Queries in PubMed and MEDLINE with Entrez
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Entering edit mode
2.4 years ago
pl640 • 0

I'm trying to set up a PubMed query using Entrez and MEDLINE to retrieve journals about a complicated subject. I want to retrieve the most relevant abstracts of articles about the effectiveness of various drugs and treatments in infantile colic. Moreover, I want to see what MESH terms are linked to the search query. My goal is to improve the search query as much as possible, so I need a way in which I can build on top of my results.

-Update, I've replaced my last code with its newest version-

I've succeeded partly in setting up the general code for extracting titles, PMIDs, MeSH terms and Abstracts of a query. I'm now trying to create a loop in which I can test different queries and their results. Does anyone know how to efficiently create a loop? Or does anyone have an useful tutorial for doing this?

#Initialisation
Entrez.api_key = "example"
Entrez.email = "example@example.com"

TERM= "infant*[mh] AND colic[majr]"

handle = Entrez.egquery(term=TERM)
record = Entrez.read(handle)
for row in record["eGQueryResult"]:
    if row["DbName"]=="pubmed":
        print(row["Count"])

handle = Entrez.esearch(db="pubmed",
                        term=TERM,
                        retmax='100',
                        sort='relevance',
                        retmode='xml',
                        mindate="2016/11",
                        maxdate="2019/02")
record = Entrez.read(handle)
handle.close()
idlist = record["IdList"]
for i in idlist:
    if i == '27631535':
        idlist.remove(i)

print(idlist)

#downloading the corresponding MEDLINE records
handle = Entrez.efetch(db="pubmed",
                       id=idlist, rettype="medline", retmode="json")
records = Medline.parse(handle)
records = list(records)
for record in records:
    #if record[PMID] == '27631535':
        #records.remove(record)
    print("title:", record.get("TI", "?"))
    print("PMID:", record.get("PMID", "?"))
    print("MeSH Terms:", record.get("MH","?"))
    #print("abstracts:", record.get("AB", "?"))
    print("")

Many thanks in advance!

Biopython Entrez Pubmed MESH medline • 929 views
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Entering edit mode

Go to PubMed and play with your query first. I suggest something like these:

  • (infantile colic[mesh] AND effectiveness) AND (drugs OR herbal* OR sugar* OR safety)
  • (infantile colic[mesh] AND treatment) AND (effectiveness OR drugs OR herbal* OR sugar* OR safety)

Remember, that parenthesis in your query are important.

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Entering edit mode

Thank you for your response, I've experimented with the queries in PubMed and I've set up a list of queries that I want to test. Do you have recommendations of how to efficiently incorporate a loop in my code to do so?

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