Limits...
Dictionary construction and identification of possible adverse drug events in Danish clinical narrative text.

Eriksson R, Jensen PB, Frankild S, Jensen LJ, Brunak S - J Am Med Inform Assoc (2013)

Bottom Line: Drugs have tremendous potential to cure and relieve disease, but the risk of unintended effects is always present.Based on the undesirable effects section from the summary of product characteristics (SPC) of 7446 drugs, we have built a Danish ADE dictionary.Moreover, this method allows synonyms to be identified and anatomical location descriptions can be merged to allow appropriate grouping of effects in the same location.

View Article: PubMed Central - PubMed

Affiliation: Department of Disease Systems Biology, Faculty of Health and Medical Sciences, NNF Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.

ABSTRACT

Objective: Drugs have tremendous potential to cure and relieve disease, but the risk of unintended effects is always present. Healthcare providers increasingly record data in electronic patient records (EPRs), in which we aim to identify possible adverse events (AEs) and, specifically, possible adverse drug events (ADEs).

Materials and methods: Based on the undesirable effects section from the summary of product characteristics (SPC) of 7446 drugs, we have built a Danish ADE dictionary. Starting from this dictionary we have developed a pipeline for identifying possible ADEs in unstructured clinical narrative text. We use a named entity recognition (NER) tagger to identify dictionary matches in the text and post-coordination rules to construct ADE compound terms. Finally, we apply post-processing rules and filters to handle, for example, negations and sentences about subjects other than the patient. Moreover, this method allows synonyms to be identified and anatomical location descriptions can be merged to allow appropriate grouping of effects in the same location.

Results: The method identified 1 970 731 (35 477 unique) possible ADEs in a large corpus of 6011 psychiatric hospital patient records. Validation was performed through manual inspection of possible ADEs, resulting in precision of 89% and recall of 75%.

Discussion: The presented dictionary-building method could be used to construct other ADE dictionaries. The complication of compound words in Germanic languages was addressed. Additionally, the synonym and anatomical location collapse improve the method.

Conclusions: The developed dictionary and method can be used to identify possible ADEs in Danish clinical narratives.

Show MeSH

Related in: MedlinePlus

Dictionary group synonyms and synonymous coordinated terms. Synonyms, inflections and spelling variants were merged into a common concept, where ordering and prepositions were omitted.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3756275&req=5

AMIAJNL2013001708F4: Dictionary group synonyms and synonymous coordinated terms. Synonyms, inflections and spelling variants were merged into a common concept, where ordering and prepositions were omitted.

Mentions: ADE locations were collapsed using the BRENDA Tissue Ontology27 structure, which maps different levels of anatomical detail and enables aggregation into organs and organ systems as shown in figure 3. A separate input file, which can be modified, controls the details of this collapsing. Alternative spellings, synonyms and inflectional variants were aggregated to the same identifier. This means that location variants like abdominal and abdomen are assigned to the same identifier, likewise decrease and reduce from the laboratory value group share one identifier. These post-coordination conversions enabled us to aggregate different variations of coordinated terms as illustrated in figure 4.


Dictionary construction and identification of possible adverse drug events in Danish clinical narrative text.

Eriksson R, Jensen PB, Frankild S, Jensen LJ, Brunak S - J Am Med Inform Assoc (2013)

Dictionary group synonyms and synonymous coordinated terms. Synonyms, inflections and spelling variants were merged into a common concept, where ordering and prepositions were omitted.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3756275&req=5

AMIAJNL2013001708F4: Dictionary group synonyms and synonymous coordinated terms. Synonyms, inflections and spelling variants were merged into a common concept, where ordering and prepositions were omitted.
Mentions: ADE locations were collapsed using the BRENDA Tissue Ontology27 structure, which maps different levels of anatomical detail and enables aggregation into organs and organ systems as shown in figure 3. A separate input file, which can be modified, controls the details of this collapsing. Alternative spellings, synonyms and inflectional variants were aggregated to the same identifier. This means that location variants like abdominal and abdomen are assigned to the same identifier, likewise decrease and reduce from the laboratory value group share one identifier. These post-coordination conversions enabled us to aggregate different variations of coordinated terms as illustrated in figure 4.

Bottom Line: Drugs have tremendous potential to cure and relieve disease, but the risk of unintended effects is always present.Based on the undesirable effects section from the summary of product characteristics (SPC) of 7446 drugs, we have built a Danish ADE dictionary.Moreover, this method allows synonyms to be identified and anatomical location descriptions can be merged to allow appropriate grouping of effects in the same location.

View Article: PubMed Central - PubMed

Affiliation: Department of Disease Systems Biology, Faculty of Health and Medical Sciences, NNF Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.

ABSTRACT

Objective: Drugs have tremendous potential to cure and relieve disease, but the risk of unintended effects is always present. Healthcare providers increasingly record data in electronic patient records (EPRs), in which we aim to identify possible adverse events (AEs) and, specifically, possible adverse drug events (ADEs).

Materials and methods: Based on the undesirable effects section from the summary of product characteristics (SPC) of 7446 drugs, we have built a Danish ADE dictionary. Starting from this dictionary we have developed a pipeline for identifying possible ADEs in unstructured clinical narrative text. We use a named entity recognition (NER) tagger to identify dictionary matches in the text and post-coordination rules to construct ADE compound terms. Finally, we apply post-processing rules and filters to handle, for example, negations and sentences about subjects other than the patient. Moreover, this method allows synonyms to be identified and anatomical location descriptions can be merged to allow appropriate grouping of effects in the same location.

Results: The method identified 1 970 731 (35 477 unique) possible ADEs in a large corpus of 6011 psychiatric hospital patient records. Validation was performed through manual inspection of possible ADEs, resulting in precision of 89% and recall of 75%.

Discussion: The presented dictionary-building method could be used to construct other ADE dictionaries. The complication of compound words in Germanic languages was addressed. Additionally, the synonym and anatomical location collapse improve the method.

Conclusions: The developed dictionary and method can be used to identify possible ADEs in Danish clinical narratives.

Show MeSH
Related in: MedlinePlus