Cargando…
RegEl corpus: identifying DNA regulatory elements in the scientific literature
High-throughput technologies led to the generation of a wealth of data on regulatory DNA elements in the human genome. However, results from disease-driven studies are primarily shared in textual form as scientific articles. Information extraction (IE) algorithms allow this information to be (semi-)...
Autores principales: | , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2022
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9235371/ https://www.ncbi.nlm.nih.gov/pubmed/35758881 http://dx.doi.org/10.1093/database/baac043 |
_version_ | 1784736302197899264 |
---|---|
author | Garda, Samuele Lenihan-Geels, Freyda Proft, Sebastian Hochmuth, Stefanie Schülke, Markus Seelow, Dominik Leser, Ulf |
author_facet | Garda, Samuele Lenihan-Geels, Freyda Proft, Sebastian Hochmuth, Stefanie Schülke, Markus Seelow, Dominik Leser, Ulf |
author_sort | Garda, Samuele |
collection | PubMed |
description | High-throughput technologies led to the generation of a wealth of data on regulatory DNA elements in the human genome. However, results from disease-driven studies are primarily shared in textual form as scientific articles. Information extraction (IE) algorithms allow this information to be (semi-)automatically accessed. Their development, however, is dependent on the availability of annotated corpora. Therefore, we introduce RegEl (Regulatory Elements), the first freely available corpus annotated with regulatory DNA elements comprising 305 PubMed abstracts for a total of 2690 sentences. We focus on enhancers, promoters and transcription factor binding sites. Three annotators worked in two stages, achieving an overall 0.73 F1 inter-annotator agreement and 0.46 for regulatory elements. Depending on the entity type, IE baselines reach F1-scores of 0.48–0.91 for entity detection and 0.71–0.88 for entity normalization. Next, we apply our entity detection models to the entire PubMed collection and extract co-occurrences of genes or diseases with regulatory elements. This generates large collections of regulatory elements associated with 137 870 unique genes and 7420 diseases, which we make openly available. Database URL: https://zenodo.org/record/6418451#.YqcLHvexVqg |
format | Online Article Text |
id | pubmed-9235371 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-92353712022-06-28 RegEl corpus: identifying DNA regulatory elements in the scientific literature Garda, Samuele Lenihan-Geels, Freyda Proft, Sebastian Hochmuth, Stefanie Schülke, Markus Seelow, Dominik Leser, Ulf Database (Oxford) Original Article High-throughput technologies led to the generation of a wealth of data on regulatory DNA elements in the human genome. However, results from disease-driven studies are primarily shared in textual form as scientific articles. Information extraction (IE) algorithms allow this information to be (semi-)automatically accessed. Their development, however, is dependent on the availability of annotated corpora. Therefore, we introduce RegEl (Regulatory Elements), the first freely available corpus annotated with regulatory DNA elements comprising 305 PubMed abstracts for a total of 2690 sentences. We focus on enhancers, promoters and transcription factor binding sites. Three annotators worked in two stages, achieving an overall 0.73 F1 inter-annotator agreement and 0.46 for regulatory elements. Depending on the entity type, IE baselines reach F1-scores of 0.48–0.91 for entity detection and 0.71–0.88 for entity normalization. Next, we apply our entity detection models to the entire PubMed collection and extract co-occurrences of genes or diseases with regulatory elements. This generates large collections of regulatory elements associated with 137 870 unique genes and 7420 diseases, which we make openly available. Database URL: https://zenodo.org/record/6418451#.YqcLHvexVqg Oxford University Press 2022-06-27 /pmc/articles/PMC9235371/ /pubmed/35758881 http://dx.doi.org/10.1093/database/baac043 Text en © The Author(s) 2022. Published by Oxford University Press. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Original Article Garda, Samuele Lenihan-Geels, Freyda Proft, Sebastian Hochmuth, Stefanie Schülke, Markus Seelow, Dominik Leser, Ulf RegEl corpus: identifying DNA regulatory elements in the scientific literature |
title | RegEl corpus: identifying DNA regulatory elements in the scientific literature |
title_full | RegEl corpus: identifying DNA regulatory elements in the scientific literature |
title_fullStr | RegEl corpus: identifying DNA regulatory elements in the scientific literature |
title_full_unstemmed | RegEl corpus: identifying DNA regulatory elements in the scientific literature |
title_short | RegEl corpus: identifying DNA regulatory elements in the scientific literature |
title_sort | regel corpus: identifying dna regulatory elements in the scientific literature |
topic | Original Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9235371/ https://www.ncbi.nlm.nih.gov/pubmed/35758881 http://dx.doi.org/10.1093/database/baac043 |
work_keys_str_mv | AT gardasamuele regelcorpusidentifyingdnaregulatoryelementsinthescientificliterature AT lenihangeelsfreyda regelcorpusidentifyingdnaregulatoryelementsinthescientificliterature AT proftsebastian regelcorpusidentifyingdnaregulatoryelementsinthescientificliterature AT hochmuthstefanie regelcorpusidentifyingdnaregulatoryelementsinthescientificliterature AT schulkemarkus regelcorpusidentifyingdnaregulatoryelementsinthescientificliterature AT seelowdominik regelcorpusidentifyingdnaregulatoryelementsinthescientificliterature AT leserulf regelcorpusidentifyingdnaregulatoryelementsinthescientificliterature |