How to Submit to dbSNP:

VII. Formatting Data for Updates and Withdrawals

Version 4.1; December 11, 2015

Updating dbSNP Submissions

You can update a submission you previously made to dbSNP by submitting update files formatted using the tags defined in the Updating the Basic Record section of this document and sending them to dbSNP at [email protected]

Below are the three most common situations where a user needs to update data previously submitted to dbSNP:

Contact information: changes can be made to an investigator's handle contact information by sending the new information to [email protected].
Publication information: send an updated publication section to [email protected]. The title field must be identical between the original submission and the submission update in order for dbSNP to match the records. If the update is the publication of an "in press" citation, then the PubMed ID (PMID) may be provided in lieu of the compete reference if it is known. The necessary information will be automatically extracted from the full citation in PubMed.
Changing the basic record: submitters should send the updated sections to [email protected] as specified below.

Updating the Basic Record

You can update a submission you previously made to dbSNP by by submitting update files formatted using the tags defined below and sending them to dbSNP at [email protected]

TYPE: BATCH_UPDATE:	To set a success rate for a batch with a previously unclassified success rate. This can potentially involve adding a population
HANDLE: <handle>	Submission handle as supplied by NCBI
BATCH: <local_batch_ID>	Report the local batch id if you didn't report it when you first submitted the batch. A local_batch_ID is simply a name you give to the set of variation assays or experiments you are submitting. The local_batch_ID allows for clear reference to the submitted set in communication between NCBI and submitters.
NEW_METHOD: <local_method_id>	Used to change the method used for the bath. Use the VALIDATION section for adding additional methods to variations. To ensure data integrity, if you use of NEW_METHOD, you will need database administrator confirmation when you load. A <local_method_id> is the identifier you or your lab uses to refer to a method for assaying variation. However, if you are,or have submitted your sequences to SRA, use your SRA experiment accession (e.g.SRX1131768) as your method ID.
SUCCESS_RATE: <percentage>
POPULATION: <local population id>	This is the identifier you or your lab uses to refer to: 1. the population of individuals used to define a SNP assay, or 2. the population that was assayed for variants Note: some population strings will be predefined, or "globally" defined, and can be used by more than one submitter. The handle for these globally defined populations is 'NCBI'. To remove ambiguity, populations will always be used as <handle>\|<population id>
COMMENT: Free text	Free text for public viewing. Anything written in this field will be shown with each SNP assay in this batch.
LINKOUT_URL: free text URL	A free text (255 char max) URL that links to the submitter's local website. NCBI requests that links to data for individual SNP records be formed by the concatenation of this URL string with the local SNP ID.
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TYPE: BATCH_REASSIGN	To change the batch id associated with a variation. This is used to move variations to a newly created batch ID with a different SUCCESS_RATE and/or population. Method ID and method_count for SNPs remain the same. New batch inherits all properties from the old batch except for NEW_SUCCESS_RATE, POPULATION, COMMENT and LINKOUT_URL as noted.
HANDLE: <handle>
OLD_BATCH: <local batch id>
NEW_BATCH: <local batch id>
NEW_SUCCESS_RATE: <percentage>
NEW_POPULATION: <population id>
COMMENT: free text
LINKOUT_URL: free text URL
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When updating the assay section, be sure to repeat the following for each variation that is reassigned. Also, repeat from VALIDATION to LINKOUT_URL for each variation validated.

SNP: <ID, ss# or local>	ID must exist in OLD_BATCH
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TYPE: VALIDATION	Used to add a new method to a variation's method history. The new batch will inherit properties from Old Batch except for NEW_SUCCESS_RATE, POPULATION, and NEW_METHOD as noted.
HANDLE: <handle>
OLD_BATCH: <local batch id>
NEW_BATCH: <local batch id>
NEW_SUCCESS_RATE:<percentage>	Probability that SNP is real, based on validation data.
NEW_METHOD: <local identifier>	ID of validation method used on a set of optional variation from given method
SNPs METHOD_EX:	Free text
NEW_POPULATION:<local identifier>
COMMENT:	optional comment
LINKOUT_URL:	optional linkout to submitter website
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SNP: <ID> (SEGREGATES=YES\|NO\|UNKNOWN; HOMOZYGOTE_FOUND=YES\|NO\|UNKNOWN)	Update of SEGREGATES and HOMOZYGOTE_FOUND is optional
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Withdrawing a Variation

You may withdraw a submission from dbSNP by by submitting withdrawal files formatted as defined below and sending them to dbSNP at [email protected]. You should note, however, that it is not possible to completely eliminate a withdrawn record from dbSNP since a submission quickly becomes permanently associated with dbSNP records and the records in other databases. Although the variant will be removed from active variant records and placed with those in deletion history, the withdrawn record will still retain its original submitted SNP (ss) ID number. If you search for a ss ID number that has been withdrawn, you will get a report that describes the submission and its withdrawal data.

Use the following Tag:Value pairs to report variations you wish to be withdrawn:

TYPE: WITHDRAWN	Used to mark a SNP as withdrawn. SNP will retain ss#, but type will change from SNP to WITHDRAWN (WD).
HANDLE: <handle>
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EVIDENCE: GeneDuplication
	Repeat both the Evidence:GeneDuplication and the SNP tag value pairs for each variation that is withdrawn for this reason.
SNP: <ID, ss# or local>
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EVIDENCE: Artifact
	Repeat both the Evidence:Artifact and the SNP tag value pairs for each variation that is withdrawn for this reason.
SNP: <ID, ss# or local>
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EVIDENCE: NotSpecified
	Repeat both the Evidence:NotSpecified and the SNP tag value pairs for each variation that is withdrawn for this reason.
SNP: <ID, ss# or local>
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EVIDENCE:AmbiguousMapLocation
	Repeat both the Evidence:AmbiguousMapLocation and the SNP tag value pairs for each variation that is withdrawn for this reason.
SNP: <ID, ss# or local>
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EVIDENCE: LowMapQuality
	Repeat both the Evidence:LowMapQuality and the SNP tag value pairs for each variation that is withdrawn for this reason.
SNP: <ID, ss# or local>
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EVIDENCE: DuplicateSubmission
	Repeat both the Evidence:DuplicateSubmission and the SNP tag value pairs for each variation that is withdrawn for this reason.
SNP: <ID, ss# or local>
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Contact dbSNP

If you do not find the answer to your submission questions in the How to Submit to dbSNP document series, contact dbSNP submissions at [email protected], and we will do our best to answer your submission question or help you solve a difficult submission problem.

Send submissions and submission questions to: [email protected]
Send submission updates to: [email protected]
Send general inquiries, etc. to: [email protected]

Titles in the How to Submit to dbSNP Series: