add rs deleted

[knmkr]

According to the official FAQ, deleted rs ids are stored in SNPHistory table. So we can query if rs ids are deleted or not based on that table.

Refs:

https://www.ncbi.nlm.nih.gov/books/NBK279185/#_FTP_Finding_Deleted_no_longer_used_refSN_

Finding Deleted (no longer used) refSNP Numbers

The “rsCurrent" field in RsMergeArch contains 129,000 rs numbers not in the ASN.1 flat files or in a dbSNP web search. Is there a list of expired rs numbers?

Let me explain how we track both merged and deleted (an entirely different process from merging) refSNP (rs) numbers, by using a hypothetical example where a “chain merge” (multiple rs numbers merge into each other) occurs:

For example, let us say rs ”A” merged into rs ”B”, and later, rs ”B” merged into rs “C”. As a result of the first merge, the entry for rs ”A” in rsCurrent is updated to rs “B”; after the second merge, rsCurrent is then updated to rs “C”. Now, if rs “C”’s submitters withdraw all the member ss numbers within the refSNP cluster rs “C”, then rs “C” will get an entry in the SNPHistory table (the SNPHistory table ONLY contains SNPs that have "become history" — that is, SNPs that have been completely deleted). Please see ftp file for SNPHistory.bcp (located in the snp/database/organism_data/species of interest directory). To find the column names for the SNPHistory table, download the human_9606_table.sql, which is located in the human organism_schema directory.

Getting back to RsMergeArch: since "withdrawing rs “C" is not a merge action, the table RsMergeArch is not updated. RsMergeArch is used to track "rs merge" actions only. I can see that this might be confusing, so when time allows, we will add the following explanation to the RsMergeAch table definition, to make the RsMergeArch.rsCurrent meaning clearer:

RsMergeArch is used to track each rs merge event.

If an rs number in RsMergeArch.rsCurrent is withdrawn from dbSNP by submitter request, then an the rs number of the same value as that in rsCurrent will be entered into the SNPHistory table (which contains deleted rs numbers only).

Please note: "rsCurrent" in RsMergeArch does not mean the "current rs number" in the current dbSNP build". (08/12/08)

https://www.ncbi.nlm.nih.gov/projects/SNP/snp_db_table_description.cgi?t=SNPHistory

dbSNP Column Description for table: SNPHistory

Table name and description

Table Description
Internal tracking table.

Table column and description

Column	Description	Type	Byte	Order
snp_id		int	4	1
create_time		smalldatetime	4	2
last_updated_time		smalldatetime	4	3
history_create_time		smalldatetime	4	4

This table/column description is last updated at: Aug 15 2005 03:26:00:000PM .