RE: [Obo-discuss] [Obi-devel] Announce a Genome and Gene Ontology (GGO)
He, Yongqun
Thanks, Chris, for your comment and references. I agree with you. Once the separate ontology paralleling the SO for molecular entities is ready, we are happy to swap out the class ‘gene’ in OGG (previously GGO) for a new one.
As you might have noticed, I just emailed and notified the name change from GGO to OGG (Ontology of Genes and Genomes).
Oliver
From: Chris Mungall [mailto:cjmu...@lbl.gov]
Sent: Tuesday, October 29, 2013 7:08 PM
To: He, Yongqun
Cc: Lindsay Cowell; <obo-d...@lists.sourceforge.net>; Ramona Walls; ggo-d...@googlegroups.com; Liu, Yue; Cathy Wu
Subject: Re: [Obo-discuss] [Obi-devel] Announce a Genome and Gene Ontology (GGO)
On Tue, Oct 29, 2013 at 7:34 AM, He, Yongqun <yong...@med.umich.edu> wrote:
However, we do have possible issue with the two terms 'gene' and 'genome' per se, because these two terms have been defined in SO. We don't mean to duplicate the two terms. We just don't know if our GGO terms have the same meanings as the
two SO terms. Below is some explanation:
For the GGO term 'gene' (GGO_0000000002), here is our definition:
"a gene is a material entity that represents the entire DNA sequence required for synthesis of a functional protein or RNA molecule."
This definition comes from the NCBI-recommended book "Molecular Cell Biology. 4th edition":
http://www.ncbi.nlm.nih.gov/books/NBK21640/
Here is a paragraph of text quoted from the above book and website:
" In molecular terms, a gene commonly is defined as the entire nucleic acid sequence that is necessary for the synthesis of a functional polypeptide. According to this definition, a gene includes more than the nucleotides encoding the amino acid sequence
of a protein, referred to as the coding region. A gene also includes all the DNA sequences required for synthesis of a particular RNA transcript. In some prokaryotic genes, DNA sequences controlling the initiation of transcription by RNA polymerase can lie
thousands of base pairs from the coding region. In eukaryotic genes, transcription-control regions known as enhancers can lie 50 kb or more from the coding region. Other critical noncoding regions in eukaryotic genes are the sequences that specify 3′ cleavage
and polyadenylation [poly(A) sites] and splicing of primary RNA transcripts. Mutations in these RNAprocessing signals prevent expression of a functional mRNA and thus of the encoded polypeptide."
I totally agree with the definition of the term 'gene' in here.
One key factor in my mind is that GGO defines 'gene' as a material entity, but I don't know if the SO 'gene' definition agrees with it. In SO, the term 'gene' (http://purl.obolibrary.org/obo/SO_0000704)
is defined as:
"A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. "
Its root term is: sequence_feature (SO_0000110), which is defined as:
"An extent of biological sequence."
Here, I don't know if the "biological sequence" in SO is also a material entity, or a "sequence information" that may be classified as an IAO 'information content entity' (ICE).
As I view it, a gene material entity can be documented by its gene sequence information. The gene sequence information is an IAO 'information content entity'. I think we will need some term like 'gene sequence information' or something similar. I don't know
if the SO:sequence fits in this category.
There will be a a separate ontology that parallels the SO for the molecular entities. I suggest the GGO class gene is swapped out for this one when it's ready. Grouping classes like "human gene" can stay in GGO, they don't really serve
much purpose other than make the hierarchy slightly less flat in a browser.
See
http://www.sciencedirect.com/science/article/pii/S1532046410000353
http://ceur-ws.org/Vol-897/session3-paper13.pdf
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