[Biopython] using efetch to return mesh terms

[Alex Garnett]

Possibly my mistake -- in the past I've interpreted strings escaped by 'u'
as encoded json. In any case, I'm still looking to get this to return mesh
terms... any advice?

Thanks,
-alex
On Nov 27, 2012 9:30 PM, "Michiel de Hoon" <mjldehoon at yahoo.com> wrote:

> It's not a json, it's just a Python dictionary.
> Best,
> -Michiel.
>
>
> --- On *Tue, 11/27/12, Alex Garnett <axfelix at gmail.com>* wrote:
>
>
> From: Alex Garnett <axfelix at gmail.com>
> Subject: Re: [Biopython] using efetch to return mesh terms
> To: "Michiel de Hoon" <mjldehoon at yahoo.com>
> Cc: "biopython" <biopython at lists.open-bio.org>
> Date: Tuesday, November 27, 2012, 11:42 PM
>
> Thanks for the quick response, Michiel.
>
> I've been trying:
>
> handle = Entrez.efetch(db="pubmed", id=pmids, rettype="medline",
> retmode="xml")
> records = Entrez.read(handle)
>
> where pmids is a list of pubmed IDs.
>
> this returns the following json:
>
> {u'MedlineCitation': DictElement({u'OtherID': [], u'OtherAbstract': [],
> u'CitationSubset': ['IM'], u'KeywordList': [], u'DateCreated': {u'Month':
> '11', u'Day':
> '20', u'Year': '2012'}, u'SpaceFlightMission': [], u'GeneralNote': [],
> u'Article': DictElement({u'ArticleDate': [], u'Pagination': {u'MedlinePgn':
> '140-54'}, u'AuthorList': ListElement([DictElement({u'LastName': 'Goupil',
> u'Initials': 'L',
> u'NameID': [], u'ForeName': 'Louise'}, attributes={u'ValidYN': u'Y'}),
> DictElement({u'LastName': 'Bekinschtein', u'Initials': 'T', u'NameID': [],
> u'ForeName': 'Tristan'}, attributes={u'ValidYN': u'Y'})],
> attributes={u'Type': u'authors', u'CompleteYN': u'Y'}), u'Language':
> ['eng'], u'PublicationTypeList': ['Journal Article'], u'Journal': {u'ISSN':
> StringElement('0003-9829', attributes={u'IssnType': u'Print'}),
> u'ISOAbbreviation': 'Arch Ital Biol', u'JournalIssue':
> DictElement({u'Volume': '150', u'Issue': '2-3', u'PubDate': {u'Month':
> 'Jun', u'Year': '2012'}}, attributes={u'CitedMedium': u'Print'}), u'Title':
> 'Archives italiennes de biologie'}, u'Affiliation': 'MRC Cognition and
> Brain Sciences Unit, 15 Chauces Road, CB2 7EF, Cambridge,UK Email:
> louisegoupil at hotmal.fr.', u'ArticleTitle': 'Cognitive processing during
> the transition to sleep.', u'ELocationID':
> [StringElement('10.4449/aib.v150i2.1247', attributes={u'ValidYN': u'Y',
> u'EIdType': u'doi'})], u'Abstract': {u'AbstractText': ['Several dramatic
> physiological and behavioural changes occur during the transition from
> wakefulness to sleep. The process is regarded as a grey area of
> consciousness between attentive wakefulness and slow wave sleep. Although
> there is evidence of neurophysiological integration decay
> as signalled by sleep EEG elements, changes in power spectra and
> coherence, thalamocortical connectivity in fMRI, and single neuron changes
> in firing patterns,
> little is known about the cognitive and behavioural dynamics of these
> transitions. Hereby we revise the body and brain physiology, behaviour and
> phenomenology of these changes of consciousness and propose an experimental
> framework to integrate the two aspects of consciousness that interact in
> the transition, wakefulness and awareness.']}}, attributes={u'PubModel':
> u'Print'}), u'PMID': StringElement('23165874', attributes={u'Version':
> u'1'}), u'MedlineJournalInfo': {u'MedlineTA': 'Arch Ital Biol', u'Country':
> 'Italy', u'NlmUniqueID': '0372441', u'ISSNLinking': '0003-9829'}},
> attributes={u'Owner': u'NLM', u'Status': u'In-Data-Review'}),
> u'PubmedData': {u'ArticleIdList': [StringElement('23165874',
> attributes={u'IdType': u'pubmed'})], u'PublicationStatus': 'ppublish',
> u'History': [DictElement({u'Month': '2', u'Day': '07', u'Year': '2012'},
> attributes={u'PubStatus': u'accepted'}), DictElement({u'Minute': '0',
> u'Month': '11', u'Day': '21', u'Hour': '6', u'Year': '2012'},
> attributes={u'PubStatus': u'entrez'}), DictElement({u'Minute': '0',
> u'Month': '11', u'Day': '21', u'Hour': '6', u'Year': '2012'},
> attributes={u'PubStatus': u'pubmed'}), DictElement({u'Minute': '0',
> u'Month': '11', u'Day': '21', u'Hour': '6', u'Year': '2012'},
> attributes={u'PubStatus': u'medline'})]}}
>
> I've tried tweaking the rettype and retmode parameters a bit, but with no
> success.
>
>
> -alex
>
>
>
> On Tue, Nov 27, 2012 at 8:38 PM, Michiel de Hoon <mjldehoon at yahoo.com<http://mc/compose?to=mjldehoon@yahoo.com>
> > wrote:
>
> Hi Alex,
> Exactly which command did you try?
> Best,
> -Michiel.
>
> --- On Tue, 11/27/12, Alex Garnett <axfelix at gmail.com<http://mc/compose?to=axfelix@gmail.com>>
> wrote:
>
> > From: Alex Garnett <axfelix at gmail.com<http://mc/compose?to=axfelix@gmail.com>
> >
> > Subject: [Biopython] using efetch to return mesh terms
> > To: "biopython" <biopython at lists.open-bio.org<http://mc/compose?to=biopython@lists.open-bio.org>
> >
> > Date: Tuesday, November 27, 2012, 10:28 PM
> > hi folks,
> >
> > quick question -- first time using biopython and I'm just
> > trying to
> > jury-rig something real quick based on tutorials.
> >
> > I can't seem to get Entrez.efetch() to return mesh terms for
> > a given
> > article, and the documentation here isn't encouraging:
> > http://www.ncbi.nlm.nih.gov/books/NBK25499/
> >
> > anything obvious I'm missing? thanks!
> >
> > -alex
> > _______________________________________________
> > Biopython mailing list  -  Biopython at lists.open-bio.org<http://mc/compose?to=Biopython@lists.open-bio.org>
> > http://lists.open-bio.org/mailman/listinfo/biopython
> >
>
>
>