Tag Me If You Can! Semantic Annotation of Biodiversity Metadata with the QEMP Corpus and the BiodivTagger

Felicitas Löffler, Nora Abdelmageed, Samira Babalou, Pawandeep Kaur, Birgitta König-Ries


Abstract
Dataset Retrieval is gaining importance due to a large amount of research data and the great demand for reusing scientific data. Dataset Retrieval is mostly based on metadata, structured information about the primary data. Enriching these metadata with semantic annotations based on Linked Open Data (LOD) enables datasets, publications and authors to be connected and expands the search on semantically related terms. In this work, we introduce the BiodivTagger, an ontology-based Information Extraction pipeline, developed for metadata from biodiversity research. The system recognizes biological, physical and chemical processes, environmental terms, data parameters and phenotypes as well as materials and chemical compounds and links them to concepts in dedicated ontologies. To evaluate our pipeline, we created a gold standard of 50 metadata files (QEMP corpus) selected from five different data repositories in biodiversity research. To the best of our knowledge, this is the first annotated metadata corpus for biodiversity research data. The results reveal a mixed picture. While materials and data parameters are properly matched to ontological concepts in most cases, some ontological issues occurred for processes and environmental terms.
Anthology ID:
2020.lrec-1.560
Volume:
Proceedings of the 12th Language Resources and Evaluation Conference
Month:
May
Year:
2020
Address:
Marseille, France
Venue:
LREC
SIG:
Publisher:
European Language Resources Association
Note:
Pages:
4557–4564
Language:
English
URL:
https://aclanthology.org/2020.lrec-1.560
DOI:
Bibkey:
Cite (ACL):
Felicitas Löffler, Nora Abdelmageed, Samira Babalou, Pawandeep Kaur, and Birgitta König-Ries. 2020. Tag Me If You Can! Semantic Annotation of Biodiversity Metadata with the QEMP Corpus and the BiodivTagger. In Proceedings of the 12th Language Resources and Evaluation Conference, pages 4557–4564, Marseille, France. European Language Resources Association.
Cite (Informal):
Tag Me If You Can! Semantic Annotation of Biodiversity Metadata with the QEMP Corpus and the BiodivTagger (Löffler et al., LREC 2020)
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PDF:
https://aclanthology.org/2020.lrec-1.560.pdf