The Distinction between Linguistic and Conceptual Semantics in Medical Terminology and its Implication for NLP-Based Knowledge Acquisition

Natural language understanding systems have to exploit various kinds of knowledge in order to represent the meaning behind texts. Getting this knowledge in place is often such a huge enterprise that it is tempting to look for systems that can discover such knowledge automatically. We describe how the distinction between conceptual and linguistic semantics may assist in reaching this objective, provided that distinguishing between them is not done too rigorously. We present several examples to support this view and argue that in a multilingual environment, linguistic ontologies should be designed as interfaces between domain conceptualizations and linguistic knowledge bases.

The Explanatory Role of Events in Causal and Temporal Reasoning in Medicine

The logic of time and the way we reason about time is intrinsically connected with the way we reason about causality. In this paper, we focus our attention on some of the less obvious ways in which reasoning about time and causality interact. It is explained why in temporal reasoning a firm distinction has to be made between the ontology, i. e., what happens, and the way we describe the ontology. Temporal events need to be redescribed in such a way that they causally explain why some of the events are followed by the others. While building a temporal/causal theory, certain events may be omitted, not because they do not play a causal role, but because they do not play an explanatory role. In doing so, it is possible to eliminate the distinction between theories representing time as dense, and theories that represent time as discrete.

A Terminological and Ontological Analysis of the NCI Thesaurus

Objective: The National Cancer Institute Thesaurus is described by its authors as “a biomedical vocabulary that provides consistent, unambiguous codes and definitions for concepts used in cancer research” and which “exhibits ontology-like properties in its construction and use”. We performed a qualitative analysis of the Thesaurus in order to assess its conformity with principles of good practice in terminology and ontology design.

Materials and Methods: We used both the on-line browsable version of the Thesaurus and its OWL-representation (version 04.08b, released on August 2, 2004), measuring each in light of the requirements put forward in relevant ISO terminology standards and in light of ontological principles advanced in the recent literature.

Results: We found many mistakes and inconsistencies with respect to the term-formation principles used, the underlying knowledge representation system, and missing or inappropriately assigned verbal and formal definitions.

Conclusion: Version 04.08b of the NCI Thesaurus suffers from the same broad range of problems that have been observed in other biomedical terminologies. For its further development, we recommend the use of a more principled approach that allows the Thesaurus to be tested not just for internal consistency but also for its degree of correspondence to that part of reality which it is designed to represent.

Perspectives on next steps in classification of oro-facial pain - part 2: role of psychosocial factors

This study was initiated by a symposium, in which the present authors contributed, organised by the International RDC/TMD Consortium Network in March 2013. The purpose of the study was to review the status of biobehavioural research - both quantitative and qualitative - related to oro-facial pain (OFP) with respect to the aetiology, pathophysiology, diagnosis and management of OFP conditions, and how this information can optimally be used for developing a structured OFP classification system for research. In particular, we address representation of psychosocial entities in classification systems, use of qualitative research to identify and understand the full scope of psychosocial entities and their interaction, and the usage of classification system for guiding treatment. We then provide recommendations for addressing these problems, including how ontological principles can inform this process.

Perspectives on next steps in classification of oro-facial pain - part 1: role of ontology

The purpose of this study was to review existing principles of oro-facial pain classifications and to specify design recommendations for a new system that would reflect recent insights in biomedical classification systems, terminologies and ontologies. The study was initiated by a symposium organised by the International RDC/TMD Consortium Network in March 2013, to which the present authors contributed. The following areas are addressed: problems with current classification approaches, status of the ontological basis of pain disorders, insufficient diagnostic aids and biomarkers for pain disorders, exploratory nature of current pain terminology and classification systems, and problems with prevailing classification methods from an ontological perspective. Four recommendations for addressing these problems are as follows: (i) develop a hypothesis-driven classification structure built on principles that ensure to our best understanding an accurate description of the relations among all entities involved in oro-facial pain disorders; (ii) take into account the physiology and phenomenology of oro-facial pain disorders to adequately represent both domains including psychosocial entities in a classification system; (iii) plan at the beginning for field-testing at strategic development stages; and (iv) consider how the classification system will be implemented. Implications in relation to the specific domains of psychosocial factors and biomarkers for inclusion into an oro-facial pain classification system are described in two separate papers.

Classifying orofacial pains: a new proposal of taxonomy based on ontology

We propose a new taxonomy model based on ontological principles for disorders that manifest themselves through the symptom of persistent orofacial pain and are commonly seen in clinical practice and difficult to manage. Consensus meeting of eight experts from various geographic areas representing different perspectives (orofacial pain, headache, oral medicine and ontology) as an initial step towards improving the taxonomy. Ontological principles were introduced, reviewed and applied during the consensus building process. Diagnostic criteria for persistent dento-alveolar pain disorder (PDAP) were formulated as an example to be used to model the taxonomical structure of all orofacial pain conditions. These criteria have the advantage of being (i) anatomically defined, (ii) in accordance with other classification systems for the provision of clinical care, (iii) descriptive and succinct, (iv) easy to adapt for applications in varying settings, (v) scalable and (vi) transferable for the description of pain disorders in other orofacial regions of interest. Limitations are that the criteria introduce new terminology, do not have widespread acceptance and have yet to be tested. These results were presented to the greater conference membership and were unanimously accepted. Consensus for the diagnostic criteria of PDAP was established within this working group. This is an initial first step towards developing a coherent taxonomy for orofacial pain disorders, which is needed to improve clinical research and care.

An evolutionary approach to realism-based adverse event representations

BACKGROUND

Part of the ReMINE project involved the creation of an ontology enabling computer-assisted decision support for optimal adverse event management.

OBJECTIVES

The ontology was required to satisfy the following requirements: 1) to be able to account for the distinct and context-dependent ways in which authoritative sources define the term 'adverse event', 2) to allow the identification of relevant risks against patient safety (RAPS) on the basis of the disease history of a patient as documented in electronic health records, and 3) to be compatible with present and future ontologies developed under the Open Biomedical Ontology (OBO) Foundry framework.

METHODS

We used as feeder ontologies the Basic Formal Ontology, the Foundational Model of Anatomy, the Ontology for General Medical Science, the Information Artifact Ontology and the Ontology of Mental Health. We further used relations defined according to the pattern set forth in the OBO Relation Ontology. In light of the intended use of the ontology for the representation of adverse events that have actually occurred and therefore are registered in a database, we also applied the principles of referent tracking.

RESULTS

We merged the upper portions of the mentioned feeder ontologies and introduced 22 additional representational units of which 13 are generally applicable in biomedicine and nine in the adverse event context. We provided for each representational unit a textual definition that can be translated into equivalent formal definitions.

CONCLUSION

The resulting ontology satisfies all of the requirements set forth. Merging the feeder ontologies, although all designed under the OBO Foundry principles, brought new insight into what the representational units of such ontologies actually denote.

A terminological and ontological analysis of the NCI Thesaurus

OBJECTIVE

The National Cancer Institute Thesaurus is described by its authors as "a biomedical vocabulary that provides consistent, unambiguous codes and definitions for concepts used in cancer research" and which "exhibits ontology-like properties in its construction and use". We performed a qualitative analysis of the Thesaurus in order to assess its conformity with principles of good practice in terminology and ontology design.

MATERIALS AND METHODS

We used both the on-line browsable version of the Thesaurus and its OWL-representation (version 04.08b, released on August 2, 2004), measuring each in light of the requirements put forward in relevant ISO terminology standards and in light of ontological principles advanced in the recent literature.

RESULTS

We found many mistakes and inconsistencies with respect to the term-formation principles used, the underlying knowledge representation system, and missing or inappropriately assigned verbal and formal definitions.

CONCLUSION

Version 04.08b of the NCI Thesaurus suffers from the same broad range of problems that have been observed in other biomedical terminologies. For its further development, we recommend the use of a more principled approach that allows the Thesaurus to be tested not just for internal consistency but also for its degree of correspondence to that part of reality which it is designed to represent.

Common sense as a key requirement for promoting the electronic healthcare record: two years of experience in the Belgian National PROREC Centre

PROREC-BE vzw is the first national PROREC centre that has been created to promote the use of high quality electronic healthcare records in line with European standards and insights. The mission of the centre is to satisfy the needs of all actors playing in the electronic healthcare record theatre. This is realised by setting up discussion fora and technical groups, and by adhering to common sense principles such as acceptance of each other's competence, looking at responsibilities instead of rights, and preferring win-win over zero-sum games. After two year of working, the Belgian PROREC centre has satisfactorily shown that working along these principles pays off, and is beneficial for all.

Syntactic-semantic tagging as a mediator between linguistic representations and formal models: an exercise in linking SNOMED to GALEN

Natural language understanding applications are good candidates to solve the knowledge acquisition bottleneck when designing large scale concept systems. However, a necessary condition is that systems are built that transform sentences into a meaning representation that is independent of the subtleties of linguistic structure that nevertheless underly the way language works. The Cassandra II syntactic-semantic tagging system fulfills this goal partially. Within the GALEN-IN-USE project, it is used to transform linguistic representations of surgical procedure expressions into conceptual representations. In this paper, the proctology chapter of the SNOMED V3.1 procedure axis was used as a testbed to evaluate the usefulness of this approach. A quantitative and qualitative analysis of the data obtained is presented, showing that the Cassandra system can indeed complement the manual modelling efforts being conducted in the GALEN-IN-USE project. The different requirements related to linguistic modelling versus conceptual modelling can partly be accounted for by using an interface ontology, of which the fine tuning will however remain an important effort.

Reconciling users' needs and formal requirements: issues in developing a reusable ontology for medicine

A common language, or terminology, for representing what clinicians have said and done is an important requirement for individual clinical systems, and it is a pre-requisite for integrating disparate applications in a distributed telematic healthcare environment. Formal representations based on description logics or closely related formalisms are increasingly used for representing medical terminologies. GALEN's experience in using one such formalism raises two major issues, as follows: how to make ontologies based on description logics easy to use and understand for both clinicians and applications developers; what features are required of the ontology and description logic if they are to achieve their aims. Based on our experience we put forward four contentions: two relating to each of these two issues, as follows: that natural language generation is essential to make a description logic based ontology accessible to users; that the description logic based ontology should be treated as an "assembly language" and accessed via "intermediate representations" oriented to users and "perspectives" adapting it to specific applications; that independence and reuse are best supported by partitioning the subsumption hierarchy of elementary concepts into orthogonal taxonomies, each of which forms a pure tree in which the branches at each level are disjoint but nonexhaustive subconcepts of the parent concept; that the expressivity of the description logic must include support for transitive relations despite the computational cost, and that this computational cost is acceptable in practice. The authors argue that these features will be necessary, though by no means sufficient, for the development of any large reusable ontology for medicine.

The distinction between linguistic and conceptual semantics in medical terminology and its implication for NLP-based knowledge acquisition

Natural language understanding systems have to exploit various kinds of knowledge in order to represent the meaning behind texts. Getting this knowledge in place is often such a huge enterprise that it is tempting to look for systems that can discover such knowledge automatically. We describe how the distinction between conceptual and linguistic semantics may assist in reaching this objective, provided that distinguishing between them is not done too rigorously. We present several examples to support this view and argue that in a multilingual environment, linguistic ontologies should be designed as interfaces between domain conceptualizations and linguistic knowledge bases.

From syntactic-semantic tagging to knowledge discovery in medical texts

In the GALEN project, the syntactic-semantic tagger MultiTALE is upgraded to extract knowledge from natural language surgical procedure expressions. In this paper, we describe the methodology applied and show that out of a randomly selected sample of such expressions coming from the procedure axis of Snomed International, 81% could be analysed correctly. The problems encountered fall in three different categories: unusual grammatical configurations within the Snomed terms, insufficient domain knowledge and different categorisation of concepts and semantic links in the domain and linguistic models used. It is concluded that the Multi-TALE system can be used to attach meaning to words that not have been encountered previously, but that an interface ontology mediating between domain models and linguistic models is needed to arrive at a higher level of independence from both particular languages and from particular domains.

From a time standard for medical informatics to a controlled language for health

CEN ENV 12381 is a European Prestandard focusing on formal representation and explicit reference of temporal information in healthcare informatics and telematics. One of its merits is not just the possibility to represent natural language expressions containing time-related information in a structured way, but also to give some mechanisms on how clinical language itself can be used to convey meaning unambiguously. As such, CEN ENV 12381 introduces the notion of 'controlled language use' in the domain of healthcare. In this paper the principles behind controlled language design and use are explained. Through a detailed study of the inconsistencies and ambiguities that arise when interpreting Snomed procedure terms in the framework of the Galen-In-Use project, it is shown that most of them can be explained as a violation of sound term-formation principles. A proposal is made to develop a controlled language for health and to use it in subsequent versions of coding and classification systems. It is expected that such an endeavour will lead to a more effective application of linguistic engineering in areas such as automatic knowledge acquisition, automatic translation, and terminology validation in the domain of healthcare informatics.

TSMI: a CEN/TC251 standard for time specific problems in healthcare informatics and telematics

Time is the most important variable in healthcare, and standards are needed about how to represent information with explicit references to time. In this paper, the European Prestandard 'TSMI: time standards for healthcare specific problems' (CEN/TC251 preENV 12381) is presented which aims to be the first contribution to this harmonisation process, focusing on 'representation' and 'explicit reference' of temporal information in healthcare. The prestandard is mainly composed of two parts. First, the basic building blocks for modelling time-related information are introduced, and a formal representation scheme proposed. In a second part, conformance rules and principles for Healthcare Data and Information as well as for Healthcare Information Systems, are covered.

From natural language to formal language: when MultiTALE meets GALEN

In the GALEN project, the syntactic-semantic tagger MultiTALE is upgraded to extract knowledge from natural language surgical procedure expressions. In this paper, we describe the methodology applied and show that out of a randomly selected sample of such expressions, 81% could be analysed correctly. The problems encountered are summarised and areas of further investigation identified.

A double-blind study of neurotropin in patients with acute ischemic stroke

Neurotropin was found to reduce brain oedema in an experimental model of brain infarction in the guinea-pig. A randomized double-blind controlled trial with Neurotropin was performed in 220 patients admitted within 24 h after an acute ischemic stroke. 35 of the neurotropin and 41 of the placebo-randomized patients had to be excluded. 10 included patients in the neurotropin and 13 in the placebo-treated group died within the study period of 15 days. A better clinical outcome was observed in the 65 included surviving neurotropin compared with the 56 placebo-treated patients. The size of the infarct and of the oedema zones was significantly more decreased on CT scans from Day 11 compared with Day 3 after stroke in the neurotropin than in the placebo treated group. Neurotropin is helpful in treating brain oedema, related to acute ischemic stroke.

The explanatory role of events in causal and temporal reasoning in medicine

The logic of time and the way we reason about time is intrinsically connected with the way we reason about causality. In this paper, we focus our attention on some of the less obvious ways in which reasoning about time and causality interact. It is explained why in temporal reasoning a firm distinction has to be made between the ontology, i.e., what happens, and the way we describe the ontology. Temporal events need to be redescribed in such a way that they causally explain why some of the events are followed by the others. While building a temporal/causal theory, certain events may be omitted, not because they do not play a causal role, but because they do not play an explanatory role. In doing so, it is possible to eliminate the distinction between theories representing time as dense, and theories that represent time as discrete.

Models for representation of terminologies and coding systems in medicine

Unification of medical coding systems is a perceived need involving a long-term task. Standards will support convergence of present coding systems towards a coherent set of tools. The Project Team "Model for Representation of Semantics" (CEN/TC251/PT003-MOSE) modeled existing tools to obtain a vocabulary apt to describe coding systems and terminologies. Requirements on faithfulness and safety, usefulness and purposiveness, coherence and integration were worked out, and the MOSE's 10 key principles for Standards in Medical Semantics were established.

Training of health care personnel towards the implementation and use of electronic health care records using integrated imaging technology

The hospital of the future will be a place in which Health Care providers of various disciplines will have access to all information about a patient in a timely fashion, and where the communication system will be able to cope with all information representations ranging through data, text, images and voice. Multimedia systems offer the facilities to cope with the specific problems of the mainly manual approach for the effective and efficient organization of information related to facts and findings in medical care. In this article we outline the training needs for future users of such systems.

Hemiballism. Clinico-pathological conference

A case of left hemiballism is presented. Besides multiple lacunar infarcts an haemorrhage in the contralateral subthalamic nucleus is shown. A short review of the literature is given with special attention to the etiology and the therapy.