unable to fetch all the documents from the api

[jmohit13]

Hi, I am using Bio 1.3.7 version to retrieve documents from the pubmed db. I observed a mismatch in the number of search results from the Pubmed search and Bio api.

Entrez.email = "test@gmail.com"
Entrez.api_key = <API_KEY>
handle = Entrez.esearch(db=DB, term=QUERY, rettype="medline")
record = Entrez.read(handle)

count = int(record['Count'])
handle = Entrez.esearch(db=DB, term=QUERY, retmax=count, rettype="medline")
record = Entrez.read(handle)

id_list = record["IdList"]

query = ((cSCC) OR (Cutaneous squamous cell carcinoma)) AND ((relapse) OR (relapse rate) OR (treatment progression))

No. of results from Bio api = 1552 No. of results from Pubmed search = 1749

For a few other queries, I observed this difference to be quite large. Can you please look into this. Thanks.

[ialbert]

This issue occasionally pops up on Biostar

• Biopython's Esearch for Pubmed does not give the same results as web search
• Xml Returned Using Efetch Differs To That Downloaded From Query At Pubmed Website

note that the problem comes from NCBI not bio or entrez direct in general. The NCBI website returns a different number of results on wether you connect from command line or via the web.