Question: How to convert data from NCBI E-utilities.efetch to python data object?
0
gravatar for MatthewP
5 months ago by
MatthewP180
China
MatthewP180 wrote:

Hello, everyone! I want to use E-utilities to get all gene information. I already get all gene UIDs and next step is use E-utils.efetch get gene record. However I find it's hard to extract informations I need from the E-utils.efetch return data. Here is one example link getting gene records from E-utils, click to see the data returned:
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=79669,10059,23548,8999
Return data looks like:

Entrezgene ::= {
  track-info {
    geneid 79669,
    status live,
    create-date std {
      year 2001,
      month 3,
      day 12
    },
    update-date std {
      year 2018,
      month 12,
      day 8
    }
  },
  type protein-coding,
  source {
    genome genomic,
    origin natural,
    org {
      taxname "Homo sapiens",
      common "human",
      db {
        {
          db "taxon", ...

The problem is I need to convert such data into python object(dict, list) to extract information I need, this is hard. I google and can't find any packages for such job. It's there some easy way? Otherwise I had to write scripts myself.

python ncbi • 370 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by MatthewP180
1

Hello MatthewP ,

the format of the return is called ASN.1. This format can be parsed and transformed in a dictionary using the ASN1.tools package for python. Have a look into the examples to see how it works.

fin swimmer

ADD REPLYlink written 5 months ago by finswimmer11k
1

It would probably be worth your while to abandon ASN.1 style results, in favour of some of the more broadly applicable formats, as discussed here for instance.

ADD REPLYlink written 5 months ago by jrj.healey13k
1
gravatar for MatthewP
5 months ago by
MatthewP180
China
MatthewP180 wrote:

Hello, I find E-utils can return xml if you set retmode=xml. Example:
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=79669,10059,23548,8999&retmode=xml
Here is all support retmode list:
https://www.ncbi.nlm.nih.gov/books/NBK25499/table/chapter4.T._valid_values_of__retmode_and/?report=objectonly
For some newbee like me.

ADD COMMENTlink written 5 months ago by MatthewP180
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