#383 New RNA interactions-related terms

[Pablo Porras]

Hi all,

These three new terms will be added to the ontology in order to allow curation of some types of RNA interactions and RNA/DNA-related features:

[Term]
id: MI:2201
name: DNA chemical modification
def: "Chemical alterations occurring at the nucleotide level in the specific DNA molecule involved in an interaction. The process can involve covalent modifications (i.e. methylations) or other forms of chemical modification." [PMID:14755292]
subset: PSI-MI_slim
synonym: "dna chemical modification" EXACT PSI-MI-short []
synonym: "DNA chemical modification" EXACT PSI-MI-alternate []
synonym: "DNA epigenetic modification" EXACT PSI-MI-alternate []
is_a: MI:0252 ! biological feature
created_by: ppm
creation_date: 2015-08-11T15:37:49Z

[Term]
id: MI:2202
name: RNA chemical modification
def: "Chemical alterations occurring at the nucleotide level in the specific RNA molecule involved in an interaction. The process can involve covalent modifications (i.e. 2'-O-methylation) or other forms of chemical modification, such as isomerizations (i.e. pseudouridylation)." [PMID:14755292]
subset: PSI-MI_slim
synonym: "post-transcriptional modification" EXACT PSI-MI-alternate []
synonym: "rna chemical modification" EXACT PSI-MI-short []
synonym: "RNA chemical modification" EXACT PSI-MI-alternate []
is_a: MI:0252 ! biological feature
created_by: ppm
creation_date: 2015-08-11T15:55:40Z

[Term]
id: MI:2203
name: primer extension assay
def: "Primer extension can be used to determine the 3' end of a given sequence of RNA. This technique requires a radiolabelled primer which is complementary to a region near the 3' end of the RNA. The primer is allowed to anneal to the RNA and reverse transcriptase is used to synthesize a strand of DNA from the RNA until it reaches the 5' end of the RNA. By denaturing the hybrid and using the extended primer DNA strand as a marker on an electrophoretic gel, it is possible to determine the transcriptional start site." [PMID:23378648]
subset: PSI-MI_slim
synonym: "primer extension assay" EXACT PSI-MI-short []
is_a: MI:1193 ! partial RNA sequence identification
created_by: ppm
creation_date: 2015-08-11T17:22:38Z

The DNA/RNA chemical modification terms aim to be general terms under which modifications to these molecules at the nucleotide level ("post-translational modifications" for nucleic acids(, such as methylations, can be added. We propose using the generic term to create a feature and then cross-reference this feature to ChEBI, which already has all these terms in place.

Any feedback welcomed. I am commiting the changes in the CV now.

Cheers,

Pablo.