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API route: from biosample id, return associated dataobject ids #667

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kheal opened this issue Sep 3, 2024 · 0 comments
Open

API route: from biosample id, return associated dataobject ids #667

kheal opened this issue Sep 3, 2024 · 0 comments
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enhancement New feature or request

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@kheal
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kheal commented Sep 3, 2024

Is your feature request related to a problem? Please describe.
The example notebook here or [here (for python)] performs a schema traversal to associate a studys's biosamples with data objects in order to collect those data objects for analysis.

Describe the solution you'd like
Ideally, from a biosample id, I would like an API call that returns all associated dataobject ids.

Example user story template:
AS A user,
IF I START WITH A LIST OF BIOSAMPLES, I have to query pooling_set(material_processing_set in berkeley schema), extraction_set(material_processing_set in berkeley schema), library_preparation_set(material_processing_set in berkeley schema), omics_processing(data_generation_set in berkeley schema), metagenome_annotation_activity_set (workflow_activity_set in berkeley schema) and keep track of ids along the way to get a list of ids to get associated data objects.

I WANT TO send a list of biosample ids and get a json of biosample id with all associated data object ids and data object types.

Acceptance Criteria

Additional context
Although this (closed issue #608) does a fair amount of work in this direction, we still do not have the functionality of going from biosample -> data object, especially for large studies like NEON.

This is related to milestone microbiomedata/issues#516 and microbiomedata/issues#496

@kheal kheal added the enhancement New feature or request label Sep 3, 2024
@kheal kheal changed the title From biosample id, return associated dataobject ids API route: from biosample id, return associated dataobject ids Sep 3, 2024
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