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The-Sequence-Ontology / SO-Ontologies

Collect of SO Ontologies
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Terms for transposons are not complete #487

Closed oushujun closed 4 years ago

oushujun commented 4 years ago

Main issue

What is this request referring to? Many transposons are not included in the SO system. Please add them for a better catalog. For SO naming and relationships please refer to the two citations below.

Parent Term transposable_element SO:0000101

Relevant Publications https://www.nature.com/articles/nrg2165 https://pubmed.ncbi.nlm.nih.gov/26709091/ Relevant discussions: https://github.com/oushujun/EDTA/issues/83

Other non-transposon repeat terms:

Parent Term repeat_region SO:0000657

Request Terms knob: cytologically observable heterochromatic regions present on chromosomes Simple_repeat: RepeatMasker defined simple repeat regions

davidwsant commented 4 years ago

Hi Shujun,

The term knob has been assigned the ID SO:0002257. The SO Browser is not updating automatically right now, but I have emailed someone to see if that can be fixed. This term is present in the ontology files in GitHub and should be added to the browser soon.

If you would like new terms as children of transposable_element, please give specific details including specific names and definitions. Please follow the format of this issue template. Please specify every name of a term along with every definition that you would like added in a single issue request.

As for simple_repeat, we do not typically add terms that refer to a program. If you would like to find a formal definition from RepeatMasker, you can add another issue request and we can look into adding that term.

Thank you,

Dave Sant