Extracting information automatically from biological literature

C Blaschke, R Hoffmann, JC Oliveros… - Comparative and …, 2001 - ncbi.nlm.nih.gov
In the past few decades, biologists have generated a large amount of data that has been
published mainly in biological journals. It is now important to be able to recover as much as …

Making your database available through Wikipedia: the pros and cons

RD Finn, PP Gardner, A Bateman - Nucleic acids research, 2012 - academic.oup.com
Wikipedia, the online encyclopedia, is the most famous wiki in use today. It contains over 3.7
million pages of content; with many pages written on scientific subject matters that include …

[PDF][PDF] Biomedical text mining for research rigor and integrity: tasks, challenges, directions

H Kilicoglu - Briefings in bioinformatics, 2018 - academic.oup.com
An estimated quarter of a trillion US dollars is invested in the biomedical research enterprise
annually. There is growing alarm that a significant portion of this investment is wasted …

Comparing the use of research resource identifiers and natural language processing for citation of databases, software, and other digital artifacts

CN Hsu, AE Bandrowski, TH Gillespie… - … in Science & …, 2019 - ieeexplore.ieee.org
The Research Resource Identifier (RRID) was introduced in 2014 to better identify
biomedical research resources and track their use across the literature, including key digital …

Understanding life sciences data curation practices via user research

A Venkatesan, N Karamanis, M Ide-Smith… - …, 2019 - f1000research.com
Background: Manual curation is a cornerstone of public biological data resources. However,
it is a time-consuming process that urgently needs supportive technical solutions in the face …

Datasets2Tools, repository and search engine for bioinformatics datasets, tools and canned analyses

D Torre, P Krawczuk, KM Jagodnik, A Lachmann… - Scientific data, 2018 - nature.com
Biomedical data repositories such as the Gene Expression Omnibus (GEO) enable the
search and discovery of relevant biomedical digital data objects. Similarly, resources such …

Database citation in supplementary data linked to Europe PubMed Central full text biomedical articles

Ş Kafkas, JH Kim, X Pi, JR McEntyre - Journal of Biomedical Semantics, 2015 - Springer
Background In this study, we present an analysis of data citation practices in full text
research articles and their corresponding supplementary data files, made available in the …

the translational Data Catalog-discoverable biomedical datasets

D Welter, P Rocca-Serra, V Grouès, N Sallam… - Scientific Data, 2023 - nature.com
The discoverability of datasets resulting from the diverse range of translational and
biomedical projects remains sporadic. It is especially difficult for datasets emerging from pre …

Evaluation of text data mining for database curation: lessons learned from the KDD Challenge Cup

AS Yeh, L Hirschman, AA Morgan - arXiv preprint cs/0308032, 2003 - arxiv.org
MOTIVATION: The biological literature is a major repository of knowledge. Many biological
databases draw much of their content from a careful curation of this literature. However, as …

Scratchpads: a data-publishing framework to build, share and manage information on the diversity of life

VS Smith, SD Rycroft, KT Harman, B Scott… - BMC bioinformatics, 2009 - Springer
Abstract Background Natural History science is characterised by a single immense goal (to
document, describe and synthesise all facets pertaining to the diversity of life) that can only …