[Feedback] Site Feedback: Gramene QTL dataset clarifications

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URL         : http://archive.gramene.org/about/index.html

Subject     : Site Feedback: Gramene QTL dataset clarifications

Name        : Max Jonkman

Email       : max.jonkman at wur.nl

Organization: Wageningen University & Researchcentre

Comments    : 

Dear sir/madam,

For the creation of an RDF database that contains rice QTL data, I have been using the QTL dataset from gramene.org. However, I have a few questions about the data itself, and I was hoping you could answer them for me, or point me to the person that could do so if not.

Both these questions relate to the dataset found at ftp://ftp.gramene.org/pub/gramene/archives/qtl/qtl39.sql.gz

1. In the trait_ontology_association table, there is a species_id column that only has values of 0 and 1. There are 10 different species_ids in the species table, but 0 is not one of them, and 2-10 are not referenced at all. Could you clarify the meaning of this column in the trait_ontology_association table?

2. In the 'qtl' table, there are columns for start and stop position. At first me and my supervisors interpreted them as absolute positions on the genome. However, there are decimals to be found, as well as a few negative numbers, and a lot actually have the same start and stop position. How do we need to interpret these numbers if I want to map them to the reference genome myself?

Hopefully you can answer my questions, it would be a huge help to my research.

Best regards,
Max Jonkman
MSc student with Systems and Synthetic Biology group of Wageningen University, the Netherlands

http://www.warelab.org/bugs/view.php?id=5406