[HTML][HTML] LSTMVoter: chemical named entity recognition using a conglomerate of sequence labeling tools

W Hemati, A Mehler - Journal of cheminformatics, 2019 - Springer
Background Chemical and biomedical named entity recognition (NER) is an essential
preprocessing task in natural language processing. The identification and extraction of …

[HTML][HTML] LeadMine: a grammar and dictionary driven approach to entity recognition

DM Lowe, RA Sayle - Journal of cheminformatics, 2015 - Springer
Background Chemical entity recognition has traditionally been performed by machine
learning approaches. Here we describe an approach using grammars and dictionaries. This …

OSPAR: A Corpus for Extraction of Organic Synthesis Procedures with Argument Roles

K Machi, S Akiyama, Y Nagata… - Journal of Chemical …, 2023 - ACS Publications
There is a pressing need for the automated extraction of chemical reaction information
because of the rapid growth of scientific documents. The previously reported works in the …

Overview of DrugProt task at BioCreative VII: data and methods for large-scale text mining and knowledge graph generation of heterogenous chemical–protein …

A Miranda-Escalada, F Mehryary, J Luoma… - Database, 2023 - academic.oup.com
It is getting increasingly challenging to efficiently exploit drug-related information described
in the growing amount of scientific literature. Indeed, for drug–gene/protein interactions, the …

[HTML][HTML] Dataset search in biodiversity research: Do metadata in data repositories reflect scholarly information needs?

F Löffler, V Wesp, B König-Ries, F Klan - PloS one, 2021 - journals.plos.org
The increasing amount of publicly available research data provides the opportunity to link
and integrate data in order to create and prove novel hypotheses, to repeat experiments or …

[HTML][HTML] MER: a shell script and annotation server for minimal named entity recognition and linking

FM Couto, A Lamurias - Journal of cheminformatics, 2018 - Springer
Named-entity recognition aims at identifying the fragments of text that mention entities of
interest, that afterwards could be linked to a knowledge base where those entities are …

The impact of domain-specific pre-training on named entity recognition tasks in materials science

N Walker, A Trewartha, H Huo, S Lee… - Available at SSRN …, 2021 - papers.ssrn.com
The massive increase in materials science publications has resulted in a bottleneck in
efficiently connecting new materials discoveries to knowledge from established literature …

FDAPT: Federated domain-adaptive pre-training for language models

L Jiang, F Svoboda, ND Lane - arXiv preprint arXiv:2307.06933, 2023 - arxiv.org
Combining Domain-adaptive Pre-training (DAPT) with Federated Learning (FL) can
enhance model adaptation by leveraging more sensitive and distributed data while …

[HTML][HTML] The RareDis corpus: a corpus annotated with rare diseases, their signs and symptoms

C Martínez-deMiguel, I Segura-Bedmar… - Journal of Biomedical …, 2022 - Elsevier
Rare diseases affect a small number of people compared to the general population.
However, more than 6,000 different rare diseases exist and, in total, they affect more than …

[HTML][HTML] Lessons learned to enable question answering on knowledge graphs extracted from scientific publications: A case study on the coronavirus literature

C Badenes-Olmedo, O Corcho - Journal of Biomedical Informatics, 2023 - Elsevier
The article presents a workflow to create a question-answering system whose knowledge
base combines knowledge graphs and scientific publications on coronaviruses. It is based …