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EO term for "untreated Control" in osmotic stress RNA seq expt #124

Open cmungall opened 10 years ago

cmungall commented 10 years ago

From Sunita Kumari: Sunita: What EO term do you use for control treatment? I mean e.g there are two samples, one has ABA treatment other is simple water treatment (no ABA), so will be used as control for ABA: EO:0007105

RNA-seq data from one of our paper http://www.ncbi.nlm.nih.gov/pubmed/22008187 We need metadata annotation for KBase, so there were ABA, PEG treatments and for control we used water and NaOH.

Original comment by: cooperl09

cmungall commented 10 years ago

Ideally in the annotation schema I would expect the following arrangement:

Type: Name Control Environment: Water/NaOH Treatment Environment: ABA/PEG

OR

Experiment | Plant Accession |sample_type | Treatment | Treatment_value 001 | Accession-1 | control | ABA | Absent 001 | Accession-1 | treated | ABA | Present/specify amount

ABA absent can be replaced with Water

But feel free to use water

Original comment by: pj37

cmungall commented 10 years ago

I think we need a class for the untreated controls.
Suggested new term: control treatment (EO:new): A plant treatment (EO:0001001) involving the application of inert factors such as water in an experiment.

we can create child terms as needed

Original comment by: cooperl09

cmungall commented 10 years ago

A plant treatment used as a reference (control) to compare the effects of other one or more treatment factor in a study.

Sometimes you have inert sometimes there is no treatment.

Original comment by: pj37