def get_pubmed_from_doi(doi): 'try to get pubmed dict for this DOI, or None if not found' import pubmed xml = pubmed.search_pubmed(doi, retmax='1', field='LID') try: d, root = pubmed.dict_from_xml(xml, pubmedID='!Id') except KeyError: # some DOI not properly indexed in pubmed?!?! xml = pubmed.search_pubmed(doi, retmax='1') try: d, root = pubmed.dict_from_xml(xml, pubmedID='!Id') except KeyError: pass else: # have to check whether title matches pubmedDict = pubmed.get_pubmed_dict(d['pubmedID']) if pubmedDict.get('title')[:50].lower() == \ doiDict.get('title')[:50].lower(): return pubmedDict else: return pubmed.get_pubmed_dict(d['pubmedID'])
def _query_external(self, pubmedID): "obtain pubmed doc data from NCBI" import pubmed return pubmed.get_pubmed_dict(str(pubmedID))
def _query_external(self, pubmedID): 'obtain pubmed doc data from NCBI' import pubmed return pubmed.get_pubmed_dict(str(pubmedID))