Upload data in tripal

Question

[felipead66]

I have installed Tripal on an online server. Can anyone tell me how to upload count data from a table?

[Michael]

Have you checked the documentation: https://tripal.readthedocs.io/en/latest/ What kind of count data?

[felipead66]

I want to add both transcriptome and protein data. It is kind of silly question since I have created the table in the "Materialized view" but I do not know how to upload the actual data. The tutorial says it is done without programming, but I cannot really see how to do it!

[Michael]

You really should read the documentation. Also, first it is count data, then protein and transcriptome, so which is it?

[felipead66]

It is protein and transcript normalized count data.

Answer 1

[Michael]

If that is gene-expression data, try the Tripal Expression extension module. This can import the data from CSV files:

Data Loaders Three loaders are provided by this module, a biosample loader, an expression loader, and a p-value loader. The biosample loader has the ability to load data from a flat file or from an xml file downloaded from NCBI. The expression loader can load expression data in column or matrix format. The p-value loader takes a csv or tsv file.

Expression Display Once expression data is loaded, a display field will be shown on each feature page that has corresponding biosamples and expression values.

The whole process might need a bit more steps than simply uploading the CSV file, but if you want to upload expression data, this is the Tripal extension to take. Follow the examples given in the documentation and if you experience problems use the github issue tracker.

[felipead66]

Thank you for your answer. Is it possible to also upload measurements? I have 10 tissues for which I have measurements such as length, lightness, acidity etc. How could I treat these measurements in Tripal?

[Michael]

Hi, it's been a while. Did you have any luck with the expression module? I am not sure if there is an extension that adds tissues and measurements. But if these are just a few measurements and not gene expression (which you could put into the expression module) I'd tend to make my life easy and just post a table on a web-page or in a publication or in Drupal. Off-loading everything into well-structured repositories and data models is certainly the "official" prescribed path, but sometimes you need to ask the question if it is worth the effort.

In my opinion, and average Tripal/Drupal site is already trending towards unmanageable complexity, with every module added, the situation gets worse.

[felipead66]

Thank you for your answers. I am having some troubles with Tripal, trying to figure out how to proceed. Now my problem is with expression data uploading. I have a matrix file with 15 samples (expression measurements). Therefore I have a matrix of 16 columns (one being the names). I have uploaded the biomaterials etc which includes 15 samples. But when I upload the matrix, I get an error specifying that "17 columns are expected but found 16". Do you have any idea why I "miss" a column?