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Consider moving away from BioStudies and query directly to Atlas #11

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pmb59 opened this issue Oct 21, 2022 · 0 comments
Open

Consider moving away from BioStudies and query directly to Atlas #11

pmb59 opened this issue Oct 21, 2022 · 0 comments

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@pmb59
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pmb59 commented Oct 21, 2022

Historically, this package queried the ArrayExpress API and more recently the ArrayExpress collection in BioStudies in search for Atlas experiments (gxa=true gives 3998 hits in BioStudies as of today).

https://www.ebi.ac.uk/biostudies/api/v1/search?&gxa=true

It is worth noting that searching in ArrayExpress doesn't search/return the entirety of Expression Atlas experiments. With the "unglue" project, the assumption that all Atlas experiments are in ArrayExpress is not true any more. For example all new GEO experiments since 2017 are not in AE/BioStudies.

It would preferable to query the Atlas REST endpoint directly, and remove the dependance on BioStudies API queries.

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