Retrieve Species name from Ensembl plants / fungi / bacteria / metazoa / protists

Question

[ignasi_11]

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

• http://rest.ensemblgenomes.org/info/genomes/division/EnsemblPlants?content-type=application/json

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

• http://rest.ensemblgenomes.org/info/genomes/division/EnsemblFungi?content-type=application/json

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!

Answer 1

[LLTommy]

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 http://rest.ensembl.org/documentation/info/species - I don't know if that is useful for you.

Answer 2

[shengweima]

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