Annotation Release NCBI Homo sapiens Version on SQL table dump annotation database

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Eah Alina Keomanee

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Oct 27, 2021, 7:04:51 PM10/27/21
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Hello ,

I am trying to figure out what Annotation Release NCBI Homo sapiens version was used to create the ncbiRefSeqSelect.txt.gz and ncbiRefSeqCurated.txt.gz files and was wonderinf if you could assist me?
Is it the same version that the current NCBI RefSeq tracks is using, which I believe is RefSeq genes from NCBI - Annotation Release NCBI Homo sapiens 109.20210514 (2021-05-18) ? 

https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ncbiRefSeqCurated.txt.gz

I appreciate any information you can provide, thank you!
Alina

Eah Alina Keomanee

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Oct 28, 2021, 12:33:43 PM10/28/21
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Hello ,

I have one follow-up question, I see that these files are also available under specific version links in the archive folder. Do you know if the current files in the SQL table dump database are in these archive files below?


Thank you,
Alina
From: Eah Alina Keomanee
Sent: Wednesday, October 27, 2021 3:56 PM
To: gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>
Subject: Annotation Release NCBI Homo sapiens Version on SQL table dump annotation database
 

Jairo Navarro Gonzalez

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Oct 29, 2021, 6:23:55 PM10/29/21
to Eah Alina Keomanee, gen...@soe.ucsc.edu

Hello,

Thank you for using the UCSC Genome Browser and sending your inquiry.

You are correct and the RefSeq version for the two files, ncbiRefSeqSelect.txt.gz and ncbiRefSeqCurated.txt.gz, is 109.20210514 (2021-05-18). It is RefSeq 109, but an update to it, made by RefSeq on 5/14/2021. The SQL table dump files you shared will always correspond to the latest version of RefSeq for that assembly. The latest version of RefSeq for hg38 and hg19 in the archive directory is:

https://hgdownload.soe.ucsc.edu/goldenPath/archive/hg38/ncbiRefSeq/109.20210514/
https://hgdownload.soe.ucsc.edu/goldenPath/archive/hg19/ncbiRefSeq/105.20201022/

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
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Jairo Navarro
UCSC Genome Browser

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Eah Alina Keomanee

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Oct 30, 2021, 6:53:11 PM10/30/21
to Jairo Navarro Gonzalez, gen...@soe.ucsc.edu
Hello Jairo,

Thank you for your quick response, that is very helpful to know! Do you know how long the archive directories will be available(the oldest ones I see are from May of this year) ? 

Thank you,
Alina
From: Jairo Navarro Gonzalez <jnav...@ucsc.edu>
Sent: Friday, October 29, 2021 3:23 PM
To: Eah Alina Keomanee <al...@biodiscovery.com>
Cc: gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>
Subject: Re: [genome] Re: Annotation Release NCBI Homo sapiens Version on SQL table dump annotation database
 

Matthew Speir

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Nov 1, 2021, 2:43:30 PM11/1/21
to Eah Alina Keomanee, Jairo Navarro Gonzalez, gen...@soe.ucsc.edu
Hello, Alina.

We have no plans to delete archive directories. For the NCBI RefSeq track, the reason the archives are only available starting from May 2021 is that is when we started the archive, not because we removed older ones.

If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Matthew Speir

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Human Cell Atlas, User Experience Researcher

UCSC Genome Browser, User Support

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Eah Alina Keomanee

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Nov 2, 2021, 1:37:29 PM11/2/21
to Matthew Speir, Jairo Navarro Gonzalez, gen...@soe.ucsc.edu
Hello Matthew,

I see, thank you for the information! This was very helpful!

Alina
From: Matthew Speir <msp...@ucsc.edu>
Sent: Monday, November 1, 2021 11:43 AM

To: Eah Alina Keomanee <al...@biodiscovery.com>
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