Question: Retrieve Species name from Ensembl plants / fungi / bacteria / metazoa / protists
gravatar for ignasi_11
4.2 years ago by
ignasi_110 wrote:

I know that I can retrieve all the information from the ensembl plant division with this link:

Same way I can also retrieve all informatino from the ensembl fungi division with the following:

And same for bacteria, metazoa and protists.

The information obtained is in JSON format and contains many fields, such as:

  • assembly_id, assembly_level, assembly_name, base_count, dbname, division, genebuild, has_genome_alignments, has_other_alignments, has_pan_compara, has_peptide_compara, has_variations, is_reference, name, serotype, species, species_id, species_taxonomy_id, strain and taxonomy_id.

Is there any way to use the Ensembl REST GET url specifying to retrieve only the "species" field? And to retrieve only many fields (such as division and assembly_name for example)?

thank you very much!

ADD COMMENTlink modified 4.2 years ago by LLTommy1.2k • written 4.2 years ago by ignasi_110
gravatar for LLTommy
4.2 years ago by
LLTommy1.2k wrote:

The script from shengweima will work I guess. However, this is getting all the data and than just pick the field you want to have - which most likely will be the only option to do it.

P.S.: Here you can get a list of species - I don't know if that is useful for you.

ADD COMMENTlink written 4.2 years ago by LLTommy1.2k
gravatar for shengweima
4.2 years ago by
shengweima60 wrote:

I have give you python script on there enter link description here

ADD COMMENTlink written 4.2 years ago by shengweima60
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