Re: [Obo-discuss] [Obi-devel] Announce a Genome and Gene Ontology (GGO)

[Chris M. <cjm...@lb...>]

On Tue, Oct 29, 2013 at 7:34 AM, He, Yongqun <yon...@me...> 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