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The-Sequence-Ontology / SO-Ontologies

Collect of SO Ontologies
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What is the difference between SO:0001659 promoter_element and SO:0000713 DNA_motif #535

Open pgaudet opened 3 years ago

pgaudet commented 3 years ago

SO term name and accession Please give the term name and accession. Example: rRNA_gene (SO:0001637)

SO:0001659 promoter_element : An element that can exist within the promoter region of a gene. SO:0000713 DNA_motif : A motif that is active in the DNA form of the sequence

Some children of DNA motif are more similar to children of 'promoter elements' - for example E_box and androgen_response_elements

Also, in other parts of the ontology (and based on GREECK feedback), 'promoter' was defined in SO are 'core promoter'. The children of promoter elements are not core promoter elements.

This branch needs some reorganization to be aligned with other parts of the ontology. Let me know if you want more specific suggestions.

@cmungall @colinlog @valwood @thomaspd @vanaukenk

Thanks, Pascale

Parent term name and accession Please give the term name and accession of the current parent. Example: ncRNA_gene (SO:0001263)

Suggested new parent term name and accession Please give the term name and accession of the parent you suggest for the term. Example: ncRNA_gene (SO:0001263)

Reason for the change Please state the reason you believe the term should be moved to a new location.

Relevant Publications Please list a number of relevant publications that support the name, definition, and ontological location of the term you are requesting. It is best if you can include a PubMed ID or the last name of the first author along with the publication year, journal-title and potentially the article title.

ValWood commented 3 years ago

"DNA motif" is not specific for transcription regulation motifs. It also includes (for example), rDNA_intergenic_spacer_element ARS_consensus_sequence mating_type_region_motif

(although the SO definition SO:0000713 DNA_motif A motif that is active in the DNA form of the sequence.

doesn't describe a motif, and I don't really understand what "is active in the DNA form of the sequence" means (this isn't the definition of a motif)

ValWood commented 3 years ago

the definition of SO:0001683 sequence_motif is : | A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance.

therefore it follows that the definition of DNA_motif aka (DNA_sequnce_motif /add synonym) should be

A DNA sequence motif is a nucleotide sequence pattern that may have biological significance.