wenliangz · November 12, 2022 06:07 · Oct 7, 2015
diff --git a/pubmed.py b/pubmed.py
@@ -0,0 +1,53 @@
+## this little script shows off the use of the pubmed API through bioconductor
+## requires installing Biopython (using pip)
+## also requires installing the DTD files for each of the Entrez API calls, 
+## but the instructions for this are given when you run the script
+
+## useful list of Entrez databases that can be queried through API
+# pmc_pubmed	PubMed citations for these articles
+# pmc_refs_pubmed	PubMed article citing PMC article
+# pmc_pmc_cites	   PMC articles that given PMC article cites
+# pmc_pmc_citedby	PMC article citing given PMC article
+# pubmed_pubmed	 Calculated set of PubMed citations similar to the selected article(s) retrieved using a word weight algorithm. 
+# pubmed_pubmed_refs    Citation referenced in PubMed article. Only valid for PubMed citations that are also in PMC.
+
+
+from Bio import Entrez
+
+Entrez.email = "[email protected]"
+
+def get_abstract(pmid):
+    handle = Entrez.efetch(db='pubmed', id=pmid, retmode='text', rettype='abstract')
+    return handle.read()
+
+def get_links_id(pmid):
+	link_list = []
+	links = Entrez.elink(dbfrom="pubmed", id=pmid, linkname="pubmed_pubmed")	
+	record = Entrez.read(links)
+
+	records = record[0][u'LinkSetDb'][0][u'Link']
+
+	for link in records:
+		link_list.append(link[u'Id'])
+
+	return link_list
+
+def get_links_term(term):
+	links = Entrez.esearch(db="pubmed", retmax = 1000, term=term)	
+	record = Entrez.read(links)
+	link_list = record[u'IdList']
+
+	return link_list
+
+
+### MAIN -----------------------
+
+print(get_links_term("Saffran JR[Author] "))
+
+print "----------------------------"
+
+print(get_abstract("26113833"))
+
+print "----------------------------"
+
+print(get_links_id("8943209"))
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