BioASQ Sub-Corpus for the Pharmacology of Epilepsy (BioPepsy)
DOI10.5281/zenodo.4680826Zenodo4680826MaRDI QIDQ6693314FDOQ6693314
Dataset published at Zenodo repository.
Publication date: 12 April 2021
Copyright license: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International
The sub corpus contains StandoffAnnotations for Drug Names and Terms from Epilepsy Ontologies with their Aggregations Recognized in the 2021 BioASQ corpus. The terms for epilepsy ontologies are from NCBO BioPortal, namely from the ontologies EpSO, ESSO, EPILONT, EPISEM and FENICS: https://bioportal.bioontology.org/ontologies/EPSO https://bioportal.bioontology.org/ontologies/ESSO https://bioportal.bioontology.org/ontologies/EPILONT https://bioportal.bioontology.org/ontologies/EPISEM https://bioportal.bioontology.org/ontologies/FENICS The dictionary for the identificatin of drug names is derived from the DrugBank vocabulary available online at https://go.drugbank.com/releases/latest#open-data. The terms were identified using a custom implementation of a UIMA-based text mining wokflow that annotates free text with the UIMA ConceptMapper. Further descriptions of this workflow can be found in the following publications: Bernd Mller, Alexandra Hagelstein: Beyond Metadata: Enriching life science publications in Livivo with semantic entities from the linked data cloud. SEMANTiCS (Posters, Demos, SuCCESS) 2016 Bernd Mller, Alexandra Hagelstein, Thomas Gbitz: Life Science Ontologies in Literature Retrieval: A Comparison of Linked Data Sets for Use in Semantic Search on a Heterogeneous Corpus. EKAW (Satellite Events) 2016: 158-161 Bernd Mller, Christoph Poley, Jana Pssel, Alexandra Hagelstein, Thomas Gbitz: LIVIVO - the Vertical Search Engine for Life Sciences. Datenbank-Spektrum 17(1): 29-34 (2017) Bernd Mller, Dietrich Rebholz-Schuhmann: Selected Approaches Ranking Contextual Term for the BioASQ Multi-label Classification (Task6a and 7a). PKDD/ECML Workshops (2) 2019: 569-580 The file format is JSON. The file content is described as follows: bioasqepilepsy2021.json - All standoff annotations for each document in the 2021 BioASQ corpus aggepilepsy2021EPSOANDDrugNames.json - aggregation of frequenciesfor all standoff annotations in documents from the 2021 BioASQ corpus that contain terms from EpSO co-occurring with at least one drug name aggepilepsy2021ESSOANDDrugNames.json- aggregation of frequenciesfor all standoff annotations in documents from the 2021 BioASQ corpus that contain terms from ESSO co-occurring with at least one drug name aggepilepsy2021EPILONTANDDrugNames.json- aggregation of frequenciesfor all standoff annotations in documents from the 2021 BioASQ corpus that contain terms from EPILONTco-occurring with at least one drug name aggepilepsy2021EPISEMANDDrugNames.json- aggregation of frequenciesfor all standoff annotations in documents from the 2021 BioASQ corpus that contain terms from EPISEMco-occurring with at least one drug name aggepilepsy2021FENICSANDDrugNames.json- aggregation of frequenciesfor all standoff annotations in documents from the 2021 BioASQ corpus that contain terms from FENICSco-occurring with at least one drug name All JSONfiles should be importable into a collection of a MongoDB. Documents are identified by their PMIDs. Please cite this data as: Mller, Bernd. BioASQ Sub-Corpus for the Pharmacology of Epilepsy (BioPEpsy) 2021. ZENODO,10.5281/zenodo.4680086
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