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Data curation for FaceBase
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Review FB00000958, FB00000959, FB00000960, FB00000961, FB00000962, and FB00000963 #87

Open robes opened 6 years ago

robes commented 6 years ago

Selleri lab has reported these datasets as ready for Hub review.

robes commented 6 years ago

My impressions

FB00000958: good FB00000959: good FB00000960: good FB00000961: good FB00000962: good FB00000963: good

They all looked good to me.

BridgetDS commented 6 years ago

I think they are fine to release as-is, but at some point it would be helpful (i.e. make them easier to find via the faceted browser) to have some way to tag these with the human/chimp genes that the enhancers are near (FOXI2, COL13A1, NARS2) -- right now they are (not terribly helpfully) listed only under mouse gene panTro4. It also feels odd to have these labeled solely as mouse data, even though that is technically true.

robes commented 6 years ago

Right. I agree with that. I want to begin a conversation with them and two other groups doing enhancer assay work and refactor this.

From: BridgetDS notifications@github.com Reply-To: informatics-isi-edu/facebase-curation reply@reply.github.com Date: Thursday, March 22, 2018 at 3:02 PM To: informatics-isi-edu/facebase-curation facebase-curation@noreply.github.com Cc: Robert Schuler schuler@ads.isi.edu, Assign assign@noreply.github.com Subject: Re: [informatics-isi-edu/facebase-curation] Review FB00000958, FB00000959, FB00000960, FB00000961, FB00000962, and FB00000963 (#87)

I think they are fine to release as-is, but at some point it would be helpful (i.e. make them easier to find via the faceted browser) to have some way to tag these with the human/chimp genes that the enhancers are near (FOXI2, COL13A1, NARS2) -- right now they are (not terribly helpfully) listed only under mouse gene panTro4. It also feels odd to have these labeled solely as mouse data, even though that is technically true.

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bugacov commented 6 years ago

FB958: Looks Good. Might be good to add Protocol to Experiment and local_indentifier to Experiment and/or biosample. If look at the file it has 3XhEt1 and the enhancer Lab Internal field says 3XhET1_pHsp68-lacZ-tdTomato. So maybe the same ID can be use in Experiment. FB959: Same comment as 958. FB960: Same comment as 958. FB961: Same comment as 958. FB962: Same comment as 958.

I think we can mark them as Curated and ask them if they can add the identifiers (which they already have in the Enhancer assay

bugacov commented 4 years ago

@robes and @BridgetDS ... Not sure what should be done about this issue.

1) Are we going to try to address the issue that Bridget about tagging w/ other genes?

2) @robes ... it seems to me that in these datasets we can add a Chromosome entry w/ the start-end position?

BridgetDS commented 4 years ago

@bugacov @robes I would say we should ask someone who is knowledgeable about enhancers for suggestions on this (probably Axel Visel, since he is one of our scientific advisors)