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Nevertheless full text processing would most certainly increase the recall of automatic processing.
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Full-text processing is planned for the future.
Although there is little benefit from full-text processing for some applications such as MeSH indexing (24), it is crucial to other tasks such as the extraction of scientific claims: a recent study showed that only 7.84% of scientific claims are reported in abstracts (25).
The curation pipeline for the CellFinder database includes the following steps (cf. Figure 1): triage of potential relevant documents, retrieval of full text, linguistic pre-processing, named-entity recognition, post-processing, relationship extraction, manual validation of the results and integration of gene expression events into the database.
We find as well that processing MEDLINE is different to processing full text articles.
A total of 66 records were selected for full text review and data processing.
The TB classifier showed difficulties when processing full text, as its performances decreased by 44%; in contrast, the ML performances only decreased by 6%.
> -wrap-foot> togethergethese these prior results not only indicate that processing full text is essential for supporting curation of genetic variants, both in proteins and DNA, but also raise doubts about the role of text mining tools in the context of real-world curation tasks.
We believe that more elaborate approaches for detecting these ignored but highly confident functional assignments (e.g. methods based on natural-language processing of full text journal articles [ 54]) would extract considerably more annotations than our simple keyword-based PubMed search (see Methods for details).
Any disagreement in the selection of abstracts was resolved by consensus or by a third reviewer (B.F .. Full text articles for review and data processing were obtained for all selected abstracts.
The interactive interface of PCorral supports curation work and interactive exploration of the full set of MEDLINE, and curators may integrate the text processing services from Whatizit into their own curation infrastructure.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com