DOI: 10.5281/zenodo.4680826
title: BioASQ Sub-Corpus for the Pharmacology of Epilepsy (BioPepsy)

description: The sub corpus contains Standoff Annotations 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 Müller, Alexandra Hagelstein: Beyond Metadata: Enriching life science publications in Livivo with semantic entities from the linked data cloud. SEMANTiCS (Posters, Demos, SuCCESS) 2016 Bernd Müller, Alexandra Hagelstein, Thomas Gübitz: 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 Müller, Christoph Poley, Jana Pössel, Alexandra Hagelstein, Thomas Gübitz: LIVIVO - the Vertical Search Engine for Life Sciences. Datenbank-Spektrum 17(1): 29-34 (2017) Bernd Müller, 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 frequencies for all standoff annotations in documents from the 2021 BioASQ corpus that contain terms from <strong>EpSO </strong>co-occurring with at least one drug name aggepilepsy2021ESSOANDDrugNames.json- aggregation of frequencies for all standoff annotations in documents from the 2021 BioASQ corpus that contain terms from <strong>ESSO </strong>co-occurring with at least one drug name aggepilepsy2021EPILONTANDDrugNames.json- aggregation of frequencies for all standoff annotations in documents from the 2021 BioASQ corpus that contain terms from <strong>EPILONT </strong>co-occurring with at least one drug name aggepilepsy2021EPISEMANDDrugNames.json- aggregation of frequencies for all standoff annotations in documents from the 2021 BioASQ corpus that contain terms from <strong>EPISEM </strong>co-occurring with at least one drug name aggepilepsy2021FENICSANDDrugNames.json- aggregation of frequencies for all standoff annotations in documents from the 2021 BioASQ corpus that contain terms from <strong>FENICS </strong>co-occurring with at least one drug name All JSON files should be importable into a collection of a MongoDB. Documents are identified by their PMIDs. Please cite this data as: Müller, Bernd. BioASQ Sub-Corpus for the Pharmacology of Epilepsy (BioPEpsy) 2021. ZENODO, 10.5281/zenodo.4680086
description: {"references": ["Bernd M\u00fcller, Dietrich Rebholz-Schuhmann: Selected Approaches Ranking Contextual Term for the BioASQ Multi-label Classification (Task6a and 7a). PKDD/ECML Workshops (2) 2019: 569-580", "Bernd M\u00fcller, Christoph Poley, Jana P\u00f6ssel, Alexandra Hagelstein, Thomas G\u00fcbitz: LIVIVO - the Vertical Search Engine for Life Sciences. Datenbank-Spektrum 17(1): 29-34 (2017)", "Bernd M\u00fcller, Alexandra Hagelstein, Thomas G\u00fcbitz: 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 M\u00fcller, Alexandra Hagelstein: Beyond Metadata: Enriching life science publications in Livivo with semantic entities from the linked data cloud. SEMANTiCS (Posters, Demos, SuCCESS) 2016"]}