This PR adds a command that downloads and preprocesses the GDA corpus, seq2rel-ds preprocess gda. The GDA corpus is contains gene-disease associations and was created with distant supervision (see here for more information).
Other changes
✨ Add a new argument, sort_ents to parse_pubtator that sorts entities according to their order of first appearance. This is important for methods like ours, which use traditional, order-sensitive loss functions.
♻️ Arguments shared by query_pubtator and parse_pubtator are now passed as **kwargs.
TODO
[X] Expand test coverage for parse_pubtator to include all of the edge cases, as well as all of the parameters to the function. Tracking in #18.
Overview
This PR adds a command that downloads and preprocesses the GDA corpus,
seq2rel-ds preprocess gda. The GDA corpus is contains gene-disease associations and was created with distant supervision (see here for more information).Other changes
sort_entstoparse_pubtatorthat sorts entities according to their order of first appearance. This is important for methods like ours, which use traditional, order-sensitive loss functions.query_pubtatorandparse_pubtatorare now passed as**kwargs.TODO
parse_pubtatorto include all of the edge cases, as well as all of the parameters to the function. Tracking in #18.