Take the 2-minute tour ×
Biology Stack Exchange is a question and answer site for biology researchers, academics, and students. It's 100% free, no registration required.

I wanted to create a tool for some fields like SIFT, Phenotype, etc..so for example I know Phenotype will have "Text" values or SIFT will have some determined values from a drop down list...but what about Chrom Positions? what are some valid sample values for that? so I can know what type I can use for it.

share|improve this question
    
(1) Since this is a purely bioinformatical question, it should be closed and re-asked on biostars.org. (2) Are you concerned with the position on a chromosome (i.e. a one-based offset like 123456) or a genomic position including the chromosome (e.g. X:123456) or? Then there’s leonardo’s answer which uses a different format to store the same information. –  Konrad Rudolph May 16 '12 at 12:44
add comment

1 Answer

up vote 2 down vote accepted

Since it sounds like you are the one designing the database, you can make this a number of ways. The simplest is probably to reduce it to two variables, likely two decimals.

See this hemoglobin example for a chromosomal locus example.

  • There are N chromosomes (23 for humans, if you like, sex chromosomes can be treated as a pair).
  • There are 2 chromatids per chromosome.
  • The part of the chromatid is either p or q (short or long arm).
  • Then there is the location on the portion of the chromatid (eg, 15.5).

Chromatid can be easily represented as a decimal, where the integer portion is the chromosome number, and the decimal portion corresponds to the chromatid and arm.

The chromosomal locus can be another decimal, such as 15.5 for the example above.

This is of course one way, and there are many other ways you could do this.

share|improve this answer
2  
This sounds a bit convoluted, to be honest. Why not use a compound type to store the separate bits of information in their respective fields? For instance, putting chromatid and arm into a decimal point number isn’t only “dirty”, it’s also unnecessarily complicated. Even if the database doesn’t support enumerations (wot?!), this could still be represented by separate bit fields. –  Konrad Rudolph May 16 '12 at 12:46
    
Yes it absolutely could, and should be done this way. This was one (crude) way to do it as the OP did not post any details as to the kind of DB or format he expected to use. –  leonardo May 16 '12 at 21:31
add comment

Your Answer

 
discard

By posting your answer, you agree to the privacy policy and terms of service.

Not the answer you're looking for? Browse other questions tagged or ask your own question.