http://www.ncbi.nlm.nih.gov/SNP/get_html.cgi?whichHtml=faq
SNP FAQ--Pubmed Nucleotide Protein Genome Structure Popset Taxonomy OMIM Books SNP Search SNP Pubmed Protein Nucleotide Structure Genome Popset OMIM Taxonomy Books Probeset 3d Domains Unists for Limits Preview/Index History Clipboard Details GENERAL dbsnp Home_page SNP Science Primer Announcements dbsnp Summary FTP SERVER Build History Handle Request DOCUMENTATION FAQ Overview How To Submit Refsnp Summary Info Database Schema html pdf Data_formats SEARCH Entrez SNP Blast SNP Main Search--Batch query By Submitter New Batches Method Population Detail Class Publication Chromosome Report Locus Information STS Markers Free_form Search Simple Advance HAPLOTYPE Specifications Sample Hapset Sample Individual SNP FAQ dbsnp Frequently Asked Questions (FAQS) General_information 1. Description of SNP database 2. Relationship between dbsnp and Genbank 3. Classes of genetic variation within the database 4. History of the database 5. Sources of the data 6. Growth_rate 7. Species represented in the database 8. Relationship between dbsnp to NIH Polymorphic Discovery Resource 9. Provisions for quality_control Searching 1. Searching db SNP 2. Batch queries 3. Searching for polymorphisms of specific genes or chromosomes Submission and Withdrawal 1. Submitting data 2. Simultaneous SNP and STS submission 3. Naming formats 4. NCBI assay ID, or ss ID 5. Reference SNP ID, or rs ID 6. Human gene nomenclature 7. Hold until published (HUP) policy 8. Withdrawing data Downloading 1. Downloading via FTP Linking to dbsnp 1. Linking to a dbsnp record General_information 1 . What is the SNP database? SNP stands for"single nucleotide polymorphism"."SNPS are the most common genetic variations and occur once every 100 to 300 bases. A key aspect of research in genetics is the association of sequence variation with heritable phenotypes. It is_expected that SNPS will accelerate the identification of disease genes by allowing researchers to look_for associations between a disease and specific differences (SNPS) in a population. This differs from the more typical approach of pedigree analysis which tracks transmission of a disease through a family. It is much easier to obtain DNA samples from a random set of individuals in a population than it is to obtain them from every member of a family over several generations. Once discovered these polymorphisms can be_used by additional laboratories, using the sequence information around the polymorphism and the specific experimental_conditions. For a current summary of information contained in the database, see the dbsnp Summary page. Back to FAQS 2. What is the relationship between dbsnp and Genbank? dbsnp is an independent database and not a division of Genbank. Although much of the data in dbsnp is not in Genbank, the dbsnp data will_be_integrated with other NCBI genomic data, and this will ultimately affect Genbank records. The sequences of dbsnp records are_expected to be_contained within the sequences of one or more Genbank records, with the Genbank records generally containing longer sequences and fewer allele designations. The integration will eventually link dbsnp records with Genbank records containing overlapping sequences deduced or stated to be from the same location. Reference dbsnp records will_be_mapped to external resources or databases and will also point back to the original dbsnp submitter records. For further information on this, see"What is a Reference SNP, or rs ID?""below. As with all NCBI projects, the data in dbsnp will_be freely available to the scientific community and made available in a variety of forms. Please see the dbsnp Home_page for further information. Back to FAQS 3. What classes of genetic variation are_included in the database? The database has_been_designed to accept several classes of genetic variation: SNPS microsatellite repeats small insertion/deletion polymorphisms dbsnp uses the term"SNP"in the much looser sense of"minor genetic variation, "so there_is no requirement or assumption about minimum allele frequencies for the polymorphisms in the database. Thus the scope of dbsnp includes disease causing CLINICAL MUTATIONS as_well_as NEUTRAL POLYMORPHISMS. Given the current activity in the discovery of general sequence variation, it is_anticipated that SNP markers with unknown selective effects will_be the vast majority of submitted records. Back to FAQS 4. When was the SNP database established? dbsnp was_launched in September of 1998. Back to FAQS 5. Where does the data come from? dbsnp accepts submissions from all laboratories and is_interested especially in mutations in genes and/or where additional biological information is_known. Major contributors to the database are_associated laboratories with the National Human Genome Research Institute (NHGRI) grants program. The NHGRI has_funded an intensive effort to collect 50,000 SNPS in three years. The grant recipients under this program include genome centers, private extra mural research labs, and private businesses. These groups are working_on a variety of aspects of new SNP discovery, new technologies for SNP detection, and rapid SNP genotyping in large samples. In_addition_to this central contribution to dbsnp, other research labs and private companies can deposit SNP information to make_it easily accessible to the research community and part_of the public_domain. We are currently designing a common data exchange format for SNP data to be_used between the central SNP databases. Back to FAQS 6 . What is the rate at which dbsnp is growing? In_general, the database grows at a rate of about 90 SNPS per month; however, large numbers of submissions by large research projects can cause uneven growth . While dbsnp welcomes data from smaller contributors, the majority of the data will probably come from a small number of large projects funded by the NHGRI grants. For this reason, it is_expected to grow in erratic jumps for the_next few years. It is_expected that there_will_be 5, 000-10,000 SNPS by the end of the first year of the funded SNP grants. For the current number of SNPS in the database, see the dbsnp Summary page. Back to FAQS 7. Which species are_represented in the database? Currently only Homo_sapiens is_represented in the database; however, the database has_been_designed to accept mutation information from any species, not just Homo_sapiens. Back to FAQS 8. How is dbsnp related_to the NIH Polymorphism Discovery Resource? The database has_been_designed to accept frequency and/or individual genotype information from any submitter-defined population, not just the NIH Polymorphism Discovery Resource (NIHDPR. The NIHDPR is_encouraged as a resource for the extra mural NIH-funded SNP grants to facilitate a more straightforward evaluation of differing discovery or genotyping methods using a consistent panel of samples. None of the frequency information currently in dbsnp comes from the NIHDPR. Back to FAQS 9. What provisions are_made for quality_control? Data validation can be_maintained for both submitted assay reports and reference SNP objects. At the level of an individual submitted assay report, dbsnp provides several fields to assess the quality of the data. For further information, please see: How to Submit, Validation fields. Back to FAQS Searching 1. How can I search dbsnp? dbsnp can be_searched both via other NCBI resources or directly. Via other NCBI resources We are developing three ways to query the database by integrating it with other NCBI resources. They are: a. by gene name/nomenclature association Query results from the Locuslink database will show a purple"V"button in SNP records have_been_mapped to the gene. Clicking on the V will take you to a list of the reference SNP records for any gene in the Locuslink database. b. by map location dbsnp is currently being_integrated to Genemap99 and the integrated physical maps that are being_constructed at NCBI . When integration is_completed, the maps may_be_browsed for SNP content in user specified regions of the map. This feature should be ready in mid May. c_as a BLAST operation on dbsnp using a candidate sequence. The sequences in dbsnp are currently being_formatted to be_searched by BLAST. Users will_be able to submit a query sequence to BLAST, and receive a list of any SNPS in the database that hit the sequence. This feature will_be ready in late May. Direct searching of dbsnp Currently, there_are six ways to search dbsnp directly: Ad_hoc Main search-search by SNP accession number, submitter SNP ID, NCBI Assay ID, or genome SNP ID. By submitter-search by submitter handle New Batches-search by local batch ID Method -search by method used by the submitter to identify the SNP Population-search by the type of population studied Publication-search by publication title Chromosome Report-reports of SNPS with STS mapping information, sorted by cray distance where possible Back to FAQS 2. Is it possible to do batch queries? There_are two means of doing batch queries: 1. Searching batches submitted by individual laboratories. This method is_used to search groups, or batches, of SNPS submitted by individual laboratories. It is possible to search by batches submitted by individual laboratories. Batches are_identified by the local batch identification code, submitter handle, number of SNPS in the submission, and the date of submission. Batches are_displayed chronologically by most recent date of submission. See the New Batches page for further information. 2. Submitting a batch of requests. This method would allow a user to submit a batch of queries, or requests. The results would then be_returned to the user's email account in ASN. 1, FASTA, XML, chromosome report, or text flatfile format. The batch of requests can be_submitted as an upload file or entered using a web interface. See the dbsnp Batch Query page for further information. Back to FAQS 3. How can I search for polymorphisms of a specific gene or chromosome? It is currently not possible to search for SNPS of a specific gene or chromosome; however, a report of mapped SNPS sorted by chromosome and fine map position is available. It is possible to look_at the map of a specific gene or chromosome and search for SNPS within that region. See"How can I search dbsnp?""for a discussion of the integrated resource features that will soon address this need. NCBI is also in_the_process_of integrating dbsnp entries with other sequence and mapping resources via BLAST and Electronic PCR (E-PCR) analysis. This analysis will attempt to associate all SNPS with a nucleotide sequence record and/or physical map contig. If the SNP is in a gene region, it will_be_annotated on the appropriate Reference Sequence or Unigene cluster. Back to FAQS Submission and Withdrawal 1. How can I submit data to the database? Independent labs can submit data directly to NCBI by following the submission procedures and suggestions found on the dbsnp How to Submit page. Back to FAQS 2. What kind_of data is_needed to submit STS and SNP data simultaneously? In_order_to submit simultaneously STS and SNP data, it is necessary to submit a batch file which includes the following sections in the indicated order. SECTION TYPE SECTION DESCRIPTION Contact CONT Submitter's name, phone_number, and other contact information for this datafile Publication PUB List of pre-press, or published articles about the markers*SNP Method METHOD Free text section for description of general method of assay*SNP Population POPULATION Description of population sample*STS Source SOURCE Description of source organism*STS Protocol PROTOCOL PCR protocol components*STS Buffer BUFFER PCR buffer components STS Record STS An STS entry using a SOURCE, PROTOCOL, BUFFER, primers and sequence*STS Method METH A section to label/decode lines in an STS Map section STS Map Data MAP Map information for the STS (and, hence, the SNP) SNP Record SNPASSAY An SNP entry using METHOD, STS, alleles and flanking sequence SNP Frequency SNPPOPUSE Frequency data for SNPASSAY in POPULATION Sections denoted with an asterisk(*)only have to be_defined and submitted once. The other sections carry the particular details for each SNP, insertion/deletion or microsatellite in a data set. Details of each section can be found in the dbsts submission instructions or the dbsnp submission instructions. Back to FAQS 3. Is_there a specific name or format I must use for submission? Individual laboratories will_be_assigned a unique handle, which is a short lab identifier, usually an acronym or abbreviated name. The handle will allow submissions to be_associated with laboratories independent of the details of who is handling a particular set of submissions from that laboratory. For more information on handles, please see: How to Submit, Handles Local SNP identifiers need only be unique within a specific handle. The combination"HANDLE LOCAL SNP ID"will_be unique within the database. There_is a 64 character limit for SNP identifiers. For more information on identifiers and examples of identifiers, please see: How to Submit, Identifiers Back to FAQS 4. What is the NCBI assay ID, or'ss'ID? The NCBI assay ID, or'ss'ID is simply an accession number assigned by NCBI to submitted SNPS. It has the format NCBI ss NCBI ASSAY ID. Note that'ss'is always in the lower_case. For more information on ss ID's please see: How To Submit, Resource Integration. Back to FAQS 5. What is a reference SNP, or'rs'ID? A reference SNP ID, or'rs'ID is an identification tag assigned by NCBI to SNPS that appear to be unique in the database. The rs ID number, or tag, is_assigned at submission. Initially, it is_expected that nearly every submission will_be_assigned a_rs ID. As the database matures, however, submitted SNP's that map to identical locations as previously submitted SNP's will_be_linked into the reference set of the existing reference SNP record. These SNP rs ID's will_be a set of features that will_be_mapped to external resources or databases including NCBI databases. The SNP rs ID number will_be_noted on the records on these external resources and databases in_order_to point users back to the original dbsnp records. A reference SNP record has the format NCBI rs NCBI SNP ID. Note that'rs'is always in the lower_case. For more information on rs ID's please see: How To Submit, Abstract Report. Back to FAQS 6. What is the official nomenclature for human genes? There_is currently no official nomenclature for human genes; however, The Human Gene Nomenclature Committee is currently trying to establish a nomenclature standard and does have_recommended a format. The Human Gene Nomenclature Committee is_accepted the authority for establishing these standards. For new genes lacking official nomenclature the research community is_encouraged to use the Nomenclature Committee web form to submit a proposed gene symbol and name, thus creating a community provided name. In_general, the research community does try to conform_to using preexisting names but these names might not be the current official nomenclature name so situations do arise where a single gene is being_called by multiple names. There_is no enforcement of this suggested nomenclature method and investigators are free to name a gene as they wish. There is no standard'format'for the official gene name, but, for human genes, the official gene symbol (an abbreviation) does have_standardized the format of capitalizing all alphabetic_characters and excluding use of non alpha/numeric characters. For_example, official symbols might look_like ABC3 but do not look_like ABC (3). Back to FAQS 7 . What is the"hold until published (HUP)" policy? dbsnp data cannot be_held confidential until publication. Note that dbsts and dbsnp have different"hold until published "or HUP policies. Submissions to dbsts can be_withheld from public view until the accession number is_published. dbsnp records, however, will_be available for public inspection when the submission process is complete, even in the case of simultaneous dbsnp/sbsts submissions. STS submissions that require HUP treatment should be_submitted separately, and prior to the SNP submission. Back to FAQS 8. Is it possible to withdraw submissions from the database? A record can not be_deleted completely from the database. The submission identification_number of all records, and the rs ID number of abstracted reference SNP records, are_incorporated into other databases (Please see"What is the NCBI assay ID or'ss'ID?""and"What is a reference SNP or'rs'ID?""above). ) These ID tags indicate source information of SNPS to users of other databases that reference the data in_question. These ID tags point the users back to dbsnp. Also, other laboratories can submit records to SNP that refer to SNPS already in the database. Because a submission quickly becomes permanently associated with other records both within dbsnp and in other databases it is not possible to completely eliminate it from the database. A record can be_marked as"withdrawn, "however, so_that a query of that SNP will indicate that the submitter has_chosen to withdraw that data. Back to FAQS Downloading 1. Is is possible to download dbsnp? dbsnp is available for downloading via the NCBI FTP server in three formats: pc compressed uncompressed unix compressed The following FTP files are available: contact. rep-Handle information and submitter contact information publicat. rep-Publications cited in the database method . rep-Assay methods defined by submitters populatn. rep-Population descriptions defined by submitters snpassay. rep-Assay reports for all SNPS in the database popuse. rep-Population frequency data induse. rep-Individual genotype data Note: this_is the data only. It is not a stand alone searchable database that includes software. Back to FAQS Linking to dbsnp 1. Is it possible to create HTML links to a particular dbsnp record? Yes. If you have a local website with more data related_to a particular SNP, it may_be useful to create a link from the local site to the ss id number of a chosen SNP record. To do so, use the following URL: http://www. ncbi. nlm. nih. gov/SNP/snp_retrieve. cgi? subsnp_id=Set the"subsnp_id"to the chosen NCBI Assay ID number. For_example, if the NCBI Assay Id number is 123, set the URL as: http://www. ncbi. nlm. nih. gov/SNP/snp_retireve. cgi? subsnp_id=123 Back to FAQS Comments or Questions? If you have further questions, comments or suggestions for improvement of this FAQ page or dbsnp please contact the NCBI Service Desk at info@ncbi. nlm . nih. gov db SNP Home NCBI Home FAQ page updated: 19 April 1999 GENERAL: Home_page Announcements dbsnp Summary Genome FTP SERVER Build History Handle Request DOCUMENTATION: FAQ Overview How To Submit Refsnp Summary Info Database Schema SEARCH: Entrez SNP Blast SNP Main Search Batch query By Submitter New Batches Method Population Publication Chromosome Report Batch Locus Info Freeform Easyform Between Marker HAPLOTYPE: Specifications Sample Hapset Sample Individual NCBI: Pubmed Entrez BLAST OMIM Taxomomy Structure Disclaimer Privacy statement Revised May 29,2002 2: 19 PM