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MaveDB API
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Unable to update dataset with new DOI information #193

Closed AYSung closed 1 month ago

AYSung commented 5 months ago

I published a score set as requested by a reviewer but the DOI linking was not working at the time. The publisher has asked that the dataset be linked to the DOI when it is published, but when I access the score set there is no way to edit the external DOI and raw read links.

afrubin commented 4 months ago

@AYSung Thanks for your report. Can you put the URN of the dataset you're having trouble with here?

If I understand correctly, you have an existing score set and want to edit the metadata so that it correctly links to to the raw reads. Is that right?

MaveDB is not able to mint DOIs, but the urn accession number given when the dataset is published will be stable and can be put in your publication.

AYSung commented 4 months ago

Hi Alan,

The URN is mavedb:00000663-a. I would like to edit the metadata to include the doi: 10.1038/s42255-024-01042-7 and a link to the raw reads at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1007392. Appreciate your help!

Best, Andrew

On Wed, May 8, 2024 at 1:42 AM Alan Rubin @.***> wrote:

@AYSung https://github.com/AYSung Thanks for your report. Can you put the URN of the dataset you're having trouble with here?

If I understand correctly, you have an existing score set and want to edit the metadata so that it correctly links to to the raw reads. Is that right?

MaveDB is not able to mint DOIs, but the urn accession number given when the dataset is published will be stable and can be put in your publication.

— Reply to this email directly, view it on GitHub https://github.com/VariantEffect/mavedb-api/issues/193#issuecomment-2099852601, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACGX27GSO4XLJUM4T5YAYV3ZBHCNJAVCNFSM6AAAAABHEGJNZGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOJZHA2TENRQGE . You are receiving this because you were mentioned.Message ID: @.***>

afrubin commented 4 months ago

@AYSung Thanks, we'll look into this and see if there's a bug stopping you from editing the metadata yourself.

I see that the DOI is to a paper. We'd rather wait until the paper has been indexed in PubMed and link it to the record that way, since that will enable searching by author and other publication attributes, as well as letting us format the reference properly on the MaveDB website. I hope that will satisfy the journal!

AYSung commented 4 months ago

Thanks, that makes sense! Should I ping you again when the paper is indexed on PubMed?

Best, Andrew

On Wed, May 8, 2024 at 10:19 PM Alan Rubin @.***> wrote:

@AYSung https://github.com/AYSung Thanks, we'll look into this and see if there's a bug stopping you from editing the metadata yourself.

I see that the DOI is to a paper. We'd rather wait until the paper has been indexed in PubMed and link it to the record that way, since that will enable searching by author and other publication attributes, as well as letting us format the reference properly on the MaveDB website. I hope that will satisfy the journal!

— Reply to this email directly, view it on GitHub https://github.com/VariantEffect/mavedb-api/issues/193#issuecomment-2101860035, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACGX27EPPZLWM7763TR6OM3ZBLTLRAVCNFSM6AAAAABHEGJNZGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMBRHA3DAMBTGU . You are receiving this because you were mentioned.Message ID: @.***>

afrubin commented 4 months ago

Yes, please do!

AYSung commented 4 months ago

Hi Alan,

The paper has been indexed on Pubmed https://pubmed.ncbi.nlm.nih.gov/38720117/ - Let me know if you need any more information and thanks again for the help!

Best, Andrew

On Wed, May 8, 2024 at 10:31 PM Alan Rubin @.***> wrote:

Yes, please do!

— Reply to this email directly, view it on GitHub https://github.com/VariantEffect/mavedb-api/issues/193#issuecomment-2101868424, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACGX27CSRFXI4R2H5FI2ASLZBLUYZAVCNFSM6AAAAABHEGJNZGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMBRHA3DQNBSGQ . You are receiving this because you were mentioned.Message ID: @.***>

jstone-dev commented 4 months ago

Hi Andrew, we wanted to let you know that the Pubmed link, DOI, and raw reads link have been added to the experiment and score set. Thanks for letting us know about this! We'll address the underlying issue that prevented you from attaching these.

Best, Jeremy

AYSung commented 4 months ago

Awesome, thank you so much!

Best, Andrew

On Sat, May 18, 2024 at 7:42 PM jstone-uw @.***> wrote:

Hi Andrew, we wanted to let you know that the Pubmed link, DOI, and raw reads link have been added to the experiment and score set. Thanks for letting us know about this! We'll address the underlying issue that prevented you from attaching these.

Best, Jeremy

— Reply to this email directly, view it on GitHub https://github.com/VariantEffect/mavedb-api/issues/193#issuecomment-2119044719, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACGX27H33VLYZZVDXP7RD2LZC7YRBAVCNFSM6AAAAABHEGJNZGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMJZGA2DINZRHE . You are receiving this because you were mentioned.Message ID: @.***>

bencap commented 1 month ago

Closing as completed based on the above discussion.