The focus of our work was not to provide yet another query tool for patient and trial data, but to enable and encourage domain experts to build machine-readable and richly annotated models of phenotypes that can later be used to build queries. An initial overhead is required to build these models. Therefore, the framework does not support rapid query building as provided by tools such as FDPG <TextLink reference="2"></TextLink>, i2b2 <TextLink reference="17"></TextLink>, or tranSMART <TextLink reference="18"></TextLink>. But there is no need for complex ETL jobs to pre-process patient or trial data. All queries are generated in the source-specific language and can be executed directly on the source system. In this work, we have focused on the query languages FHIR Search and SQL. However, the concept described here can also be used in conjunction with other query languages by implementing appropriate query adapters. Admittedly, the required mapping to source systems may be difficult for some database schemas or APIs – or even impossible in some cases if essential data is missing (e.g., terminology codes). However, the resulting framework is lightweight and has no requirements for the storage of patient data, and aspects such as data privacy can be handled by the source systems.</Pgraph></TextBlock>
<TextBlock linked="yes" name="Conclusions">
<MainHeadline>Conclusions</MainHeadline><Pgraph>We have developed a methodology for modelling phenotypes and retrieving the corresponding data elements from patient data management systems and clinical research systems. The required tasks are clearly divided between domain experts and IT specialists. This computer-assisted approach can improve disease detection and clinical trial recruitment.</Pgraph></TextBlock>
<TextBlock linked="yes" name="Notes">
<MainHeadline>Notes</MainHeadline><SubHeadline>Terminology- and Ontology-based Phenotyping (TOP) Framework </SubHeadline><Pgraph>Source code for frontend and backend is available at <Hyperlink href="https://github.com/Onto-Med/top-frontend">https://github.com/Onto-Med/top-frontend</Hyperlink> and <Hyperlink href="https://github.com/Onto-Med/top-backend">https://github.com/Onto-Med/top-backend</Hyperlink>. A user manual can be found at <Hyperlink href="https://onto-med.github.io/top-deployment">https://onto-med.github.io/top-deployment</Hyperlink>.</Pgraph><SubHeadline>Competing interests</SubHeadline><Pgraph>The authors declare that they have no competing interests.</Pgraph><SubHeadline>Funding</SubHeadline><Pgraph>This work was supported by the German Federal Ministry of Education and Research as part of the projects SMITH TOP (reference number: 01ZZ2018) and SMITH (reference number: 01ZZ1803A).</Pgraph></TextBlock>
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<Caption><Pgraph><Mark1>Figure 1: Overview of the TOP Framework. Domain experts use the graphical user interface to browse existing phenotype classes, create new ones and execute algorithms based on them. IT specialists provide data source adapters and mappings that enable generating source system-specific queries. External terminology servers can be incorporated.</Mark1></Pgraph></Caption>
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<Caption><Pgraph><Mark1>Figure 2: Screenshot of the TOP Framework web application. Shown is the repository ‘BMI Example’ that contains a simple phenotype model of the body mass index (BMI). On the left side, all phenotype definitions contained in the repository are displayed in a tree structure. And on the right side, a form to edit the definition of the phenotype ‘BMI’ is shown.</Mark1></Pgraph></Caption>
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