I am new to python and would like to extract abstracts from pubmed using the entrez system from the bio package.
I got the esearch to give me my UIDs (stored in my_list_ges) and I can also download an entry using efetch.
Now, however, the result is a list of dictionaries and the entries look like a dictionary but I cannot access them:
Entrez.email= "my-email@provider.sth"
handle=Entrez.efetch(db="pubmed",id=my_list_ges[0],rettype="null",retmode="xml")
record = Entrez.read(handle)
abstract=record["Abstract"]
handle.close()
The result is a TypeError:
TypeError: list indices must be integers, not str
And I get a KeyError when trying to retrieve 'Abstract' from the first record:
>>> record[0]["Abstract"]
KeyError: 'Abstract'
This is weird, because in the result of the esearch I could easily access my UIDs by a dictionary
The structure of record[0] is:
{u'MedlineCitation': DictElement({
u'OtherID': [],
u'OtherAbstract': [],
u'CitationSubset': ['IM'],
u'KeywordList': [],
u'DateCreated': {u'Month': '03', u'Day': '17', u'Year': '2016'},
u'SpaceFlightMission': [],
u'GeneralNote': [],
u'Article':
DictElement({
u'ArticleDate': [
DictElement({u'Month': '03', u'Day': '16', u'Year': '2016'}, attributes={u'DateType': u'Electronic'})],
u'Pagination': {u'MedlinePgn': 'e0151666'},
u'AuthorList': ListElement([
DictElement({
u'LastName': "O'Neill",
u'Initials': 'KE',
u'Identifier': [],
u'AffiliationInfo': [{
u'Affiliation': 'MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, SCRM Building, 5 Little France Drive, Edinburgh, EH16 4UU, UK.',
u'Identifier': []}],
u'ForeName': 'Kathy E'
}, attributes={u'ValidYN': u'Y'}),
DictElement({
u'LastName': 'Bredenkamp',
u'Initials': 'N', u'Identifier': [],
u'AffiliationInfo': [{
u'Affiliation': 'MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, SCRM Building, 5 Little France Drive, Edinburgh, EH16 4UU, UK.',
u'Identifier': []}],
u'ForeName': 'Nicholas'}, attributes={u'ValidYN': u'Y'}),
DictElement({
u'LastName': 'Tischner',
u'Initials': 'C',
u'Identifier': [],
u'AffiliationInfo': [{
u'Affiliation': 'MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, SCRM Building, 5 Little France Drive, Edinburgh, EH16 4UU, UK.',
u'Identifier': []}],
u'ForeName': 'Christin'}, attributes={u'ValidYN': u'Y'}),
DictElement({
u'LastName': 'Vaidya',
u'Initials': 'HJ',
u'Identifier': [],
u'AffiliationInfo': [{
u'Affiliation': 'MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, SCRM Building, 5 Little France Drive, Edinburgh, EH16 4UU, UK.',
u'Identifier': []}],
u'ForeName': 'Harsh J'}, attributes={u'ValidYN': u'Y'}),
DictElement({
u'LastName': 'Stenhouse',
u'Initials': 'FH',
u'Identifier': [],
u'AffiliationInfo': [{
u'Affiliation': 'MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, SCRM Building, 5 Little France Drive, Edinburgh, EH16 4UU, UK.',
u'Identifier': []}], u'ForeName': 'Frances H'}, attributes={u'ValidYN': u'Y'}),
DictElement({
u'LastName': 'Peddie',
u'Initials': 'CD',
u'Identifier': [],
u'AffiliationInfo': [{
u'Affiliation': 'MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, SCRM Building, 5 Little France Drive, Edinburgh, EH16 4UU, UK.',
u'Identifier': []}],
u'ForeName': 'C Diana'}, attributes={u'ValidYN': u'Y'}),
DictElement({
u'LastName': 'Nowell',
u'Initials': 'CS',
u'Identifier': [],
u'AffiliationInfo': [{
u'Affiliation': 'MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, SCRM Building, 5 Little France Drive, Edinburgh, EH16 4UU, UK.',
u'Identifier': []}],
u'ForeName': 'Craig S'}, attributes={u'ValidYN': u'Y'}),
DictElement({
u'LastName': 'Gaskell',
u'Initials': 'T',
u'Identifier': [],
u'AffiliationInfo': [{
u'Affiliation': 'MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, SCRM Building, 5 Little France Drive, Edinburgh, EH16 4UU, UK.',
u'Identifier': []}],
u'ForeName': 'Terri'}, attributes={u'ValidYN': u'Y'}),
DictElement({
u'LastName': 'Blackburn',
u'Initials': 'CC',
u'Identifier': [],
u'AffiliationInfo': [{
u'Affiliation': 'MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, SCRM Building, 5 Little France Drive, Edinburgh, EH16 4UU, UK.',
u'Identifier': []}], u'ForeName': 'C Clare'}, attributes={u'ValidYN': u'Y'})],
attributes={u'Type': u'authors', u'CompleteYN': u'Y'}),
u'Language': ['eng'],
u'PublicationTypeList': [StringElement('Journal Article', attributes={u'UI': u'D016428'})],
u'Journal': {
u'ISSN': StringElement('1932-6203', attributes={u'IssnType': u'Electronic'}),
u'ISOAbbreviation': 'PLoS ONE',
u'JournalIssue': DictElement({
u'Volume': '11',
u'Issue': '3',
u'PubDate': {u'Year': '2016'}}, attributes={u'CitedMedium': u'Internet'}),
u'Title': 'PloS one'},
u'ArticleTitle': 'Foxn1 Is Dynamically Regulated in Thymic Epithelial Cells during Embryogenesis and at the Onset of Thymic Involution.',
u'ELocationID': [StringElement('10.1371/journal.pone.0151666', attributes={u'ValidYN': u'Y', u'EIdType': u'doi'})],
u'Abstract': {u'AbstractText': ['--Unnecessarily long abstract removed --']}}, attributes={u'PubModel': u'Electronic-eCollection'}),
u'PMID': StringElement('26983083', attributes={u'Version': u'1'}),
u'MedlineJournalInfo': {
u'MedlineTA': 'PLoS One',
u'Country': 'United States',
u'NlmUniqueID': '101285081',
u'ISSNLinking': '1932-6203'}}, attributes={u'Owner': u'NLM', u'Status': u'In-Data-Review'}),
u'PubmedData': {
u'ArticleIdList': [
StringElement('10.1371/journal.pone.0151666', attributes={u'IdType': u'doi'}),
StringElement('PONE-D-15-47173', attributes={u'IdType': u'pii'}),
StringElement('26983083', attributes={u'IdType': u'pubmed'})],
u'PublicationStatus': 'epublish',
u'History': [
DictElement({u'Month': '', u'Day': '', u'Year': '2016'}, attributes={u'PubStatus': u'ecollection'}),
DictElement({u'Month': '10', u'Day': '28', u'Year': '2015'}, attributes={u'PubStatus': u'received'}),
DictElement({u'Month': '3', u'Day': '2', u'Year': '2016'}, attributes={u'PubStatus': u'accepted'}),
DictElement({u'Month': '3', u'Day': '16', u'Year': '2016'}, attributes={u'PubStatus': u'epublish'}),
DictElement({u'Minute': '0', u'Month': '3', u'Day': '17', u'Hour': '6', u'Year': '2016'}, attributes={u'PubStatus': u'entrez'}),
DictElement({u'Minute': '0', u'Month': '3', u'Day': '18', u'Hour': '6', u'Year': '2016'}, attributes={u'PubStatus': u'pubmed'}),
DictElement({u'Minute': '0', u'Month': '3', u'Day': '18', u'Hour': '6', u'Year': '2016'}, attributes={u'PubStatus': u'medline'})]}
}
I don't know much about what the "right" thing to do in this situation is (not familiar with biopython), but the reason you are getting the KeyError in that the 'Abstract' key is nested in the 'MedlineCitation' dictionary:
record[0]['MedlineCitation']['Article']['Abstract']
Should give you something like:
{'AbstractText': ['--Unnecessarily long abstract removed --']}