Infrastructure for Semantic Annotation in the Genomics Domain

Mahmoud El-Haj, Nathan Rutherford, Matthew Coole, Ignatius Ezeani, Sheryl Prentice, Nancy Ide, Jo Knight, Scott Piao, John Mariani, Paul Rayson, Keith Suderman

Abstract
We describe a novel super-infrastructure for biomedical text mining which incorporates an end-to-end pipeline for the collection, annotation, storage, retrieval and analysis of biomedical and life sciences literature, combining NLP and corpus linguistics methods. The infrastructure permits extreme-scale research on the open access PubMed Central archive. It combines an updatable Gene Ontology Semantic Tagger (GOST) for entity identification and semantic markup in the literature, with a NLP pipeline scheduler (Buster) to collect and process the corpus, and a bespoke columnar corpus database (LexiDB) for indexing. The corpus database is distributed to permit fast indexing, and provides a simple web front-end with corpus linguistics methods for sub-corpus comparison and retrieval. GOST is also connected as a service in the Language Application (LAPPS) Grid, in which context it is interoperable with other NLP tools and data in the Grid and can be combined with them in more complex workflows. In a literature based discovery setting, we have created an annotated corpus of 9,776 papers with 5,481,543 words.
Anthology ID:
2020.lrec-1.855
Volume:
Proceedings of the Twelfth Language Resources and Evaluation Conference
Month:
May
Year:
2020
Address:
Marseille, France
Editors:
Nicoletta Calzolari, Frédéric Béchet, Philippe Blache, Khalid Choukri, Christopher Cieri, Thierry Declerck, Sara Goggi, Hitoshi Isahara, Bente Maegaard, Joseph Mariani, Hélène Mazo, Asuncion Moreno, Jan Odijk, Stelios Piperidis
Venue:
LREC
SIG:
Publisher:
European Language Resources Association
Note:
Pages:
6921–6929
Language:
English
URL:
https://aclanthology.org/2020.lrec-1.855
DOI:
Bibkey:
Cite (ACL):
Mahmoud El-Haj, Nathan Rutherford, Matthew Coole, Ignatius Ezeani, Sheryl Prentice, Nancy Ide, Jo Knight, Scott Piao, John Mariani, Paul Rayson, and Keith Suderman. 2020. Infrastructure for Semantic Annotation in the Genomics Domain. In Proceedings of the Twelfth Language Resources and Evaluation Conference, pages 6921–6929, Marseille, France. European Language Resources Association.
Cite (Informal):
Infrastructure for Semantic Annotation in the Genomics Domain (El-Haj et al., LREC 2020)
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https://preview.aclanthology.org/nschneid-patch-1/2020.lrec-1.855.pdf
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