RESOURCE GUIDE

About SLGVD

Sri Lankan Genome Variation Database (SLGVD) is a database of Single Nucleotide Polymorphisms (SNPs) found in Sinhalese, Sri Lankan Tamils and Moors, the three major ethnic groups in the Sri Lankan population. The database was designed confirming to guidelines issued by the Human Genome Variation Society (HGVS)¹.

Genetic data stored in the database is annotated with chromosomal location, gene name and gene symbol. Each genetic variation links with the relevant entries of Online Mendelian Inheritance in Man (OMIM), SNP (Single Nucleotide Polymorphisms) and Genbank databases at National Center of Biotechnology Institute (NCBI). For each variation, genotype, genotype frequencies and allele frequencies of different ethnic groups are represented in numerical and graphical format.

Guidelines followed by SLGVD developers

To organize genetic data in the database we have

• used a unique identifier for each genetic variation
• reported the source for each genetic data
• characterized genomic context of variant data
• described each genetic variation
  

SNP ID given by the NCBI SNP database is used as the unique identifier for variations stored in our database. Using this identifier variation data stored in the database can be accessed independently.

Sources from which genetic data is extracted are stored in the database for each variation. When the data is obtained from published articles, names of authors and citations are mentioned. When data is obtained from a participating laboratory the submitter is mentioned.

Genomic context of any database should be defined by specifying the species name from which the data is Derived. SLGVD is a repository of Homo sapiens sapiens (human) data. In addition to that, homologues variations in other species to human variations in SLGVD are also presented.

Description of the allelic variant forms the core of our database. For each genetic variation, genotypes, genotype frequencies, alleles and allele frequencies are given. The reference sequence of the gene for each variation is provided with the accession number and linked with the NCBI Genbank database where researches can access sequence data and gene annotation. Chromosomal location of the gene with genetic variation is also provided. Each record in the SLGVD is linked with the relevant entries of the NCBI SNP database. So that researches have access to the reference subsequence for the region with the genetic variation. As variation data in SLGVD is linked with the relevant entries of NCBI OMIM database, researches, physicians concerned with genetic disorders and advanced students in science and medicine can collect further information from computerized database version of Victor McKusicks book, Mendelian Inheritance in Man, provided through the National Center for Biotechnology Information.

Data Retrieval

The database can be searched using the gene symbol, the name of the gene or the SNP ID of the variation.

Data Submission

Submitters require a Submitter ID prior to submitting SNP data to the SLGVD. To request a “Submitter ID” please complete the submitter ID request form and send it to submitterid-request@hgucolombo.net. A confirmation email will be sent to the contact email address in the form.

Please click here to download the template SUBMITTER ID REQUEST FORM.


Once you receive a Submitter ID you can start submitting you data using the Submitter ID. To submitt SNP data prepare submission file with your data and send it to slgvd-subs@hgucolombo.net.

Please click here to download the template SUBMISSION FILE.


You will received a submission report from SLGVD with updated database entries or list of errors encountered during processing your submission file via SLGVD pipeline. You can resubmit the corrected file to slgvd-subs@hgucolombo.net in the latter case.



Please use this link for direct data submission

Sample Record

References

[1] Scriver CR, Nowacki PM, Lehvaslaiho H. Guidelines and recommendations for content, structure, and deployment of mutation databases. Hum Mutat. 1999;13(5):344-50.