ArticleDatabase : the journal of biological databases and curation2014
Processing biological literature with customizable Web services supporting interoperable formats.
Article in Database : the journal of biological databases and curation, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
9 citing papers in PubMed.
- A survey on clinical natural language processing in the United Kingdom from 2007 to 2022.NPJ digital medicine · 2022Review
- Thalia: semantic search engine for biomedical abstracts.Bioinformatics (Oxford, England) · 2019Article
- A semantic-based workflow for biomedical literature annotation.Database : the journal of biological databases and curation · 2017Article
- PubMedPortable: A Framework for Supporting the Development of Text Mining Applications.PloS one · 2016Article
- BioC viewer: a web-based tool for displaying and merging annotations in BioC.Database : the journal of biological databases and curation · 2016Article
- Text mining resources for the life sciences.Database : the journal of biological databases and curation · 2016Review
- Europe PMC: a full-text literature database for the life sciences and platform for innovation.Nucleic acids research · 2015Article
- Optimising chemical named entity recognition with pre-processing analytics, knowledge-rich features and heuristics.Journal of cheminformatics · 2015Article
- Supporting the annotation of chronic obstructive pulmonary disease (COPD) phenotypes with text mining workflows.Journal of biomedical semantics · 2015Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Web services have become a popular means of interconnecting solutions for processing a body of scientific literature. This has fuelled research on high-level data exchange formats suitable for a given domain and ensuring the interoperability of Web services. In this article, we focus on the biological domain and consider four interoperability formats, BioC, BioNLP, XMI and RDF, that represent domain-specific and generic representations and include well-established as well as emerging specifications. We use the formats in the context of customizable Web services created in our Web-based, text-mining workbench Argo that features an ever-growing library of elementary analytics and capabilities to build and deploy Web services straight from a convenient graphical user interface. We demonstrate a 2-fold customization of Web services: by building task-specific processing pipelines from a repository of available analytics, and by configuring services to accept and produce a combination of input and output data interchange formats. We provide qualitative evaluation of the formats as well as quantitative evaluation of automatic analytics. The latter was carried out as part of our participation in the fourth edition of the BioCreative challenge. Our analytics built into Web services for recognizing biochemical concepts in BioC collections achieved the highest combined scores out of 10 participating teams. Database URL: http://argo.nactem.ac.uk.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.