Display extra details from new PHAF file

[kimrutherford]

See: pombase/pombase-chado#1066

• allele variant ( add url for genotype format variant syntax)
• condition details:
  • Temperature (degrees C)
  • Chemical or agent (concentration units)
• Chemical or agent dose
• Phenotype score / Phenotype score units
  • fitness_log2(0.123)
  • normalised_difference(-0.4234)
  • stored as properties in Chado (in feature_cvtermprop)

---

Edit: Some documentation

[kimrutherford]

How's this for displaying the extra condition details?

The prototype is here: https://desktop.kmr.nz/term/FYPO:0000797

[manulera]

Ah yes! That looks good

[kimrutherford]

Looks good!

Great. The changes will be visible in the morning.

We may need to tweak the formatting a bit because sometimes the details wrap onto the next line and look odd:

[ValWood]

When we announce this we should say that the temperature and concentration can only be collected for HTP submission at present , and update the docs there to specify exactly the format for including temperature and concentration and score.

https://www.pombase.org/documentation/phenotype-data-bulk-upload-format

[kimrutherford]

The changes will be visible in the morning.

That's working now. Here's good example: https://pombase.org/genotype/alg6delta

[ValWood]

I wonder if we could tidy the syntax of these fields a little so that it will be consistent when I document that these values are allowed for HTP data

Percentage are usually (0.1%) but occasionally 2 % (with or without space)

Molarity is usually (20mM) but sometimes (20 mM) (with or without space)

Somemtimes (2.5 % v/v) and sometimes  (2 % (w/v)) ( different use of brackets)

Just on https://pombase.org/genotype/alg6delta

Is it usual to mix molarity, ratio µg/ml, percentages in a single study?

Anyway, just standardizing use of spaces and brackets would be helpful.

[kimrutherford]

I wonder if we could tidy the syntax of these fields a little so that it will be consistent when I document that these values are allowed for HTP data

Moved to: pombase/curation#3627

[kimrutherford]

Still need to display:

• Chemical or agent dose - already covered by the values attached to the FYECO terms
• Phenotype score / Phenotype score units:
  • fitness_log2(0.123)
  • normalised_difference(-0.4234)

We also have "allele variant" from the PHAF files. Maybe that doesn't need to be displayed?

[ValWood]

"allele variant"
what is that ? isn't it just the allele description?

[kimrutherford]

"allele variant"
what is that ? isn't it just the allele description?

They are the longer allele descriptions using chromosome coordinates like this:

III:g.217516_218406del

We haven't included these strings for all alleles yet but there are examples in the last column of this file:

pombe-embl/external_data/phaf_files/chado_load/htp_phafs/PMID_34984977_phaf.tsv

[ValWood]

I don't think we need to display it one the gene pages , but it could eventually be added to the allele pages as additional information?

[kimrutherford]

Yep, maybe on the allele pages at some point. But it's probably more useful as bulk download data in the PHAF files.

[kimrutherford]

• Phenotype score / Phenotype score units:
  • fitness_log2(0.123)
  • normalised_difference(-0.4234)

Should these be display on the website?

Should we display them in the same style as extensions like we do for severity ("has severity high")?:

normalised_difference -0.4234
fitness_log2 0.123

[ValWood]

I'm not sure @manulera will these be meaningful to users?

[manulera]

Hi both,

I think this may make sense in the publication pages, to compare two phenotypes since these numbers are only relevant when comparing phenotypes obtained in the same experiment. Not critical, but it can be neat.

In the gene page I don't think they would be useful.

[ValWood]

That's a good plan, only on the publication page for this detail.

[kimrutherford]

I think this may make sense in the publication pages, to compare two phenotypes since these numbers are only relevant when comparing phenotypes obtained in the same experiment. Not critical, but it can be neat.

Thanks Manu. Good plan.

That's a good plan, only on the publication page for this detail.

That's implemented and will be on the main site tomorrow. The new column is only visible in the detailed view and only on this page: https://www.pombase.org/reference/PMID:34984977

Let me know if the column name needs changing.

Unfortunately that page is still slow to load but I'm working on it: #2100

[kimrutherford]

If there's anything needed, let's open new issues.