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The utility and usability of the eFIP web interface were also evaluated during the BioCreative Workshop.
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This section describes the three distinct aspects of the eFIP method: (i) the eFIP extraction system; (ii) the online interface and (iii) the development of a use case.
The test set was manually curated by PRO curators without the use of the eFIP interface.
The overview of the eFIP system pipeline is illustrated in Figure 1.
We will improve the performance of the eFIP text mining with several enhancements.
To demonstrate the use of the eFIP system, we explored phosphorylation-dependent interactions involving 14-3-3 14-3-3 14-3-3
This averages to 104 min for manual curation and 42.5 min for eFIP-based curation, an ∼2.5-fold speed-up with the usage of the eFIP text mining interface.
In this article, we described an enhanced version of the eFIP system for the extraction of PPIs of phosphorylated proteins.
For the evaluation involving the use of the eFIP annotation interface (i.e. BioCreative Set 2 and BioCreative Set 3), the biocurators were asked to log in and mark as relevant or irrelevant the results proposed by eFIP, and to add any other textual evidence that was missed by eFIP.
The use of the eFIP interface provided a significant speed-up (∼2.5-fold) for time to completion of the curation task.
The subsections were shown to three biocurators of the PRO database, who are familiar with the output format of the eFIP system.
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