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EBISPOT / efo

Github repo for the Experimental Factor Ontology (EFO)
https://www.ebi.ac.uk/efo/
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HCA-critical: Review 'experimental process' branch #12

Closed siiraa closed 6 years ago

siiraa commented 6 years ago

Especially transciption profile assays. Need a proper classification and axiomatisation. Need new terms for single-cell assays, find classification + axioms.

siiraa commented 6 years ago

Duplicate of #4

siiraa commented 6 years ago

There is a relevant thread here - https://www.ebi.ac.uk/panda/jira/browse/FGPTO-610

Maria Keays requested this a while back: We are getting single-cell RNA-seq experiments in ArrayExpress and would like to be able to search for them easily later on -- so we thought if we could add a new term somewhere under study design (EFO_0001426) for them that would help. This would then go in the IDF "Experimental Design" field with things like "time series design" etc.

We wondered about having a new ArrayExpress experiment type but this would be confusing, as under ArrayExpress experiment type we have e.g. "RNA-seq of coding RNA", but you can have single-cell RNA-seq experiments that are "RNA-seq of coding RNA" or "RNA-seq of non-coding RNA" (and conceivably other types ...). So we thought that the decision to profile RNA taken from a single cell or from a whole tissue fits better under "study design" given what else is already under there -- but open to suggestions if you think it doesn't fit there.

siiraa commented 6 years ago

Relevant to assay/protocol review: https://www.ebi.ac.uk/panda/jira/browse/FGPTO-700

Add new term "antigen binding on array protocol"

This is mainly for ArrayExpress submitters who have data sets on peptide arrays. We have protocol term "hybridization protocol" (http://www.ebi.ac.uk/efo/EFO_0003790) or "nucleic acid hybridization to array protocol" (http://www.ebi.ac.uk/efo/EFO_0003815) for nucleic acids but no equivalent for peptides/proteins. Submitters of such data sets don't think the term "hybridization" is appropriate for their experiments since the term is exclusively for nucleic acids.

The definition for "antigen binding on array protocol" can be:

A protocol describing the binding of target proteins or peptides to a fixed peptide probe on the array.

siiraa commented 6 years ago

@daniwelter - you might find having a look through the slides here useful to reviewing methods needed in the scope of HCA. https://commonfund.nih.gov/sites/default/files/Breakouts-June28_508.pdf

Many of the assays/methods mentioned here are already in EFO, can benefit from better organization thought.