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Milestone - Integrate metadata enrichment into sample interface (3.3) #473

Open ssarrafan opened 1 year ago

ssarrafan commented 1 year ago

Support for metadata enrichment and enhancement We will take the proof-of-concept metadata enrichment routine71 developed in the Pilot (see Standards for FAIR Multi-omics Data), and integrate this into the NMDC Submission Portal to support streamlining metadata input and augmentation (Submission Portal, Milestone 3.3). Streamlining this work will reduce barriers for the scientific community to engage and use this resource, increasing the potential data we will receive from individual submissions. These methods will support features such as auto-suggesting values for various fields based on minimal information entered (e.g., using the geolocation field to suggest environment values or mining the study abstract to suggest terms). Measurements is an area where historical metadata has been poorly captured (12), and plan to make use of the quantulum package72 to suggest corrections for incorrectly entered quantity data.

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see #474

ssarrafan commented 7 months ago

@cmungall due in Q4 so removing from this Quarter but may still need an update for the DOE quarterly report.

aclum commented 2 months ago

Check to see what existing code can be used. Possible fields to autopopulate are elevation, geograph location name from lat,long, etc.

ssarrafan commented 2 months ago

@cmungall can you please add an update on this milestone? It's due this quarter, by September.

ssarrafan commented 2 months ago

Per the planning meeting today @cmungall will follow up with @pkalita-lbl on how this could be done and what the actual estimate of effort/time would be for this.

ssarrafan commented 1 month ago

Met with Chris, Alicia and Emiley today. @cmungall said he's discussed an approach for this with @pkalita-lbl. I will follow up with Patrick to see if we can assign this issue to him next sprint.

pkalita-lbl commented 1 month ago

Discussed this with @cmungall in a 1:1 yesterday. We decided that a good starting point to demonstrate progress on this milestone in Q4 2024 would be:

I don't think all of that will be completed by the end of Q4 2024, but we will have some progress by then.

ssarrafan commented 1 month ago

Moving to new sprint @cmungall @pkalita-lbl

pkalita-lbl commented 3 weeks ago

I created separate issues for the work outlined above:

I am going to move this issue out of the current sprint and move the task I'm actually working on into it.

ssarrafan commented 1 week ago

@cmungall @pkalita-lbl Is there anything I can report on for this DOE report on this milestone? Or do we need to reschedule it to another quarter?

pkalita-lbl commented 1 week ago