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The challenge organizers provided manually annotated abstracts from PubMed (10,000 abstracts), of which 3,500 abstracts were used as a training set, 3,500 abstracts were used as a development set, and 3,000 abstracts were used as a test set.
Having a sufficient number of manually annotated abstracts is now our priority.
In this article, we have presented the first corpus of manually annotated abstracts using the HPO.
It contains 500 manually annotated abstracts with 95 mutations in 55 abstracts.
The authors reach a recall of 0.96 and precision of 1.0 on 50 manually annotated abstracts for miRNA mention identification.
As mentioned in Section 5.2.2, only one or two manually annotated abstracts are shown in DIP as an evidence of an interaction.
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The corpus consists of 10,000 manually annotated Medline abstracts divided in a training set and a development set (3,500 abstracts each), and a test set (3,000 abstracts).
For the third test, as we did not have access to the annotator used by GoPubMed, we manually annotated 50 randomized abstracts from the results seen on GoPubMed's Web site.
To this purpose, we are developing a web annotation tool that allows healthcare professionals to manually annotate Medline abstracts.
This corpus was recently developed by a team of 14 annotators and comprises 793 PubMed abstracts, manually annotated for disease mentions and corresponding Medical Subject Headings (MeSH®) or Online Mendelian Inheritance in Man® (OMIM®) concepts.
This dataset or corpus consists of abstracts manually annotated by an undergraduate research assistant (S.L).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com