Suppr超能文献

生物学家使用正式语言写作的新理由。

New reasons for biologists to write with a formal language.

机构信息

Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, Basel 4070, Switzerland.

出版信息

Database (Oxford). 2022 Jun 3;2022. doi: 10.1093/database/baac039.

Abstract

Current biological writing is afflicted by the use of ambiguous names, convoluted sentences, vague statements and narrative-fitted storylines. This represents a challenge for biological research in general and in particular for fields such as biological database curation and text mining, which have been tasked to cope with exponentially growing content. Improving the quality of biological writing by encouraging unambiguity and precision would foster expository discipline and machine reasoning. More specifically, the routine inclusion of formal languages in biological writing would improve our ability to describe, compile and model biology.

摘要

当前的生物写作受到模糊名称、复杂句子、模糊陈述和叙事拟合故事情节的影响。这对一般的生物研究,特别是生物数据库编纂和文本挖掘等领域构成了挑战,这些领域的任务是应对呈指数级增长的内容。通过鼓励清晰和精确来提高生物写作的质量将促进说明性学科和机器推理。更具体地说,在生物写作中常规地使用形式语言将提高我们描述、编译和建模生物学的能力。

相似文献

1
New reasons for biologists to write with a formal language.
Database (Oxford). 2022 Jun 3;2022. doi: 10.1093/database/baac039.
3
Automated assembly of molecular mechanisms at scale from text mining and curated databases.
Mol Syst Biol. 2023 May 9;19(5):e11325. doi: 10.15252/msb.202211325. Epub 2023 Mar 20.
4
BELTracker: evidence sentence retrieval for BEL statements.
Database (Oxford). 2016 May 12;2016. doi: 10.1093/database/baw079. Print 2016.
5
Survey of Natural Language Processing Techniques in Bioinformatics.
Comput Math Methods Med. 2015;2015:674296. doi: 10.1155/2015/674296. Epub 2015 Oct 7.
6
Natural language processing pipelines to annotate BioC collections with an application to the NCBI disease corpus.
Database (Oxford). 2014 Jun 16;2014. doi: 10.1093/database/bau056. Print 2014.
7
Extraction of causal relations based on SBEL and BERT model.
Database (Oxford). 2021 Feb 18;2021. doi: 10.1093/database/baab005.
8
OntoMate: a text-mining tool aiding curation at the Rat Genome Database.
Database (Oxford). 2015 Jan 25;2015. doi: 10.1093/database/bau129. Print 2015.
9
BioC interoperability track overview.
Database (Oxford). 2014 Jun 30;2014. doi: 10.1093/database/bau053. Print 2014.
10
Improved chemical text mining of patents with infinite dictionaries and automatic spelling correction.
J Chem Inf Model. 2012 Jan 23;52(1):51-62. doi: 10.1021/ci200463r. Epub 2011 Dec 28.

本文引用的文献

1
STonKGs: a sophisticated transformer trained on biomedical text and knowledge graphs.
Bioinformatics. 2022 Mar 4;38(6):1648-1656. doi: 10.1093/bioinformatics/btac001.
2
Opinion: Standardizing gene product nomenclature-a call to action.
Proc Natl Acad Sci U S A. 2021 Jan 19;118(3). doi: 10.1073/pnas.2025207118.
3
How a torrent of COVID science changed research publishing - in seven charts.
Nature. 2020 Dec;588(7839):553. doi: 10.1038/d41586-020-03564-y.
5
Ten tips for a text-mining-ready article: How to improve automated discoverability and interpretability.
PLoS Biol. 2020 Jun 1;18(6):e3000716. doi: 10.1371/journal.pbio.3000716. eCollection 2020 Jun.
6
Biomedical event extraction with a novel combination strategy based on hybrid deep neural networks.
BMC Bioinformatics. 2020 Feb 6;21(1):47. doi: 10.1186/s12859-020-3376-2.
7
Re-curation and rational enrichment of knowledge graphs in Biological Expression Language.
Database (Oxford). 2019 Jan 1;2019. doi: 10.1093/database/baz068.
8
Twenty-First Century Biological Nomenclature-The Enduring Power of Names.
Integr Comp Biol. 2018 Dec 1;58(6):1122-1131. doi: 10.1093/icb/icy060.
9
A global network of biomedical relationships derived from text.
Bioinformatics. 2018 Aug 1;34(15):2614-2624. doi: 10.1093/bioinformatics/bty114.
10
From word models to executable models of signaling networks using automated assembly.
Mol Syst Biol. 2017 Nov 24;13(11):954. doi: 10.15252/msb.20177651.

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验