PhenCode: Guidelines for data conversion

There are some things the LSDB curators or teams can do to facilitate adding their data to the Locus Variants track. The data should be in a computer-friendly format such as tab-delimited. Suggested fields include a variant ID, HGVS-style name, common name, nucleotide change, amino acid change, and phenotype. Other helpful information could include disease association, base change type (substitution, deletion, insertion, duplication, or complex), location (exon, intron, 5' UTR, 3' UTR, or not within known transcription unit), and whether the coordinates are precise or estimated. In addition, the GenBank accession numbers for the reference sequences used to describe the variants are essential.

If all of this information is available, it is generally simple for the PhenCode staff to obtain the genomic coordinates and convert the data to the format needed for adding it to the track. If pieces such as the HGVS-style name are missing but the nucleotide change is given, the data can still be used but will require some extra work.

Providing links from the Genome Browser back to the source LSDB is easy, if the LSDB has been designed to allow direct links. Just give the PhenCode staff an ID (or other unique URL suffix) for each variant, plus the base URL to which these should be appended, and the links can be automatically generated and included with the variant details. It is possible for one variant to link to several pages if desired; for example the details page can have links to both the source LSDB and to OMIM.

Linking from the LSDB to the Genome Browser is also not difficult. There are several entry points that can be used, so the first decision is what you want the user to see when the link is followed. The simplest approach is just a general link to the Browser's home page ( The most powerful solution is to create a custom track on-the-fly that contains the result of a user's query at the LSDB. This not only highlights a subset of the Locus Variants track, but can also control other aspects of the display, including which build is used and which tracks are open. (See the PhenCode examples for some screen shots.) UCSC provides detailed help for creating custom tracks. Between these two extremes there are many options; feel free to contact Belinda image of email address if you need assistance.