Pubmed-ReferencePMID-citedPMCID_Search

A tool to get the reference pmid and cited pmcid and cited pmid of the give PMID list.

py function name： ‘searchRefCitPMID.py’

install dependency

run
pip install -r requirements.txt

usage

firstly, switch the work directory to the py function directory.

one Example:
cd C:\Users\Username\Desktop\searchRefCitPMID

secondly, running the py function as the following form.

one Example:
Python searchRefCitPMID.py -i PMIDexample1.txt

the help document of the py function 'searchRefCitPMID.py' is as follows:

Python searchRefCitPMID.py -h

Searching the reference PMID and cited PMCID,if necessary,change the cited PMCID to PMID

output filenames                    : reference_cited_PMID_Result.txt
PMCID-PMID converting INFO fileName : PMCID-PMID Converting Data.txt

optional arguments :
  -h    --help    show this help message and exit
  -i    I         inputFile directory,"csv" or "txt" types.
  -coln INN       column name of pmid in inputFile,         default: pubmed_id
  -api  API       APIkey,                                   default: 3d20b15ed393b63857232da6279e8cd94708  , this API key may not be useful in the future.
  -t    T         tool,                                     default: my_tool
  -e    E         email,                                    default: [email protected]
  -cv   CV        weather convert the cited PMCID to PMID,  default: True   , if don't need, set 'False'.

the output data are in the "Result" directory

"pmid to reference pmid.csv"

"pmid to cited pmcid.csv"

"pmid to cited pmid.csv"

"pmcid to pmid.csv"