docanalysis flags

`docanalysis` flags

--run_pygetpapers -> queries EuropePMC via pygetpapers --query --hits and project_name required
--query -> query to pygetpapers
-hits -> numbers of papers to download from pygetpapers
--project_name -> name of CProject folder (if pygetpapers is already run) or
--section -> section of paper from which you want to extract information (entities and/or key phrases)
--dictionary -> ami dictionary containing terms to narrow down sentences to extract entities from (semi-supervised entity extraction)
--entity_extraction -> extracts specified entities chosen from a list of entities (CARDINAL, DATE, EVENT, FAC, GPE, LANGUAGE, LAW, LOC, MONEY, NORP, ORDINAL, ORG, PERCENT, PERSON, PRODUCT, QUANTITY, TIME, WORK_OF_ART, GGP, SO, TAXON, CHEBI, GO, CL)
--key_phrase_extraction -> gives a list of keyphrases extracted either from specific sections or sentences for each paper in CProject. (unsupervised keyphrase extraction)
--make_ami_dict -> makes separate dictionaries from keyphrases and entities extracted. Merges duplicate entries into one