ArticleBMC bioinformatics2008
Natural language processing in aid of FlyBase curators.
Article in BMC bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 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
17 citing papers in PubMed.
- The alliance of genome resources: transforming comparative genomics.Mammalian genome : official journal of the International Mammalian Genome Society · 2023Review
- Data libraries - the missing element for modeling biological systems.The FEBS journal · 2020Review
- Biocuration: Distilling data into knowledge.PLoS biology · 2018Article
- Automated PDF highlighting to support faster curation of literature for Parkinson's and Alzheimer's disease.Database : the journal of biological databases and curation · 2017Article
- Mining clinical attributes of genomic variants through assisted literature curation in Egas.Database : the journal of biological databases and curation · 2016Article
- Biocuration with insufficient resources and fixed timelines.Database : the journal of biological databases and curation · 2015Article
- Egas: a collaborative and interactive document curation platform.Database : the journal of biological databases and curation · 2014Article
- Annotating the biomedical literature for the human variome.Database : the journal of biological databases and curation · 2013Article
- Text-mining solutions for biomedical research: enabling integrative biology.Nature reviews. Genetics · 2012Review
- PMRD: a curated database for genes and mutants involved in plant male reproduction.BMC plant biology · 2012Article
- Text mining for literature review and knowledge discovery in cancer risk assessment and research.PloS one · 2012Article
- Argo: an integrative, interactive, text mining-based workbench supporting curation.Database : the journal of biological databases and curation · 2012Article
- Using ODIN for a PharmGKB revalidation experiment.Database : the journal of biological databases and curation · 2012Article
- Opportunities for text mining in the FlyBase genetic literature curation workflow.Database : the journal of biological databases and curation · 2012Article
- BioCreative III interactive task: an overview.BMC bioinformatics · 2011Article
- A comparison and user-based evaluation of models of textual information structure in the context of cancer risk assessment.BMC bioinformatics · 2011Article
- The first step in the development of Text Mining technology for Cancer Risk Assessment: identifying and organizing scientific evidence in risk assessment literature.BMC bioinformatics · 2009Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
backgroundDespite increasing interest in applying Natural Language Processing (NLP) to biomedical text, whether this technology can facilitate tasks such as database curation remains unclear.
resultsPaperBrowser is the first NLP-powered interface that was developed under a user-centered approach to improve the way in which FlyBase curators navigate an article. In this paper, we first discuss how observing curators at work informed the design and evaluation of PaperBrowser. Then, we present how we appraise PaperBrowser's navigational functionalities in a user-based study using a text highlighting task and evaluation criteria of Human-Computer Interaction. Our results show that PaperBrowser reduces the amount of interactions between two highlighting events and therefore improves navigational efficiency by about 58% compared to the navigational mechanism that was previously available to the curators. Moreover, PaperBrowser is shown to provide curators with enhanced navigational utility by over 74% irrespective of the different ways in which they highlight text in the article.
conclusionWe show that state-of-the-art performance in certain NLP tasks such as Named Entity Recognition and Anaphora Resolution can be combined with the navigational functionalities of PaperBrowser to support curation quite successfully.
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What OpenQuestion holds
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.