Genotypic and Phenotypic data

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Genotypic and Phenotypic data

Jonathan Arvisais
Hi,

Is there a Tripal module/extension that can be used to upload phenotypic or genotypic data, similar than the tool to upload fasta and GFF?

Is there also a Tripal module to display genotypic and phenotypic data

Thank you!

Jonathan

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Re: Genotypic and Phenotypic data

Lacey-Anne Sanderson
Hi Jonathan,

Short Answer: These tools are currently in development. 

Loading the Data: There aren't any genotype/phenotype specific loaders at this time. However, you can load the data using the Tripal Bulk Loader (Available in the Development Version of Tripal -git clone http://git.drupal.org/sandbox/spficklin/1337878.git tripal). I am currently in the process of creating a tutorial for the Tripal Bulk Loader and will reply to this thread when it's available. Essentially the Tripal Bulk Loader allows you to load any tab-delimited file by creating a template which describes chado database records and mappings from spreadsheet columns to chado fields. You can also indicate foreign keys and set constants.

Viewing the Data:  There aren't any modules available for viewing either genotypes or phenotypes stored in the Natural Diversity tables of chado. Dorrie Main's group at Washington State University is currently working on a module that will display phenotypes although I don't know how far away that is from being released.

I have created a KnowPulse Genotype module (available from my drupal sandbox: http://drupal.org/sandbox/laceysanderson/1341246) that doesn't use standard chado tables to store the genotypes. I found that using the Natural Diversity module to store genotypic data took too much space on our server due to the large number of records required. As such this module doesn't use the natural diversity module tables but instead uses a kp_stock_genotype table to link genotypes (stored in chado.genotype and linked to features via feature_genotype) to germplasm (stock) and a project. The module creates all the database tables it needs, has an administrative interface and exposes genotypes to Views 2 -providing genotype-specific filters and fields. This module is currently being used in our production site (KnowPulse) although it is still under active development -new features are being added monthly, sometimes weekly. To see it in action, go to: http://knowpulse2.usask.ca/portal/genotype/Cultivated-Lentil/comparison?add_germplasm_genotype%5B0%5D%5Bstock_name%5D=CDC+Redberry&add_germplasm_genotype%5B0%5D%5Bstock_id%5D=58&add_germplasm_genotype%5B0%5D%5Borganism_id%5D=4&add_germplasm_genotype%5B1%5D%5Bstock_name%5D=CDC+Robin&add_germplasm_genotype%5B1%5D%5Bstock_id%5D=6749&add_germplasm_genotype%5B1%5D%5Borganism_id%5D=4&add_germplasm_genotype%5B2%5D%5Bstock_name%5D=L01-827A&add_germplasm_genotype%5B2%5D%5Bstock_id%5D=9727&add_germplasm_genotype%5B2%5D%5Borganism_id%5D=465&add_germplasm_genotype%5Badd_stock%5D%5Borganism_id%5D=%3CANY%3E&add_germplasm_genotype%5Badd_stock%5D%5Bstock_name%5D=&polymorphic%5Bfirst%5D=58&polymorphic%5Bsecond%5D=9727&library=All which shows genotypes for 3 Lentil lines for markers polymorphic between CDC Redberry and L01-827A (2 of the lines shown). Notice that you can add as many lines as you want to this display (others include ILL 8006, 964a-46 and Eston-A). Also, if you click on any marker in the list you will see a list of genotypes and a summary of alleles, flanking SNPs and a marked up backbone sequence showing nearby SNPs are available. Keep in mind, this module doesn't provide all of the flexibility of the Natural Diversity Schema (ie: it doesn't allow you to attach protocols or experiment details to individual genotypes although this information can be stored at the project level by using projectprop) and as such, you should really consider your needs and whether this reduced schema will handle them before use.

Hope this helps!
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-2430
Room 3D10 Agriculture
Department of Plant Sciences
University of Saskatchewan

On 2012-01-27, at 10:32 AM, Jonathan Arvisais wrote:

Hi,

Is there a Tripal module/extension that can be used to upload phenotypic or genotypic data, similar than the tool to upload fasta and GFF?

Is there also a Tripal module to display genotypic and phenotypic data

Thank you!

Jonathan
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