new phenotype evidence codes

[pombase-admin]

Hi Kim, could you please add the 3 terms below to phenotype evidence?

I am also wondering if we should replace 'northern' with something more general?

[Term] id: ECO:0000333 name: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence def: "A type of protein assay evidence where proteins are separated according to their electrophoretic mobility." [ECO:MCC, PubMed:4861258] comment: Electrophoretic mobility is a function of both the length and charge of a protein. The protein sample is linearized with sodium dodecyl sulfate (SDS), an anionic detergent. Typically, polypeptides bound with SDS possess an even distribution of charge per unit mass, and subsequent fractionation is by size. synonym: "SDS-PAGE evidence" EXACT [] is_a: ECO:0000039 ! protein assay evidence created_by: mchibucos creation_date: 2012-07-31T14:56:43Z

[Term] id: ECO:0000334 name: particle size and count assay evidence def: "A type of direct assay evidence resulting from an assay where both the size of and number of particles in a sample are determined." [ECO:MCC] comment: An example of an instrument used to analyze particle sizes and counts is the Beckman Coulter. Z Series system. is_a: ECO:0000002 ! direct assay evidence created_by: mchibucos creation_date: 2012-07-31T15:19:32Z

[Term] id: ECO:0000335 name: substance quantification evidence def: "A type of direct assay evidence where the quantity of a substance used as part of an assay is measured." [ECO:MCC] comment: Two examples of substance quantification assay are (i) measuring how much of a radiolabelled compound is taken up by a cell and (ii) measuring how much of a substrate is turned over by a given enzyme. is_a: ECO:0000002 ! direct assay evidence created_by: mchibucos creation_date: 2012-07-31T15:52:46Z

Original comment by: Antonialock

[pombase-admin]

Some for me too, please:

[Term] id: ECO:0000336 name: competitive growth assay evidence def: "A type of biological assay evidence in which a mutated strain of a microorganism, such as a yeast or bacterium, is grown competitively with wild-type cells and the relative fitness of the strains is assessed." [GOC:MAH, PMID:14718172, PMID:20537132] synonym: "fitness profiling" EXACT [GOC:MAH, PMID:20537132] is_a: ECO:0000094 ! biological assay evidence created_by: mchibucos creation_date: 2012-08-24T12:03:58Z

[Term] id: ECO:0000337 name: gel electrophoresis evidence def: "A type of direct assay evidence where molecules have been sorted according to their size and charge by moving through a gel in the presence of an electric field." [ECO:MCC, wikipedia:Gel_electrophoresis] comment: Molecules typically separated include DNA, RNA, or protein. The gel is typically made of agarose, polyacrylamide, or starch. is_a: ECO:0000002 ! direct assay evidence created_by: mchibucos creation_date: 2012-08-24T12:11:51Z

[Term] id: ECO:0000338 name: pulsed-field gel electrophoresis evidence def: "Gel electrophoresis evidence that employs alternately pulsed, perpendicularly oriented electrical fields, at least one of which is inhomogeneous, to separate large DNA molecules on an agarose gel." [PMID:6373014] synonym: "PFGE" EXACT [] is_a: ECO:0000337 ! gel electrophoresis evidence created_by: mchibucos creation_date: 2012-08-24T12:34:01Z

[Term] id: ECO:0000339 name: two-dimensional agarose gel electrophoresis evidence def: "Gel electrophoresis evidence where DNA molecules are electrophoresed on a low percentage agarose gel followed by high voltage electrophoresis on a higher percentage agarose gel in the presence of ethidium bromide." [PMID:8594382] comment: The first dimension gel is intentionally run at low voltage in low percentage agarose to separate DNA molecules in proportion to their mass. The second dimension is run at high voltage in a gel of higher agarose concentration in the presence of ethidium bromide so that the mobility of a non-linear molecule is drastically influenced by its shape. synonym: "2-D agarose gel electrophoresis" EXACT [] is_a: ECO:0000337 ! gel electrophoresis evidence created_by: mchibucos creation_date: 2012-08-24T12:42:37Z

[Term] id: ECO:0000340 name: plasmid maintenance assay evidence def: "Experimental evidence from an assay in which a mitotically stable plasmid (or minichromosome) is introduced into cells, cells are grown without selection for several generations, the proportion of cells that retain the plasmid is then determined (by comparing colony numbers on selective versus non-selective media), and the loss per generation calculated." [ECO:MCC, PMID:6323245] synonym: "minichromosome maintenance assay evidence" EXACT [PMID:6323245] is_a: ECO:0000006 ! experimental evidence created_by: mchibucos creation_date: 2012-08-24T13:27:58Z

Thanks! m

Original comment by: mah11

[pombase-admin]

if you add gel electrophoresis evidence then I won't need SDS-gel evidence (I thought we were going to try to keep these to a minimum?)

Original comment by: Antonialock

[pombase-admin]

me too, perhaps "gel electrophoresis evidence" is sufficient?

Original comment by: ValWood

[pombase-admin]

Well, for the two I planned to use (PFGE and 2D agarose), lumping into generic "gel electrophoresis" would lose a lot of specificity. Anyone who really needs that specificity ought to read the papers anyway, so it probably isn't a huge loss from our point of view. Given that we've had a user ask for "tetrad analysis" rather than just use "cell growth assay" for viability, though, I wonder if we're just postponing the inevitable ... it would not surprise me in the least if the people who go to the trouble to do 2D agarose gels (and they are fiddly!) want to say so specifically when they annotate their papers.

m

Original comment by: mah11

[pombase-admin]

There is a bit of rationale for this one:

>Given that we've had a user ask for "tetrad analysis" rather than just use "cell growth assay" for viability, though, I wonder if we're just postponing the inevitable

a proportion of the deletions are probably incorrect and this indicates an additional check. although I think all of the deletion as have gone through tetrad dissection so this is kind of moot, and I have cone with the "cell growth assay parent " here. In retrospect think that the fact that it is confirmed by another group in another paper is enough and I don't think we really need the tetrad term...... val

Original comment by: ValWood

[pombase-admin]

Could someone summarise this with a list of the term names to add?

Original comment by: kimrutherford

[pombase-admin]

Please add these:

ECO:0000334 particle size and count assay evidence ECO:0000335 substance quantification evidence ECO:0000336 competitive growth assay evidence (synonym: fitness profiling) ECO:0000337 gel electrophoresis evidence ECO:0000340 plasmid maintenance assay evidence

For now, we've decided not to add the more specific electrophoresis terms after all (I'll continue storing the additional info on the wiki).

cheers! m

Original comment by: mah11

[pombase-admin]

(oops, just noticed particle size and count assay is already in)

also, once you've added gel electrophoresis, you could remove sodium dodecyl sulfate polyacrylamide gel electrophoresis (unless Val & Antonia change their minds about lumping vs. splitting ...)

Original comment by: mah11

[pombase-admin]

I vote for lumping as much as poss to keep the list manageable, so remove that one.

Original comment by: ValWood

[pombase-admin]

OK, I've added those codes. Please close the ticket if they look OK.

Original comment by: kimrutherford

[pombase-admin]

• status: open --> open-fixed

Original comment by: kimrutherford

[pombase-admin]

• status: open-fixed --> closed-fixed

Original comment by: ValWood

[pombase-admin]

at the moment there are two substance quantification codes: substance quantification evidence & substance quantification. These should be merged.

Sodium dodecyl sulfate gel electrophoresis appears in a parenthesis

Original comment by: Antonialock

[pombase-admin]

• status: closed-fixed --> open-invalid

Original comment by: Antonialock

[pombase-admin]

I've removed "substance quantification" and "sodium dodecyl sulfate polyacrylamide gel electrophoresis" from the evidence list in the test tool. It will change in the main tool next time I update.

Original comment by: kimrutherford

[pombase-admin]

• status: open-invalid --> open-fixed

Original comment by: kimrutherford

[pombase-admin]

Don't remove the term sodium dodecyl sulfate polyacrylamide gel electrophoresis completely, just remove the parenthesis around the term

Original comment by: Antonialock

[pombase-admin]

I've put "sodium dodecyl sulfate polyacrylamide gel electrophoresis" back. Where (which page) are you seeing parentheses?

Original comment by: kimrutherford

[pombase-admin]

there was a parenthesis around it in the allele interface.

It's gone now so no sweat!

Original comment by: Antonialock

[pombase-admin]

That's weird. Let me know if you see it again.

Can this be closed now?

Original comment by: kimrutherford

[pombase-admin]

afaik yes, closing

Original comment by: Antonialock

[pombase-admin]

• status: open-fixed --> closed-fixed

Original comment by: Antonialock