Re: [SO-devel] C/V/D/J_gene_segment ontology

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Hi Karen,

> We could reverse the relation to be has_part if every X_gene_segment has_part exon

I think that's roughly what I had in mind, although I'm hesitant to start strictly requiring an exon part for every X_gene_segment. I haven't spent much time working through the SO tree. Is that the relationship of exon to mRNA? That's not clear to me from this page (likely due to my ignorance):
http://www.sequenceontology.org/browser/current_svn/term/SO:0000234

-Terence

________________________________
From: Karen Eilbeck [kei...@ge...]
Sent: Thursday, January 22, 2015 3:41 PM
To: SO developers
Subject: Re: [SO-devel] C/V/D/J_gene_segment ontology

Hi Terrance
Great suggestions and questions.

Off  the top of my head, without diving into the ontology,
exon part_of x_gene_segment?
would read as every exon part of some X_gene_segment, which is not true.

We could reverse the relation to be has_part if every X_gene_segment has_part exon
We could also subtype exon,
X_exon part_of X_gene_segment

I need to dive into this some more.
I will get back to you.

--Karen

On Jan 22, 2015, at 1:18 PM, Murphy, Terence (NIH/NLM/NCBI) [C] wrote:

Hi All,

I have a couple of questions about C/V/D/J_gene_segment features, which may be split over multiple intervals. Here’s an example in GenBank flatfile format (from NG_000002.1):

     gene<http://www.ncbi.nlm.nih.gov/nuccore/18860922?from=9381&to=9859&sat=4&sat_key=133151457>            9381..9859

                     /gene="IGLV4-69"

                     /gene_synonym="IGLV469; V5-6"

                     /note="immunoglobulin lambda variable 4-69"

                     /db_xref="GeneID:28784<http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=28784>"

                     /db_xref="HGNC:HGNC:5921<http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=HGNC:5921>"

                     /db_xref="IMGT/GENE-DB:IGLV4-69<http://www.imgt.org/IMGT_GENE-DB/GENElect?species=Homo+sapiens&query=2+IGLV4-69>"

     CDS<http://www.ncbi.nlm.nih.gov/nuccore/18860922?itemid=6&sat=4&sat_key=133151457>             join(9381..9429,9550..9859)

                     /gene="IGLV4-69"

                     /gene_synonym="IGLV469; V5-6"

                     /exception="rearrangement required for product"

                     /codon_start=1

                     /db_xref="GeneID:28784<http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=28784>"

                     /db_xref="HGNC:HGNC:5921<http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=HGNC:5921>"

                     /db_xref="IMGT/GENE-DB:IGLV4-69<http://www.imgt.org/IMGT_GENE-DB/GENElect?species=Homo+sapiens&query=2+IGLV4-69>"

     V_segment<http://www.ncbi.nlm.nih.gov/nuccore/18860922?itemid=7&sat=4&sat_key=133151457>       join(9381..9429,9550..9859)

                     /gene="IGLV4-69"

                     /gene_synonym="IGLV469; V5-6"

                     /standard_name="IGLV4-69"

Our GFF3 writer is currently using the same-ID/multiple-rows format for these segment features, like this:

NG_000002.1     RefSeq  gene    9381    9859    .       +       .       ID=gene2
NG_000002.1     RefSeq  CDS     9381    9429    .       +       0       ID=cds1;Parent=gene2
NG_000002.1     RefSeq  CDS     9550    9859    .       +       2       ID=cds1;Parent=gene2
NG_000002.1     RefSeq  V_gene_segment  9381    9429    .       +       .       ID=id562;Parent=gene2;part=1/2
NG_000002.1     RefSeq  V_gene_segment  9550    9859    .       +       .       ID=id562;Parent=gene2;part=2/2

I know some parsers expect IDs to be unique per row except for CDS rows, so this could be a problem. We’re looking at switching to using a parent/child format using exon features, mimicking mRNAs, like this:

NG_000002.1     RefSeq  gene    9381    9859    .       +       .       ID=gene2
NG_000002.1     RefSeq  CDS     9381    9429    .       +       0       ID=cds1;Parent=gene2
NG_000002.1     RefSeq  CDS     9550    9859    .       +       2       ID=cds1;Parent=gene2
NG_000002.1     RefSeq  V_gene_segment  9381    9859    .       +       .       ID=id564;Parent=gene2
NG_000002.1     RefSeq  exon    9381    9429    .       +       .       ID=id565;Parent=id564
NG_000002.1     RefSeq  exon    9550    9859    .       +       .       ID=id566;Parent=id564

I expect this would solve the duplicate ID problem.

I have two questions:
1)      From my read of the SO terms it doesn’t look like exon would be a valid child for gene segments. Am I mis-reading the SO definitions? Should they be changed to allow exon part_of *_gene_segment?
2)      Similarly, the CDS feature in this case seems like it should be a child of the V_gene_segment, and again CDS doesn’t appear to be a valid child. Should that be added as well?

-Terence

-----
Terence Murphy, Ph.D.
Staff Scientist
NCBI/NLM/NIH/DHHS

--
Have you seen NIH’s new genomes FTP site, including >45k assemblies?
http://www.ncbi.nlm.nih.gov/news/08-26-2014-new-genomes-FTP-live/

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Karen Eilbeck
Associate Professor
Department of Biomedical Informatics, University of Utah