Cannot Extract Some Information Using Ucsc Table Browser
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13.1 years ago
User 6659 ▴ 970

Hello

This is a very practical question. I've been looking at the UCSC browser and going through some online tutorials. However I couldn't see how to do something like get the human SNPs in dbSNP, say dbSNP 131, that have a link to an OMIM entry.

I am not specifically looking to answer this biological question (get the snps associated with a disease) but I was curious as to why i couldn't answer this question using the table browser.

It turns out you have to know what tables are related to the 'known gene' table that contain the information pertaining to OMIM. How do you find the tables that might contain the information you want? Do you have to look at the database schema to find tables whose names contain words relevant to information you are interested in. So if i wanted to get GO terms i would look for table names containing GO. Is there some crucial document that I am missing such as a schema description. I have seen this document but I presume there are too many tables to maintain this.

I'm also not sure how you know if the data you want is in an annotation track or a table. I'm presuming data with coordinates is in tracks and 'annotation' data is accessed via the auxiliary tables.

thanks

ucsc dbsnp gene • 2.7k views
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13.1 years ago
Treylathe ▴ 950

As a general answer, UCSC does have a 'track search' (look at buttons below location box on UCSC genome gateway page, but I don't think that is fully what you need as it searches track names and descriptions and not the tables.

Your best bet so far is to search through the old description file you linked to and/or the table schema, or to perhaps query the database directly? Not the easiest solution.

In answer to your specific example, the UCSC Preview browser does have an OMIM SNP track: http://genome-preview.ucsc.edu/cgi-bin/hgTracks?clade=mammal&org=Human&db=hg19&position=chr21%3A33%2C031%2C597-33%2C041%2C570&hgt.suggest=&pix=800&Submit=submit&hgsid=2560128

that includes that data.

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do you know why the omim track is only available under the preview browser?

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does the preview browser represent changes to the genome browser, the development of new tracks or both? I wasn't sure why the omim track would only be available under the preview browser and not the main browser

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it represents changes to the browser including new tracks (ie, both), they are tracks and changes that are quite ready for prime time (and should be taken with that grain of salt).

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