Add instructions for authors for Strain and Variation sections

[draciti]

We want to capture genotype info for strains, variations, and transgenes, also species. Add a sentence to explain to authors how to enter the data: Enter the strain name followed by genotype followed by species, separated by comma. e.g. PMD153, (vhp-1(sa366) II; egIs1 [dat-1p::GFP]), C. elegans

@draciti find a couple of examples for alleles, one CRISPR and a regular one find also an example for transgenes

[draciti]

Text for New Alleles box: e.g. dpy-5(e61), C.elegans CRISPR alleles: e.g. bus-50(e5001[bus-50::gfp]), C. elegans

Text for New Strains box: e.g. PMD153, (vhp-1(sa366) II; egIs1 [dat-1p::GFP]), C. elegans

Text for New Transgenes box: e.g.: eaIs15, [Ppie-1::HIM-5::GFP::pie-1], C. elegans

@vanaukenk please take a look. A couple of questions:

1. In the proposal at the beginning of the ticket wa wanted to add a sentence such as: Enter the strain name followed by genotype followed by species, separated by comma. Are we still keeping the sentence or shall we simply put the example?
2. Do we need to check in with Paul D to see if the examples are ok? I took the allele examples from the WB nomenclature page.
3. For transgenes do we want to include an extrachromosomal example as well?

Thanks

[vanaukenk]

Thanks @draciti These look good.

For the questions:

1. I'd keep the sentence; it could be helpful. And maybe we should even write a sentence for alleles (and transgenes), e.g. Enter the gene name followed by the allele in parentheses; for CRISPR alleles, include the knock-in construct. (If that makes sense).
2. We could always double-check with Paul D. just to make sure these look okay and maybe also to see if we need to update the WB nomenclature page to include CRISPR alleles.
3. Good idea - an extrachromosomal example, if curators will want them, would be good.

[draciti]

Writing the updated text here not to lose track, will also send to Paul D via email: Text for New Alleles box: Enter the gene and allele name followed by species, separated by comma. e.g. dpy-5(e61), C.elegans For CRISPR alleles include the knock-in construct, followed by species, separated by comma. e.g. bus-50(e5001[bus-50::gfp]), C. elegans

Text for New Strains box: Enter the strain name followed by genotype followed by species, separated by comma. e.g. PMD153, (vhp-1(sa366) II; egIs1 [dat-1p::GFP]), C. elegans

Text for New Transgenes box: Enter the transgene name followed by genotype followed by species, separated by comma. e.g.: eaIs15, [Ppie-1::HIM-5::GFP::pie-1], C. elegans For extrachromosomal arrays: sqEx67, [rgef-1p::mcherry::GFP::lgg-1 + rol-6], C. elegans

[draciti]

@valearna below the text suggestions, approved by Hinxton:

Text for New Alleles box: Enter the gene and allele name followed by strain and species, separated by comma. e.g. flu-4(e1004), CB1004, C.elegans For CRISPR alleles include the knock-in construct, followed by species, separated by comma. e.g. bus-50(e5001[bus-50::gfp]), C. elegans

Text for New Strains box: Enter the strain name followed by genotype followed by species, separated by comma. e.g. PMD153, (vhp-1(sa366) II; egIs1 [dat-1p::GFP]), C. elegans

Text for New Transgenes box: Enter the transgene name followed by genotype followed by species, separated by comma. e.g.: eaIs15, [Ppie-1::HIM-5::GFP::pie-1], C. elegans For extrachromosomal arrays: sqEx67, [rgef-1p::mcherry::GFP::lgg-1 + rol-6], C. elegans

[draciti]

To discuss: ask to specify species only for non elegans entities? @valearna @vanaukenk

[vanaukenk]

As an author, I think I would find it easier if instructions were uniform, regardless of species.

At this point, we are still largely dealing with C. elegans entities, but if it's easier for Hinxton, I'd be in favor of just asking authors to include species until we can come up with a more clever way to handle this.

Also, do we want authors to add strains for the CRISPR alleles as well?

[draciti]

Also, do we want authors to add strains for the CRISPR alleles as well?

Instructions updated below: Text for New Alleles box: Enter the gene and allele name followed by strain and species, separated by comma. e.g. flu-4(e1004), CB1004, C.elegans For CRISPR alleles include the knock-in construct, followed by strain and species, separated by comma. e.g. hmg-3(bar24[hmg-3::3xHA]), BAT1560, C. elegans

Text for New Strains box: Enter the strain name followed by genotype followed by species, separated by comma. e.g. PMD153, (vhp-1(sa366) II; egIs1 [dat-1p::GFP]), C. elegans

Text for New Transgenes box: Enter the transgene name followed by genotype followed by species, separated by comma. e.g.: eaIs15, [Ppie-1::HIM-5::GFP::pie-1], C. elegans For extrachromosomal arrays: sqEx67, [rgef-1p::mcherry::GFP::lgg-1 + rol-6], C. elegans

[draciti]

As an author, I think I would find it easier if instructions were uniform, regardless of species.

Sounds good

[draciti]

Can Paul D implement a check to make sure entities will be captured correctly? example, if an author does not include a strain e.g. flu-4(e1004), C.elegans Can the script recognize that there is only one comma and output a warning that one of the required fields is missing? @Paul-Davis

[Paul-Davis]

@draciti I'm sure we can handle it

[draciti]

Enter the gene and allele name followed by strain and species, separated by comma. e.g. flu-4(e1004), CB1004, C. elegans. For CRISPR alleles include the knock-in construct, followed by strain and species, separated by comma. e.g. hmg-3(bar24[hmg-3::3xHA]), BAT1560, C. elegans.

Text for New Strains box: Enter the strain name followed by genotype followed by species, separated by comma. e.g. PMD153, (vhp-1(sa366) II; egIs1 [dat-1p::GFP]), C. elegans

Text for New Transgenes box: Enter the transgene name followed by genotype followed by species, separated by comma. e.g.: eaIs15, [Ppie-1::HIM-5::GFP::pie-1], C. elegans For extrachromosomal arrays: sqEx67, [rgef-1p::mcherry::GFP::lgg-1 + rol-6], C. elegans

[draciti]

Change text: Enter one transgene per line. If possible,...

that applies to transgenes, strains, alleles explanatory text. Also, New transgenes section C. elegans should be italicized.

[draciti]

Looks good. Closing