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dcppc / data-stewards

Questions and answers about TOPmed, GTEx, and AGR resources.
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Team Phosphorus - Metadata file for MGI Gene expression data #16

Open nsuvarnaiari opened 6 years ago

nsuvarnaiari commented 6 years ago

We (Team Phosphorus) are looking for a metadata file for gene expression data consisting of MGI genes accessions, associated Mouse Developmental Anatomy Ids and MGI assay accessions (and any other metadata associated with gene expression). This information is missing in the downloadable files on MGI website. Could we get help on this. Thanks!!!!! Suvvi

JoelRichardson commented 6 years ago

Hello @nsuvarnaiari and team, You can get this info from MouseMine (maintained by MGI) via web services. Here's an example that downloads 10 rows of expression for one gene: http://www.mousemine.org/mousemine/service/template/results?name=Gene_Expression&constraint1=GXDExpression.feature&op1=LOOKUP&value1=Pax6&extra1=&format=tab&size=10

Is this close to what you're after? If so, we can talk about how to get 'everything'.

nsuvarnaiari commented 6 years ago

Yes @JoelRichardson , this is what I am looking for.

JoelRichardson commented 6 years ago

Is a simple file download of "everything" what you're after? Or an API where you can retrieve customized subsets dynamically?