Entrez.esummary ('gene' db): 如何从 DictElement 中检索 uid？

Question

我正在尝试从 NCBI Entrez Gene 数据库中检索和保存基因摘要，并且也想保留 uid，但是，尽管它在那里，但我找不到从结果中检索它的正确方法.见下文（注意：显然不是我在这里使用的有效电子邮件地址）：

from Bio import Entrez
Entrez.email = "bogus@bogus.com"
handle = Entrez.esummary(db="gene", id="79001")
record = Entrez.read(handle)
handle.close()
for k in record["DocumentSummarySet"]['DocumentSummary'][0].keys():
    print k

这些是关键：

Status, NomenclatureSymbol, OtherDesignations, Mim, Name, NomenclatureName, CurrentID, GenomicInfo, OtherAliases, Summary, GeneWeight, GeneticSource, MapLocation, ChrSort, ChrStart, LocationHist, Organism, NomenclatureStatus, Chromosome, Description

但是如果您查看元素本身 (record["DocumentSummarySet"]['DocumentSummary'][0])，您会注意到最后的 attributes={u'uid': u'79001'}：

DictElement(
    {u'Status': '0',
     u'NomenclatureSymbol': 'VKORC1',
     u'OtherDesignations': 'phylloquinone epoxide reductase',
     u'Mim': ['608547'],
     u'Name': 'VKORC1',
     u'NomenclatureName': 'vitamin K epoxide reductase complex subunit 1',
     u'CurrentID': '0',
     u'GenomicInfo': [
         {u'ChrAccVer': 'NC_000016.10',
          u'ChrLoc': '16',
          u'ExonCount': '4',
          u'ChrStop': '31090841',
          u'ChrStart': '31094998'}],
     u'OtherAliases': 'EDTP308, MST134, MST576, VKCFD2, VKOR',
     u'Summary': 'This gene [...] variants. [provided by RefSeq, Aug 2015]',
     u'GeneWeight': '46017',
     u'GeneticSource': 'genomic',
     u'MapLocation': '16p11.2',
     u'ChrSort': '16',
     u'ChrStart': '31090841',
     u'LocationHist': [
        {u'AssemblyAccVer': 'GCF_000001405.33',
         u'ChrAccVer': 'NC_000016.10',
         u'AnnotationRelease': '108',
         u'ChrStop': '31090841',
         u'ChrStart': '31094998'}],
     u'Organism': {
         u'CommonName': 'human',
         u'ScientificName': 'Homo sapiens',
         u'TaxID': '9606'},
     u'NomenclatureStatus': 'Official',
     u'Chromosome': '16',
     u'Description': 'vitamin K epoxide reductase complex subunit 1'},
     attributes={u'uid': u'79001'})

但 'attributes' 不是键之一。我还没有找到一种方法来访问保存在属性中的 uid。有人有想法吗？

Answer 1

attributes只是DictElement的一个属性，你可以用标准点访问它：

record["DocumentSummarySet"]['DocumentSummary'][0].attributes

Entrez.esummary ('gene' db): 如何从 DictElement 中检索 uid？

Entrez.esummary ('gene' db): how to retrieve uid from DictElement?

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