The proposal has been made to obsolete DNA methylation & children, as well as their regulation terms:
GO:0006306 DNA methylation
GO:0032775 DNA methylation on adenine
GO:0032776 DNA methylation on cytosine
GO:0090116 C-5 methylation of cytosine
GO:0010424 DNA methylation on cytosine within a CG sequence
GO:0010426 DNA methylation on cytosine within a CHH sequence
GO:0010425 DNA methylation on cytosine within a CNG sequence
GO:0090124 N-4 methylation of cytosine
The reason for obsoletion is that these represent molecular functions. Consider:
GO:0009008 DNA-methyltransferase activity
GO:0003886 DNA (cytosine-5-)-methyltransferase activity
GO:0051718 DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates
GO:0051719 DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates
GO:0051720 DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates'
GO:0009007 site-specific DNA-methyltransferase (adenine-specific) activity
GO:0015667 site-specific DNA-methyltransferase (cytosine-N4-specific) activity
GO:0120328 ATP-dependent DNA (cytosine-5-)-methyltransferase activity
GO:0044030 regulation of DNA methylation
GO:1905642 negative regulation of DNA methylation
GO:1905643 positive regulation of DNA methylation
The reason for obsoletion is that these terms represent regulation of a molecular function. Consider 'GO:0040029 epigenetic regulation of gene expression' or a child.
Dear all,
The proposal has been made to obsolete DNA methylation & children, as well as their regulation terms:
GO:0006306 DNA methylation GO:0032775 DNA methylation on adenine GO:0032776 DNA methylation on cytosine GO:0090116 C-5 methylation of cytosine GO:0010424 DNA methylation on cytosine within a CG sequence GO:0010426 DNA methylation on cytosine within a CHH sequence GO:0010425 DNA methylation on cytosine within a CNG sequence GO:0090124 N-4 methylation of cytosine
The reason for obsoletion is that these represent molecular functions. Consider:
GO:0009008 DNA-methyltransferase activity GO:0003886 DNA (cytosine-5-)-methyltransferase activity GO:0051718 DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates GO:0051719 DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates GO:0051720 DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates' GO:0009007 site-specific DNA-methyltransferase (adenine-specific) activity GO:0015667 site-specific DNA-methyltransferase (cytosine-N4-specific) activity GO:0120328 ATP-dependent DNA (cytosine-5-)-methyltransferase activity
GO:0044030 regulation of DNA methylation GO:1905642 negative regulation of DNA methylation GO:1905643 positive regulation of DNA methylation
The reason for obsoletion is that these terms represent regulation of a molecular function. Consider 'GO:0040029 epigenetic regulation of gene expression' or a child.
Annotations are here: https://github.com/geneontology/go-annotation/issues/4729
ARUK-UCL 1 BHF-UCL 6 ComplexPortal 8 EcoCyc 3 MGI 15 ParkinsonsUK-UCL 1 RGD 11 TAIR 22 ZFIN 15 InterPro: 6
I'd like to proceed with the obsoletion on December 22nd, 2023.
You can comment on the ticket: https://github.com/geneontology/go-ontology/issues/26602
Thanks, Pascale