| 1. |
- Vihinen, Mauno
(författare)
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Variation ontology: annotator guide.
- 2014
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Ingår i: Journal of Biomedical Semantics. - : Springer Science and Business Media LLC. - 2041-1480. ; 5:1
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Tidskriftsartikel (refereegranskat)abstract
- Systematic representation of information related to genetic and non-genetic variations is required to allow large scale studies, data mining and data integration, and to make it possible to reveal novel relationships between genotype and phenotype. Although lots of variation data is available it is often difficult to use due to lack of systematics.
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| 2. |
- Alirezaie, Marjan, 1980-, et al.
(författare)
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Automated reasoning using abduction for interpretation of medical signals
- 2014
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Ingår i: Journal of Biomedical Semantics. - : BioMed Central. - 2041-1480. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- This paper proposes an approach to leverage upon existing ontologies in order to automate the annotation of time series medical data. The annotation is achieved by an abductive reasoner using parsimonious covering theorem in order to determine the best explanation or annotation for specific user defined events in the data. The novelty of this approach resides in part by the system’s flexibility in how events are defined by users and later detected by the system. This is achieved via the use of different ontologies which find relations between medical, lexical and numerical concepts. A second contribution resides in the application of an abductive reasoner which uses the online and existing ontologies to provide annotations. The proposed method is evaluated on datasets collected from ICU patients and the generated annotations are compared against those given by medical experts.
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| 3. |
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| 4. |
- Dalianis, Hercules, et al.
(författare)
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De-identifying Swedish clinical text - refinement of a gold standard and experiments with Conditional random fields
- 2010
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Ingår i: Journal of Biomedical Semantics. - : BioMed Central. - 2041-1480. ; 1:6
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Tidskriftsartikel (refereegranskat)abstract
- Background In order to perform research on the information contained in Electronic Patient Records (EPRs), access to the data itself is needed. This is often very difficult due to confidentiality regulations. The data sets need to be fully de-identified before they can be distributed to researchers. De-identification is a difficult task where the definitions of annotation classes are not self-evident. Results We present work on the creation of two refined variants of a manually annotated Gold standard for de-identification, one created automatically, and one created through discussions among the annotators. The data is a subset from the Stockholm EPR Corpus, a data set available within our research group. These are used for the training and evaluation of an automatic system based on the Conditional Random Fields algorithm. Evaluating with four-fold cross-validation on sets of around 4-6 000 annotation instances, we obtained very promising results for both Gold Standards: F-score around 0.80 for a number of experiments, with higher results for certain annotation classes. Moreover, 49 false positives that were verified true positives were found by the system but missed by the annotators. Conclusions Our intention is to make this Gold standard, The Stockholm EPR PHI Corpus, available to other research groups in the future. Despite being slightly more time-consuming we believe the manual consensus gold standard is the most valuable for further research. We also propose a set of annotation classes to be used for similar de-identification tasks.
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| 5. |
- Henriksson, Aron, et al.
(författare)
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Synonym extraction and abbreviation expansion with ensembles of semantic spaces
- 2014
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Ingår i: Journal of Biomedical Semantics. - : Springer Science and Business Media LLC. - 2041-1480. ; 5:6
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Tidskriftsartikel (refereegranskat)abstract
- Background: Terminologies that account for variation in language use by linking synonyms and abbreviations to their corresponding concept are important enablers of high-quality information extraction from medical texts. Due to the use of specialized sub-languages in the medical domain, manual construction of semantic resources that accurately reflect language use is both costly and challenging, often resulting in low coverage. Although models of distributional semantics applied to large corpora provide a potential means of supporting development of such resources, their ability to isolate synonymy from other semantic relations is limited. Their application in the clinical domain has also only recently begun to be explored. Combining distributional models and applying them to different types of corpora may lead to enhanced performance on the tasks of automatically extracting synonyms and abbreviation-expansion pairs. Results: A combination of two distributional models – Random Indexing and Random Permutation – employed in conjunction with a single corpus outperforms using either of the models in isolation. Furthermore, combining semantic spaces induced from different types of corpora – a corpus of clinical text and a corpus of medical journal articles – further improves results, outperforming a combination of semantic spaces induced from a single source, as well as a single semantic space induced from the conjoint corpus. A combination strategy that simply sums the cosine similarity scores of candidate terms is generally the most profitable out of the ones explored. Finally, applying simple post-processing filtering rules yields substantial performance gains on the tasks of extracting abbreviation-expansion pairs, but not synonyms. The best results, measured as recall in a list of ten candidate terms, for the three tasks are: 0.39 for abbreviations to long forms, 0.33 for long forms to abbreviations, and 0.47 for synonyms. Conclusions: This study demonstrates that ensembles of semantic spaces can yield improved performance on the tasks of automatically extracting synonyms and abbreviation-expansion pairs. This notion, which merits further exploration, allows different distributional models – with different model parameters – and different types of corpora to be combined, potentially allowing enhanced performance to be obtained on a wide range of natural language processing tasks.
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| 6. |
- Lambrix, Patrick, et al.
(författare)
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A unified approach for debugging is-a structure and mappings in networked taxonomies
- 2013
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Ingår i: Journal of Biomedical Semantics. - : BioMed Central. - 2041-1480. ; 4
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundWith the increased use of ontologies and ontology mappings in semantically-enabled applications such as ontology-based search and data integration, the issue of detecting and repairing defects in ontologies and ontology mappings has become increasingly important. These defects can lead to wrong or incomplete results for the applications.ResultsWe propose a unified framework for debugging the is-a structure of and mappings between taxonomies, the most used kind of ontologies. We present theory and algorithms as well as an implemented system RepOSE, that supports a domain expert in detecting and repairing missing and wrong is-a relations and mappings. We also discuss two experiments performed by domain experts: an experiment on the Anatomy ontologies from the Ontology Alignment Evaluation Initiative, and a debugging session for the Swedish National Food Agency.ConclusionsSemantically-enabled applications need high quality ontologies and ontology mappings. One key aspect is the detection and removal of defects in the ontologies and ontology mappings. Our system RepOSE provides an environment that supports domain experts to deal with this issue. We have shown the usefulness of the approach in two experiments by detecting and repairing circa 200 and 30 defects, respectively.
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| 7. |
- Nyström, Mikael, 1977-, et al.
(författare)
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Enriching a primary health care version of ICD-10 using SNOMED CT mapping
- 2010
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Ingår i: Journal of Biomedical Semantics. - London, United Kingdom : BioMed Central. - 2041-1480. ; 1:7
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Tidskriftsartikel (refereegranskat)abstract
- Background: In order to satisfy different needs, medical terminology systems musthave richer structures. This study examines whether a Swedish primary health careversion of the mono-hierarchical ICD-10 (KSH97-P) may obtain a richer structureusing category and chapter mappings from KSH97-P to SNOMED CT and SNOMEDCT’s structure. Manually-built mappings from KSH97-P’s categories and chapters toSNOMED CT’s concepts are used as a starting pointResults: The mappings are manually evaluated using computer-producedinformation and a small number of mappings are updated. A new and polyhierarchicalchapter division of KSH97-P’s categories has been created using thecategory and chapter mappings and SNOMED CT’s generic structure. In the newchapter division, most categories are included in their original chapters. Aconsiderable number of concepts are included in other chapters than their originalchapters. Most of these inclusions can be explained by ICD-10’s design. KSH97-P’scategories are also extended with attributes using the category mappings andSNOMED CT’s defining attribute relationships. About three-fourths of all conceptsreceive an attribute of type Finding site and about half of all concepts receive anattribute of type Associated morphology. Other types of attributes are less common.Conclusions: It is possible to use mappings from KSH97-P to SNOMED CT andSNOMED CT’s structure to enrich KSH97-P’s mono-hierarchical structure with a polyhierarchicalchapter division and attributes of type Finding site and Associatedmorphology. The final mappings are available as additional files for this paper.
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| 8. |
- Allvin, Helen, et al.
(författare)
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Characteristics of Finnish and Swedish intensive care nursing narratives : a comparative analysis to support the development of clinical language technologies
- 2011
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Ingår i: Journal of Biomedical Semantics. - 2041-1480. ; 2:S1, s. 1-11
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Tidskriftsartikel (refereegranskat)abstract
- Background: Free text is helpful for entering information into electronic health records, but reusing it is a challenge. The need for language technology for processing Finnish and Swedish healthcare text is therefore evident; however, Finnish and Swedish are linguistically very dissimilar. In this paper we present a comparison of characteristics in Finnish and Swedish free-text nursing narratives from intensive care. This creates a framework for characterising and comparing clinical text and lays the groundwork for developing clinical language technologies. Methods: Our material included daily nursing narratives from one intensive care unit in Finland and one in Sweden. Inclusion criteria for patients were an inpatient period of least five days and an age of at least 16 years. We performed a comparative analysis as part of a collaborative effort between Finnish- and Swedish-speaking healthcare and language technology professionals that included both qualitative and quantitative aspects. The qualitative analysis addressed the content and structure of three average- sized health records from each country. In the quantitative analysis 514 Finnish and 379 Swedish health records were studied using various language technology tools. Results: Although the two languages are not closely related, nursing narratives in Finland and Sweden had many properties in common. Both made use of specialised jargon and their content was very similar. However, many of these characteristics were challenging regarding development of language technology to support producing and using clinical documentation. Conclusions: The way Finnish and Swedish intensive care nursing was documented, was not country or language dependent, but shared a common context, principles and structural features and even similar vocabulary elements. Technology solutions are therefore likely to be applicable to a wider range of natural languages, but they need linguistic tailoring. Availability: The Finnish and Swedish data can be found at: http://www.dsv.su.se/ hexanord/data/
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| 9. |
- Friberg Heppin, Karin, 1963
(författare)
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MedEval — A Swedish medical test collection with doctors and patients user groups
- 2011
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Ingår i: Journal of Biomedical Semantics. - 2041-1480. ; 2:3
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Tidskriftsartikel (refereegranskat)abstract
- Background Test collections for information retrieval are scarce. Domain specific test collections even more so, and medical test collections in the Swedish language non-existent prior to the making of the MedEval test collection. Most research in information retrieval has been performed in the English language, thus most test collections contain English documents. However, English is morphologically poor compared to many other European languages and a number of interesting and important aspects have not been investigated. Building a medical test collection in Swedish opens new research opportunities. Methods This article describes the making of and potential uses of MedEval, a Swedish medical test collection with assessments, not only for topical relevance, but also for target reader group: Doctors or Patients. A user of the test collection may choose if she wishes to search in the Doctors or the Patients scenario where the topical relevance assessments have been adjusted with consideration to user group, or to search in a scenario which regards only topical relevance. In addition to having three user groups, MedEval, in its present form, has two indexes, one where the terms are lemmatized and one where the terms are lemmatized and the compounds split and the constituents indexed together with the whole compound. Results Differences discovered between the documents written for medical professionals and documents written for laypersons are presented. These differences may be utilized in further studies of retrieval of documents aimed at certain groups of readers. Differences between the groups of documents are, for example, that professional documents have a higher ratio of compounds, have a greater average word length and contain more multi-word expressions. An experiment is described where the user scenarios have been utilized, searching with expert terms and lay terms, separately and in combination in the different scenarios. The tendency discovered is that the medical expert gets best results using expert terms and the lay person best results using lay terms, but also quite good results using expert terms or lay and expert terms in combination. Conclusions The many features of MedEval gives a variety of research possibilities, such as comparing the effectiveness of search terms when it comes to retrieving documents aimed at the different user groups or to study the effect of compound decomposition in retrieval of documents. As Swedish, the language of MedEval, is a morphologically more complex language than English, it is possible to study additional aspects of the effect of natural language processing in information retrieval, for example utilizing different inflectional word forms in the retrieval of expert vs lay documents. MedEval is the first Swedish test collection of the medical domain. Availability The Department of Swedish at the University of Gothenburg is in the process of making the MedEval test collection available to academic researchers.
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| 10. |
- Skeppstedt, Maria
(författare)
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Negation detection in Swedish clinical text : An adaption of NegEx to Swedish
- 2011
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Ingår i: Journal of Biomedical Semantics. - 2041-1480. ; 2:S3, s. 1-12
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Tidskriftsartikel (refereegranskat)abstract
- Background: Most methods for negation detection in clinical text have been developed for English text, and there is a need for evaluating the feasibility of adapting these methods to other languages. A Swedish adaption of the English rule-based negation detection system NegEx, which detects negations through the use of trigger phrases, was therefore evaluated. Results: The Swedish adaption of NegEx showed a precision of 75.2% and a recall of 81.9%, when evaluated on 558 manually classified sentences containing negation triggers, and a negative predictive value of 96.5% when evaluated on 342 sentences not containing negation triggers. Conclusions: The precision was significantly lower for the Swedish adaptation than published results for the English version, but since many negated propositions were identified through a limited set of trigger phrases, it could nevertheless be concluded that the same trigger phrase approach is possible in a Swedish context, even though it needs to be further developed. Availability: The triggers used for the evaluation of the Swedish adaption of NegEx are available at http://people.dsv.su.se/~mariask/resources/triggers.txt and can be used together with the original NegEx program for negation detection in Swedish clinical text.
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