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Re: [Obo-discuss] genetic feature zygosity terms
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From: Doug h. <dh...@cs...> - 2008-11-06 17:38:36
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Let me restate my initial needs. I am interested in using the terms 'heterozygous' and 'homozygous' in a phenote configuration to specify the status of genetic features while describing a genotype...as in allele m124 is heterozygous and allele b45 is homozygous in this double mutant genotype. To do this, each genetic feature pertinent to explicitly describing the genotype must have it's zygosity explicitly captured. Because I intend to use this in phenote, the terms 'heterozygous' and 'homozygous' must be used in an ontology so they can be made available in phenote. At ZFIN we currently handle these details in our data model. However, I am developing a phenote config that laboratories (without direct access to curate in ZFIN) can use to capture the details of numerous genotypes they develop in mutant screens etc. If it is done properly, then we will be able to load the data into ZFIN directly as captured by researchers using phenote....that is the hope anyway. For my purposes I care little about whether these are SO terms, PATO terms, genetic context terms, or cross products. I only care that they represent the zygosity of individual genetic features so genotypes can be explicitly described. -Doug Richard H. Scheuermann , Ph.D. wrote: > So the issue is dealing with genotype at the gene/allele level versus > the genome level. I think we tend to be a little sloppy about > distinguishing between the two. > > Richard > > On Nov 6, 2008, at 9:53 AM, Michael Ashburner wrote: > >> I agree with David. The way to do this is to *explicily* represent >> genotypes. >> >> Michael >> On 6 Nov 2008, at 09:29, David Sutherland wrote: >> >>> On Thu, 6 Nov 2008, Richard H. Scheuermann , Ph.D. wrote: >>> >>> Hi Richard, >>> >>>> I think it might be better to describe these as type of genotypes >>>> rather than types of alleles. Something like: >>>> >>>> name: heterozygous_genotype >>>> def: "A heterozygous genotype is a genotype of a diploid genome is >>>> which one >>>> allele differs from its counterpart on the other chromosome due to >>>> nucleotide sequence variation." >>>> >>>> name: homozygous_genotype >>>> def: "A homozygous genotype is a genotype of a diploid genome is >>>> which one >>>> allele is identical to its counterpart on the other chromosome in its >>>> nucleotide sequence." >>>> >>>> name: hemizygous_genotype >>>> def: "A hemizygous genotype is a genotype of a diploid genome is >>>> which one >>>> allele is missing from one chromosome whereas its counterpart is >>>> present on the other chromosome." >>>> >>> >>> A few questions: How would you use these to represent a genotype where >>> one locus is homozygous and a second is heterozygous? >>> >>> How would you distinguish transheterozygotes from mutation/+ >>> (evolutionary >>> biologists would of course dispute the reality of this distinction, but >>> model organism biologists usually expect it.) >>> >>> And what is to be gained from this approach instead of representing >>> gentypes explicitly? >>> >>> Cheers, >>> >>> David >>>> Richard >>>> >>>> >>>> On Nov 6, 2008, at 4:18 AM, Colin Batchelor wrote: >>>> >>>>> [cc:ed to song-devel in case anyone relevant isn't already on these >>>>> lists] >>>>> >>>>> Suzanna Lewis writes: >>>>> >>>>>> Alternatively Chris thinks that the SO might be the most appropriate >>>>>> place for these terms, and I can see this side as well (and now am >>>>>> tending towards SO). >>>>>> >>>>>> However neither of SO nor "context" currently have these terms and >>>>>> they definitely need a home somewhere. >>>>>> >>>>>> Colin & Karen & David: where do you think these terms should live? >>>>> >>>>> I think they could fit in as children of allele (SO:0001023), current >>>>> definition "An allele is one of a set of coexisting sequence >>>>> variants of >>>>> a gene." >>>>> >>>>> How do these look? (The wording needs improved.) >>>>> >>>>> name: heterozygous_allele >>>>> def: "A heterozygous allele on a chromosome in a diploid genome is one >>>>> that differs from its counterpart on the other chromosome." >>>>> intersection_of: SO:0001023 ! allele >>>>> intersection_of: has_quality PATO:new ! heterozygous >>>>> >>>>> name: homozygous_allele >>>>> def: "A homozygous allele on a chromosome in a diploid genome is one >>>>> that is identical to its counterpart on the other chromosome." >>>>> intersection_of: SO:0001023 ! allele >>>>> intersection_of: has_quality PATO:new ! homozygous >>>>> >>>>> Don't know what to do about hemizygous; sorry. >>>>> >>>>> Alan Ruttenberg adds: >>>>> >>>>>> It could go in PATO (relational quality?). There is precedent with >>>>> terms >>>>>> like diploid and haploid. >>>>> >>>>> "heterozygous", "homozygous" and "hemizygous" go into PATO and the SO >>>>> terms are cross-products. >>>>> >>>>> Best wishes, >>>>> Colin. >>>>> >>>>> -- >>>>> Dr Colin Batchelor MChem MRSC, Team Leader, Informatics R&D >>>>> Informatics Department, >>>>> Royal Society of Chemistry, Thomas Graham House, Cambridge UK CB4 0WF >>>>> bat...@rs... <mailto:bat...@rs...> t: +44 1223 432280 >>>>> >>>>> >>>>> >>>>> DISCLAIMER: >>>>> >>>>> This communication (including any attachments) is intended for the >>>>> use of the addressee only and may contain confidential, privileged >>>>> or copyright material. It may not be relied upon or disclosed to >>>>> any other person without the consent of the RSC. If you have >>>>> received it in error, please contact us immediately. Any advice >>>>> given by the RSC has been carefully formulated but is necessarily >>>>> based on the information available, and the RSC cannot be held >>>>> responsible for accuracy or completeness. In this respect, the RSC >>>>> owes no duty of care and shall not be liable for any resulting >>>>> damage or loss. The RSC acknowledges that a disclaimer cannot >>>>> restrict liability at law for personal injury or death arising >>>>> through a finding of negligence. The RSC does not warrant that its >>>>> emails or attachments are Virus-free: Please rely on your own >>>>> screening. >>>>> >>>>> ---------------------------------------------------------------------- >>>>> --- >>>>> This SF.Net email is sponsored by the Moblin Your Move Developer's >>>>> challenge >>>>> Build the coolest Linux based applications with Moblin SDK & win >>>>> great prizes >>>>> Grand prize is a trip for two to an Open Source event anywhere in >>>>> the world >>>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >>>>> <http://moblin-contest.org/redirect.php?banner_id=100&url=/> >>>>> _______________________________________________ >>>>> Obo-discuss mailing list >>>>> Obo...@li... >>>>> <mailto:Obo...@li...> >>>>> https://lists.sourceforge.net/lists/listinfo/obo-discuss >>>> >>>> ------------------------------------------------------------------------ >>>> ------------------------ >>>> >>>> Richard H. Scheuermann, Ph.D. >>>> Chief, Division of Biomedical Informatics >>>> Director, Division of Translational Pathology >>>> John H. Childers Professorship in Pathology >>>> Department of Pathology >>>> U.T. Southwestern Medical Center >>>> 5323 Harry Hines Blvd. >>>> Dallas, TX 75390-9072 >>>> >>>> phone: 214-648-4115 >>>> FAX: 214-648-4070 >>>> email: ric...@ut... >>>> <mailto:ric...@ut...> >>>> http://pathcuric1.swmed.edu/Research/scheuermann.html >>>> >>>> >>>> >>>> >>> >>> >>> ------------------------------------------------------------------------- >>> This SF.Net email is sponsored by the Moblin Your Move Developer's >>> challenge >>> Build the coolest Linux based applications with Moblin SDK & win >>> great prizes >>> Grand prize is a trip for two to an Open Source event anywhere in >>> the world >>> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >>> <http://moblin-contest.org/redirect.php?banner_id=100&url=/> >>> _______________________________________________ >>> Obo-discuss mailing list >>> Obo...@li... >>> <mailto:Obo...@li...> >>> https://lists.sourceforge.net/lists/listinfo/obo-discuss >> > > ------------------------------------------------------------------------------------------------ > > Richard H. Scheuermann, Ph.D. > Chief, Division of Biomedical Informatics > Director, Division of Translational Pathology > John H. Childers Professorship in Pathology > Department of Pathology > U.T. Southwestern Medical Center > 5323 Harry Hines Blvd. > Dallas, TX 75390-9072 > > phone: 214-648-4115 > FAX: 214-648-4070 > email: ric...@ut... > <mailto:ric...@ut...> > http://pathcuric1.swmed.edu/Research/scheuermann.html > > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > ------------------------------------------------------------------------ > > _______________________________________________ > Obo-discuss mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-discuss > -- Doug Howe, Ph.D. ZFIN Scientific Curator Zebrafish Nomenclature Coordinator |