The following directories will be created and populated with the
described output --
Step Class/Operation Path Description
------ -------------------------- ------------------- ---------------------------------------------------------------
1 SemanticScholarConverter semantic-scholar/ Dataset of JSON files and metadata file from Semantic Scholar
2 REACH reach/papers NXML, CSV/TSV, or plain text input for REACH.
3 reach/output FRIES output (events, entities, sentences triplet).
4 FriesMerger fries/merged Triplet files merged into one FRIES file.
5 FriesFilter fries/filtered FRIES files with at least one such event.
6 FriesReference fries/references Fries Files with \"Reference\" field appended.
-
$HOME/Documents/reach-to-frextis the "rootDir" directory as specified in REACH's "application.conf" file.restart.logis a list of filenames that have already been processed for a given operation, and may safely be skipped. -
Root directory (timestamped directory created every Sem. Scholar download (weekly Cron job) -- only need to process new files).
$HOME/Documents/reach-to-frext/current -> 2020-04-01T12:00:00 │ ├── semantic-scholar (1) │ │ │ ├── c1ad13d83e926979dbf2bbe52e4944082f28dfea.json │ └── metadata.csv │ ├── reach │ │ │ ├── papers (2) │ │ └── PMC1616946.txt │ │ └── restart.log (only process new files from dataset). │ │ │ ├── output (3) │ │ ├── PMC1616946.entities.json │ │ ├── PMC1616946.events.json │ │ ├── PMC1616946.sentences.json │ │ └── restart.log │ │ │ └── reach.log │ └── fries │ ├── merged (4) │ ├── PMC1616946.fries.json │ └── restart.log │ ├── filtered (5) │ ├── PMC1616946.fries.json │ └── restart.log │ └── references (6) ├── PMC1616946.fries.json └── restart.log