Medical Data Integration and the Semantic Annotation of Medical Protocols

Berlanga, Rafael; Jiménez-Ruiz, Ernesto; Nebot, Victoria; Manset, David; Branson, Andrew; Hauer, Tamás; McClatchey, Richard; Rogulin, Dmitry; Shamdasani, Jetendr; Zillner, Sonja; Freund, Joerg

doi:10.1109/cbms.2008.90

Cited by 11 publications

(14 citation statements)

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“…Efforts to improve consumerfriendliness of clinical text have focused on providing contextualized explanation and links to educational materials in Pap smear reports [4], contextulized links to health providers [12] and text translation [5]. This study is exploring the utility of automatic semantic annotations [6] in the form of synonyms and dynamic hyperlinks to aid consumers in reading their discharge summaries.Semantic annotations have been used to assist health professionals for their information retrieval [7,8]. However, the utility of semantic annotations from medical report text to aid consumers in reading and accessing information has received little attention.…”

Section: Introductionmentioning

confidence: 99%

SemLink — Dynamic generation of hyperlinks to enhance patient readability of discharge summaries

Adnan

Warren

Orr

2013

Proceedings of the 26th IEEE International Symposium on Computer-Based Medical Systems

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Discharge Summaries contains vocabulary that is difficult to understand for consumers. We used semantic annotation in SemLink to dynamically generate synonyms and hyperlinks to appropriate Internet resources for difficult terms in discharge summary text to make the text more comprehensible to consumers. This paper describes our semantic annotation approach and evaluates our automatic hyperlink generation algorithm in terms of success in locating web pages to hyperlink for difficult terms in the Clinical Management sections of a corpus of 200 discharge summary texts. The system achieved 95% success in hyperlinking topically relevant web resources to the difficult terms; 83% of the hyperlinks could be restricted to resources of reading grade-level 8 or less with no reduction in relevance. In the context of discharge summaries we find automated hyperlinking to provide a good level of performance in leveraging openly available resources to aid consumer interpretation of difficult terms.

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Section: Introductionmentioning

confidence: 99%

SemLink — Dynamic generation of hyperlinks to enhance patient readability of discharge summaries

Adnan

Warren

Orr

2013

Proceedings of the 26th IEEE International Symposium on Computer-Based Medical Systems

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“…In this section we describe the main experimental results achieved in the application of the proposed methodology to the construction of HeCTh. As previously mentioned, the vocabulary extraction is mainly guided by medical protocols [23] and related literature [39,45]. For the latter, we have build three collections of PubMed abstracts, namely: JIA (8,029 abstracts), TOF (7,967 abstracts) and BT (3,666 abstracts).…”

Section: Resultsmentioning

confidence: 99%

“…The knowledge acquisition in HeC is mainly based on a set of medical protocols (e.g. patient data forms) [23].…”

Section: Knowledge Acquisitionmentioning

confidence: 99%

Engineering in the Life Sciences, 9-12

2018

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This paper is intended to explore how to use terminological resources for ontology engineering. Nowadays there are several biomedical ontologies describing overlapping domains, but there is not a clear correspondence between the concepts that are supposed to be equivalent or just similar. These resources are quite precious but their integration and further development are expensive. Terminologies may support the ontological development in several stages of the lifecycle of the ontology; e.g. ontology integration. In this paper we investigate the use of terminological resources during the ontology lifecycle. We claim that the proper creation and use of a shared thesaurus is a cornerstone for the successful application of the Semantic Web technology within life sciences. Moreover, we have applied our approach to a real scenario, the Health-e-Child (HeC) project, and we have evaluated the impact of filtering and reorganizing several resources. As a result, we have created a reference thesaurus for this project, named HeCTh.

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“…The developed prototype included the Uniprot database [34], PubMed abstracts related to the diseases studied in the project, and the HeC patient database [35]. Recently, the external web service SCAIView [36] was also integrated to provide alternative protein-disease associations mined from the literature [37].…”

Section: Resultsmentioning

confidence: 99%

Exploring and linking biomedical resources through multidimensional semantic spaces

2012

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BackgroundThe semantic integration of biomedical resources is still a challenging issue which is required for effective information processing and data analysis. The availability of comprehensive knowledge resources such as biomedical ontologies and integrated thesauri greatly facilitates this integration effort by means of semantic annotation, which allows disparate data formats and contents to be expressed under a common semantic space. In this paper, we propose a multidimensional representation for such a semantic space, where dimensions regard the different perspectives in biomedical research (e.g., population, disease, anatomy and protein/genes).ResultsThis paper presents a novel method for building multidimensional semantic spaces from semantically annotated biomedical data collections. This method consists of two main processes: knowledge and data normalization. The former one arranges the concepts provided by a reference knowledge resource (e.g., biomedical ontologies and thesauri) into a set of hierarchical dimensions for analysis purposes. The latter one reduces the annotation set associated to each collection item into a set of points of the multidimensional space. Additionally, we have developed a visual tool, called 3D-Browser, which implements OLAP-like operators over the generated multidimensional space. The method and the tool have been tested and evaluated in the context of the Health-e-Child (HeC) project. Automatic semantic annotation was applied to tag three collections of abstracts taken from PubMed, one for each target disease of the project, the Uniprot database, and the HeC patient record database. We adopted the UMLS Meta-thesaurus 2010AA as the reference knowledge resource.ConclusionsCurrent knowledge resources and semantic-aware technology make possible the integration of biomedical resources. Such an integration is performed through semantic annotation of the intended biomedical data resources. This paper shows how these annotations can be exploited for integration, exploration, and analysis tasks. Results over a real scenario demonstrate the viability and usefulness of the approach, as well as the quality of the generated multidimensional semantic spaces.

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Medical Data Integration and the Semantic Annotation of Medical Protocols

Cited by 11 publications

References 11 publications

SemLink — Dynamic generation of hyperlinks to enhance patient readability of discharge summaries

SemLink — Dynamic generation of hyperlinks to enhance patient readability of discharge summaries

Engineering in the Life Sciences, 9-12

Exploring and linking biomedical resources through multidimensional semantic spaces

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Medical Data Integration and the Semantic Annotation of Medical Protocols

Cited by 11 publications

References 11 publications

SemLink &#x2014; Dynamic generation of hyperlinks to enhance patient readability of discharge summaries

SemLink &#x2014; Dynamic generation of hyperlinks to enhance patient readability of discharge summaries

Engineering in the Life Sciences, 9-12

Exploring and linking biomedical resources through multidimensional semantic spaces

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Product

Resources

About

SemLink — Dynamic generation of hyperlinks to enhance patient readability of discharge summaries

SemLink — Dynamic generation of hyperlinks to enhance patient readability of discharge summaries