Trying to get a complete list of all the ISH ID experiments for the mouse brain

Technical
1

Hi,

I was just wondering how to easily get a complete list of all the ISH ID experiments for the mouse brain.
I have tried different ways through API queries but it is difficult to get the complete list because ID figures go so high. I did not find this information in the documentation as well.

Could you please help me to get such a list?

Many thanks in advance,
Best,
Sebastien

2

Hi @spiluso!

You can get the full list of ISH mouse experiments by slightly modifying one of the examples that is listed in this page:

Specifically, they provide this particular query to get all the ISH mouse experiments in csv format:

http://api.brain-map.org/api/v2/data/query.csv?criteria=
model::SectionDataSet,
rma::criteria,[failed$eqfalse],products[abbreviation$eq'Mouse'],treatments[name$eq'ISH'],genes,plane_of_section,
rma::options,
[tabular$eq'plane_of_sections.name+as+plane','genes.acronym+as+gene','data_sets.id+as+section_data_set_id'],
[order$eq'plane_of_sections.name,genes.acronym,data_sets.id']
&num_rows=50&start_row=0

This will get you the first 50 experiments, which is the default if you omit the num_rows=50 option. You can change that to num_rows=all to get the full list of experiments (26079, in this case).

I hope this helps.

Cheers,
Nico

1 Like
3

Hi @ndefrancesco,

Excellent, that was exactly what I was looking for!
I am very grateful for your help, which will make me save a lot of time and ressources!

Many thanks,
Best,
Sebastien

1 Like
4

Hi again,

Just a quick note about the list of experiments you provide through this command. It seems that one ID appears twice in a row in this list: ID 78153149 at positions 24785 and 24786. This would give a total number of 26078 experiments.

Hope it could be useful.
Best,
Sebastien