#783 New term request: Transcript expression location detection by Hybridization Chain Reaction

[Paul Thomas]

Another term requested for FaceBase.

1. Suggested term name: Transcript expression location detection by Hybridization Chain Reaction.
2. Synonyms: Transcript expression location detection by fluorescent HCR.
3. Definition: An assay in which the location (e.g. anatomical/tissue) of a transcript is detected by a multiplexed fluorescent in situ hybridization, based on orthogonal amplification with hybridization chain reactions (HCR). RNA probes complementary to mRNA targets trigger chain reactions in which fluorophore-labeled RNA hairpins self-assemble into tethered fluorescent amplification polymers.
4. Definition source: PMID 21037591
5. Parent term: suggest to be a child of the existing term "fluorescent in situ hybridization". This is a similar technique to FISH (fluorescence in-situ hybridization) when FISH is applied to RNA, but as described right now in OBI, FISH is described as applying to DNA (which is understandable as this is its most common application), so the current term could be renamed "Genomic location detection by FISH". You might consider another parent, something like "transcript expression location detection assay", with a further parent "molecular location detection assay", as I don't see anything like this in the ontology (though I could easily just have overlooked it!).
6. Example of usage: PMID 25977364: "Multiplexed imaging of mRNA expression using fluorescent hybridization chain reaction (HCR) quantitatively confirmed the expression profiles of lead cells"
7. Editors: Paul D. Thomas, Yang Chai

[Chris Stoeckert]

Discussed on Nov. 23 call. OK with this term. Does not appear to be PCR but is related to FISH. Current FISH in OBI is specific to chromosomal structure. Need to change.
AI: add a tracker for OBI_0001683 to relabel and add a general FISH class.
AI: CS come up with a proposed logical axiom.

[Chris Stoeckert]

Added to OBI. Made a subclass of in-situ hybridization.