ArticlePloS one2014
Knowledge extraction and semantic annotation of text from the encyclopedia of life.
Article in PloS one, 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.
- The changing landscape of text mining: a review of approaches for ecology and evolution.Proceedings. Biological sciences · 2024Review
- Past and future uses of text mining in ecology and evolution.Proceedings. Biological sciences · 2022Review
- Biodiversity Observations Miner: A web application to unlock primary biodiversity data from published literature.Biodiversity data journal · 2019Article
- Semi-automatic Extraction of Plants Morphological Characters from Taxonomic Descriptions Written in Spanish.Biodiversity data journal · 2018Article
- The importance of digitized biocollections as a source of trait data and a new VertNet resource.Database : the journal of biological databases and curation · 2016Article
- Topology of Innovation Spaces in the Knowledge Networks Emerging through Questions-And-Answers.PloS one · 2016Article
- ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life.Bioinformatics (Oxford, England) · 2015Article
- Finding our way through phenotypes.PLoS biology · 2015Article
- The Encyclopedia of Life v2: Providing Global Access to Knowledge About Life on Earth.Biodiversity data journal · 2014Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Numerous digitization and ontological initiatives have focused on translating biological knowledge from narrative text to machine-readable formats. In this paper, we describe two workflows for knowledge extraction and semantic annotation of text data objects featured in an online biodiversity aggregator, the Encyclopedia of Life. One workflow tags text with DBpedia URIs based on keywords. Another workflow finds taxon names in text using GNRD for the purpose of building a species association network. Both workflows work well: the annotation workflow has an F1 Score of 0.941 and the association algorithm has an F1 Score of 0.885. Existing text annotators such as Terminizer and DBpedia Spotlight performed well, but require some optimization to be useful in the ecology and evolution domain. Important future work includes scaling up and improving accuracy through the use of distributional semantics.
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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.