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The Ontology for Biomedical Investigations
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New term request: enhancer reporter gene assay #764

Closed obi-bot closed 7 years ago

obi-bot commented 8 years ago

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. Suggested term name: 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.
  2. Synonyms: enhancer reporter gene assay
  3. Definition: An assay in which expression of a reporter gene is detected that was inserted under the control of an enhancer of interest.
  4. Definition source: PMID 24614317
  5. Parent term: suggest new term "reporter gene assay" (Definition: An assay in which expression of a reporter gene is detected that was inserted under the control of a regulatory sequence of interest.), with the existing term "Promoter activity detection by reporter gene assay" as a child of this same parent.
  6. Example of usage: PMID 19268701: "we experimentally concatenated up to four enhancers from different genes and used a transgenic mouse assay to compare the in vivo activity of these compound elements with that of the single modules"
  7. Editors: Paul D. Thomas, Yang Chai

Reported by: thomaspd1

Original Ticket: obi/obi-terms/781

obi-bot commented 8 years ago

Proposed by Jie Z.: Has_specified_output some (‘data item’ and is about SO:enhancer (http://purl.obolibrary.org/obo/SO_0000165)) Evaluant role ‘inheres in’ some DNA

We (CS and JZ) agree with proposed new term as parent: "reporter gene assay". Note that IEDB has 'reporter gene assay' as alternative label for 'promoter activity detection by reporter gene assay' (http://purl.obolibrary.org/obo/OBI_0000913) but we want to point out that reporter gene assays can be used for more than promoter activity as this term request illustrates.

Term to add: "reporter gene assay" definition: An assay in which expression is detected of a reporter gene that was inserted under the control of a regulatory sequence of interest. JZ suggests: preferred label: reporter gene detection assay (CS common usage is reporter gene assay)

Original comment by: cstoeckert

obi-bot commented 8 years ago

Discussed on Nov 23 call. Agreed to create a general parent class of reporter gene assay. AI: Chris to add.

Original comment by: cstoeckert

obi-bot commented 8 years ago

Original comment by: cstoeckert

obi-bot commented 8 years ago

Added term to OBI.

Original comment by: cstoeckert