Three genetic characteristics terms needed by MO

[obi-bot]

Genetic Characteristics related MGED ontology (MO) terms are used to describe the characteristics of samples in a microarray experiment. To facilitate the terms to be added to OBI, we provide the use cases, definitions of our requested MO terms.

Driving use case of the MGED ontology (MO) is MAGE-TAB files.

MAGE-TAB format files are simple tab-delimited spreadsheet files used to describe a microarray experiment. They typically contain some annotations using the MO.

Two types of MAGE-TAB files we are focusing on now: - IDF file - describing the experiment design, contact details, variables and protools - SDRF file - a spreadsheet with columns that describe samples, annotations, protocol references, hybridizations and data

The following fields in either IDF or SDRF files are generally required to use MO terms: - Experiment design - Experiment factor type - Characteristics - Protocol types - Protocol parameters - Material type

For more details about MAGE-TAB files, please check: http://www.ebi.ac.uk/microarray/doc/help/MAGE-TAB.html

Genetic Characteristics related MO terms are used to describe the characteristics of samples in a microarray experiment. These MO terms can be found in SDRF files, characteristics columns.

The genetic characteristics of samples may vary in different groups as experimental factors. So, these MO terms can be used as Experiment factor type in IDF files and found in experimental factor value columns in SDRF files.

Below some examples of genetic characteristics related MO terms used in MAGE-TAB files are listed. All these files can be found on ArrayExpress website.

Experiment link can direct you to the summary page of a microarray experiment on ArrayExpress. In either Experimental factors or Sample attributes fields, you can see some MO terms I mentioned in the use cases (need to click plus sign to expand the details of the experiment).

The link to IDF or SDRF files are also provided to view the usage of the MO terms in MAGE-TAB files. You may need to download and open SDRF files using Excel for better view, especially when SDRF files contain many columns.

Some MO term labels may not be accurate or appropriate according to their usage. Please focus on the use cases. We'd like to improve their labels and/or definitions to fit their usage in MAGE-TAB files.

MO terms request to be added to OBI 1. Genotype 2. wild_type 3. Haplotype

Use cases of Genotype and wild_type

Use case 1: Experiment: http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=E-MEXP-853 SDRF file: http://www.ebi.ac.uk/microarray-as/ae/files/E-MEXP-853/E-MEXP-853.sdrf.txt Characteristics [Genotype]: wild_type

Use case 2: Experiment: http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=E-TABM-56 SDRF file: http://www.ebi.ac.uk/microarray-as/ae/files/E-TABM-56/E-TABM-56.sdrf.txt Characteristics [Genotype]: wild_type

Use case 3: Experiment: http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=E-ATMX-16 IDF file: http://www.ebi.ac.uk/microarray-as/ae/files/E-ATMX-16/E-ATMX-16.idf.txt Experimental Factor Type, genotype

SDRF file: http://www.ebi.ac.uk/microarray-as/ae/files/E-ATMX-16/E-ATMX-16.sdrf.txt Characteristics [Genotype]: wild_type Characteristics [Genotype]: ncbitax ATMYC2 over-expression (ncbitax ATMYC2 over-expression is not MO term)

Use case 4: Experiment: http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=E-GEOD-1301 IDF file: http://www.ebi.ac.uk/microarray-as/ae/files/E-GEOD-1301/E-GEOD-1301.idf.txt Experimental Factor Type, genotype

SDRF file: http://www.ebi.ac.uk/microarray-as/ae/files/E-GEOD-1301/E-GEOD-1301.sdrf.txt Characteristics [Genotype]: wild_type Characteristics [Genotype]: IL-13 knockout (IL-13 knockout is not MO term)

Genotype used in above 4 use cases can refer to an organism or an allele.

Use cases of Genotype and Haplotype

Use case 1: Experiment: http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=E-GEOD-590 IDF file: http://www.ebi.ac.uk/microarray-as/ae/files/E-GEOD-590/E-GEOD-590.idf.txt Experimental Factor Type, genotype

SDRF file: http://www.ebi.ac.uk/microarray-as/ae/files/E-GEOD-1301/E-GEOD-1301.sdrf.txt Characteristics [Genotype]: USF1 protective haplotype (USF1 protective haplotype is not MO term) Characteristics [Genotype]: USF1 susceptibility haplotype (USF1 susceptibility haplotype is not MO term)

Use case 2: Experiment: http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=E-TABM-119 SDRF file: http://www.ebi.ac.uk/microarray-as/ae/files/E-TABM-119/E-TABM-119.sdrf.txt Characteristics [Haplotype]: 1 MYCN copy per haploid genome

Use case 3: Experiment: http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=E-MEXP-2280 SDRF file: http://www.ebi.ac.uk/microarray-as/ae/files/E-MEXP-2280/E-MEXP-2280.sdrf.txt Characteristics [Haplotype]: APOE haplotype: 32; MAPT haplotype: H1/H1 (APOE haplotype, MAPT haplotype are not MO terms) Characteristics [Haplotype]: APOE haplotype: 43; MAPT haplotype: H1/H1 Characteristics [Haplotype]: APOE haplotype: 33; MAPT haplotype: H1/H1

Genotype used in use case 1 refer to a single chromosome.

Term definitions and their suggested superclass in OBI

All three terms were used to describe attributes of samples. So suggest to add under "quality" in OBI. "genotype" can be used as independent variable as well. Need to think how to link it to OBI:independent variable specification in the future.

1. Genotype MO definition: The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment. SO definition: A genotype is a variant genome, complete or incomplete. (xref: wiki page) wiki definition: The genotype is the genetic constitution of a cell, an organism, or an individual

Suggested definition: a quality of an individual cell or organism that is determined by the total set of its genetic information encoded in its chromosomal, plasmid, viral or other genetic material.(Discussed on Dec 15, 2009 dev call.)

2. wild type MO definition: The genotype or phenotype that is found in nature or in standard laboratory stocks for a given organism. wiki definition: Wild type refers to the phenotype of the typical form of a species as it occurs in nature.

Suggested definition: use MO definition.

3. haplotype MO definition: The genotype of a single chromosome (i.e., the haploid genotype) that is known and relevant to the experiment being performed. SO definition: A haplotype is one of a set of coexisting sequence variants of a haplotype block. wiki definition: A haplotype is a combination of alleles at multiple loci that are transmitted together on the same chromosome. Haplotype may refer to as few as one locus or to an entire chromosome depending on the number of recombination events that have occurred between a given set of loci.

Suggested definition: use MO definition

Some of these terms have been submitted and discussed in tracker item: http://sourceforge.net/tracker/?func=detail&aid=2896768&group\_id=177891&atid=886178

Reported by: zhengj2007

Original Ticket: obi/obi-terms/487

[obi-bot]

See also https://sourceforge.net/tracker/?func=detail&aid=1899832&group\_id=177891&atid=886178

Original comment by: mcourtot

[obi-bot]

Discussed with Chris. We found the 'Genotype' associated with some genetic modification process.

We'd add the following MO terms into OBI under OBI_0600043 genetic transformation. gene_knock_in A genetic transformation whereby a functional gene, or a functional part of a gene, is inserted into an organism', e.g. by recombination, P-element insertion.

gene_knock_out A genetic transformation that the modified organism renders a gene non-functional e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods.

transfection a genetic modification that Introduce genetic material into an organism often in the form of a plasmid. (be parent of OBI_0600060 DNA transfection)

chromosomal_substitution A state/condition describing a cell, or organism, in which all, or part, of a chromosome from a donor replaces that of the recipient. Examples include strains created by repeated backcrossing as well as those created by recombinant methods. For single gene insertion, use the term gene_knock_in.

induced_mutation The modification of the genetic material (either coding or non-coding) of an organism by mutagenic compounds or irradiation.

Question: We'd like to add restriction to the modification. For example, gene_knock in and knock out. We would like to say that they are some modification that is about allele/gene. chromosomal_substitution is a modification that is about multiple alleles/genes or locus. How can we add this restriction?

According to the definition of genetic modification in Wikipedia, it involves the use of recombinant DNA techniques, but does not include traditional animal and plant breeding or mutagenesis.

Does OBI genetic transformation cover induced_mutation and breeding generated genetic variation? It sames not according to its logical definition. achieves_planned_objective 'material transformation objective'.

If not, where can these terms be added? We need a way to pull all these terms out for some software implementations.

Original comment by: zhengj2007

[obi-bot]

See tracker item: https://sourceforge.net/tracker/?func=detail&aid=3087730&group\_id=177891&atid=886178

Original comment by: zhengj2007

[obi-bot]

• status: open --> closed

Original comment by: zhengj2007