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The Ontology for Biomedical Investigations
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New terms requested for FaceBase #763

Closed obi-bot closed 7 years ago

obi-bot commented 8 years ago

Hi, I'm trying to get new terms to describe some of the data in the FaceBase resource (this project is funded by NIH/NIDCR, website at facebase.org).

  1. Enhancer activity detection by reporter gene assay. There is currently a term for "Promoter activity detection by reporter gene assay" so this could be added as a sibling. The parent could be Reporter gene assay, which is currently a synonym, but this could be changed.
  2. Chromatin modifier-associated region identification by ChIP-Seq assay. There is currently a term for "transcription factor binding site identification by ChIP-Seq assay" so this could be added as a sibling. This is meant to cover chromatin modifiers like EP300, which is a histone acetyltransferase. So it is not a histone modification, but is the enzyme that adds a histone modification. The term can refer to GO:0016568
  3. Transcript expression location detection by Hybridization Chain Reaction. The paper describing this assay is http://www.nature.com/nbt/journal/v28/n11/full/nbt.1692.html. 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). You might consider as a new 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!).

Thanks, Paul Thomas pdthomas@usc.edu

Reported by: thomaspd1

Original Ticket: obi/obi-terms/780

obi-bot commented 8 years ago

Thanks for the term submissions. I'm glad to see details about how the new terms would fit into OBI.

We're working on a set of guidelines to streamline the term submission process. Could you please take a look, and use the guidlines to submit one ticket per term request?

http://obi-ontology.org/page/OBI_term_guidelines

Feedback on the guidelines is also appreciated.

Original comment by: jamesaoverton

obi-bot commented 8 years ago

Original comment by: cstoeckert

obi-bot commented 8 years ago

These have been individually discussed and approved.

Original comment by: cstoeckert