PubMed-PubTator-API-Script

API script with flexible query and simple EDA and analysis with PubMed and PubTator Trying to retrieve PMID from PubMed and then to retrieve annotated genes/proteins and diseases from PubTator.

What's this?

This is the python script use for get huge PubMed data from NCBI API.
Document is here. https://www.ncbi.nlm.nih.gov/books/NBK25501/
You have to read below term before use this script.
https://www.nlm.nih.gov/databases/download/terms_and_conditions.html

All code

You can see all code and viz at below link.
https://nbviewer.jupyter.org/github/tatsuya-takahashi/PubMed-API-Script/blob/master/PubMed.ipynb

How to use

You can set your own parameter to fetch PubMed data.
You can analyze data as you like. This sample indicates simple EDA.

# const
BASEURL_INFO = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi'
BASEURL_SRCH = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi'
BASEURL_FTCH = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi'

# parameters
SOURCE_DB    = 'pubmed'     #pubmed, nuccore, nucest, nucgss, popset, protein
TERM         = 'cancer'     # Entrez text query. 
DATE_TYPE    = 'pdat'       # Type of date used to limit a search. The allowed values vary between Entrez databases, but common values are 'mdat' (modification date), 'pdat' (publication date) and 'edat' (Entrez date). Generally an Entrez database will have only two allowed values for datetype.
MIN_DATE     = '2018/01/01' # yyyy/mm/dd
MAX_DATE     = '2019/12/31' # yyyy/mm/dd
SEP          = '|'
BATCH_NUM    = 1000

# seed
RANDOM_STATE = 42
np.random.seed(RANDOM_STATE)

What's output?

pubmed_article.csv

PMID
JournalTitle
Title
doi
Abstract
Language
Year_A
Month_A
Day_A
Year_PM
Month_PM
Day_PM
Status
MeSH
MeSH_UI KeywordI
Keyword

pubmed_author.csv

authorId
PMID
name
identifier
identifierSource

pubmed_affiliation.csv

authorId
affiliation

HiroH23/PubMed-API-Script