Duplicate Pubtator Annotations

wzkariampuzha commented 2 years ago

Right now Pubtator annotates the title and the abstract and returns annotations with duplicate infos_identifier numbers. These need to be removed and new annotations need to be able to added only if they are have not already been added to that article.

Constraints

Cannot lowercase the text before sending it to Pubtator due to case differences in the gene space.
Instead of Title and Abstract, we are allowed to concatenate title+abstract, however, it would be better if these were still kept separate.
This needs to be written in the weekly update function
Existing duplicate Pubtator annotations need to be removed.

brandon-gong commented 2 years ago

Assuming two nodes are duplicates iff they have the exact same (case sensitive) infons_identifier, infons_type, and text.
Remove type from PubtatorAnnotation nodes

brandon-gong commented 2 years ago

https://gist.github.com/brandon-gong/05164652f0ad286f4f3ca710532ba264

brandon-gong commented 2 years ago

https://gist.github.com/brandon-gong/a08d0fd7ab4e0a116e46fa6506cfb2aa

qianzhu2018 commented 2 years ago

almost done

ncats / RDAS

Duplicate Pubtator Annotations #3