Add allele properties

[mbrush]

Transferred from: NIF-11599 Original Reporter: Nicole Washington

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We need a section of GENO that records the properties of an "allele" on phenotype/gene expression. These "alleles" could be genetic changes or externally applied changes (like morpholinos/RNAi, transient transfection).

The kinds of things that need to be included here are:

1. up/down (over/under) expression For example, as resulting from Transgenic/Actin promoter (up expression) or RNAi (down expression)
2. hypermorph (genetic changes that result in increased phenotype).
3. hypomorph (genetic changes that result in decreased phenotype).
4. environmentally-dependent (resulting from drugs, temperature, etc.). changes in phenotype are only observed when an allele is exposed to a particular environment. 4b. temperature-specific. different phenotypes are observed when this allele is exposed to a different temperature.

An allele can have >1 of the above properties. For example, I believe that a single allele might be hypomorphic at one temp, and hypermorphic at another. There may need to be specific subtypes for each of these, but i think these are the general layout of the classes.

[pnrobinson]

"hypomorph" etc. is not a genotype this is a consequence of a genotype at a biochemical level.

Please also note that there is a good ontology that covers things like this

http://variationontology.org/

--Peter

Dr. med. Peter N. Robinson, MSc. Professor of Medical Genomics Professor in the Bioinformatics Division of the Department of Mathematics and Computer Science of the Freie Universität Berlin Institut für Medizinische Genetik und Humangenetik Charité - Universitätsmedizin Berlin Augustenburger Platz 1 13353 Berlin Germany +4930 450566006 Mobile: 0160 93769872 peter.robinson@charite.de http://compbio.charite.de http://www.human-phenotype-ontology.org Introduction to Bio-Ontologies: http://www.crcpress.com/product/isbn/9781439836651 I have learned from my mistakes, and I am sure I can repeat them exactly ORCID ID:http://orcid.org/0000-0002-0736-9199 Scopus Author ID 7403719646 Appointment request: http://doodle.com/pnrobinson

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Von: mbrush [notifications@github.com] Gesendet: Freitag, 16. Januar 2015 01:46 An: monarch-initiative/GENO-ontology Betreff: [GENO-ontology] Add allele properties (#3)

Transferred from: NIF-11599https://support.crbs.ucsd.edu/browse/NIF-11599 Original Reporter: Nicole Washington

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We need a section of GENO that records the properties of an "allele" on phenotype/gene expression. These "alleles" could be genetic changes or externally applied changes (like morpholinos/RNAi, transient transfection).

The kinds of things that need to be included here are:

1. up/down (over/under) expression For example, as resulting from Transgenic/Actin promoter (up expression) or RNAi (down expression)
2. hypermorph (genetic changes that result in increased phenotype).
3. hypomorph (genetic changes that result in decreased phenotype).
4. environmentally-dependent (resulting from drugs, temperature, etc.). changes in phenotype are only observed when an allele is exposed to a particular environment. 4b. temperature-specific. different phenotypes are observed when this allele is exposed to a different temperature.

An allele can have >1 of the above properties. For example, I believe that a single allele might be hypomorphic at one temp, and hypermorphic at another. There may need to be specific subtypes for each of these, but i think these are the general layout of the classes.

— Reply to this email directly or view it on GitHubhttps://github.com/monarch-initiative/GENO-ontology/issues/3.

[mbrush]

GENO covers lots of concepts related to genotypes, including attributes of variants such as these. We are coordinating with the Sequence Ontology to implement such terms in SO or GENO for community re-use. Vario overlaps largely with SO (where we would rather put these things). And at present, I don't think either Vario or SO implements classes like this.

[mbrush]

A hierarchy/requirements from our Wormbase contacts (2015-06-02):

[kyook]

Here are terms that we will be using for the time being in WB to describe allele functional effects. I look forward to getting them in sync with GENO terms. I will send you an obo file via e-mail.

[mellybelly]

I'd also like to have protein effects, such as becoming constituently active

[mbrush]

see also the 'allelic requirement' and 'mutation consequence' slides in the deck here for other requirements: https://www.clinicalgenome.org/site/assets/files/2757/fitzpatrick_ddg2p.pdf . . .has some concepts not currently in GENO, but related to allele properties, mode of inheritance, and zygosity. ClinGen GenCC WG also shared slides with similar 'Allelic Requirement' terms (that were distinction from their 'Inheritance Pattern' terms).

Also consider terms Paul created for M Might's work?