Add new PHAF columns

[kimrutherford]

• Ploidy - needs to be mandatory (add to all files
• allele variant ( add url for genotype format variant syntax)
• Use Condition column
  • Temperature (degrees C)
  • Chemical or agent (concentration units)
• Chemical or agent dose
• Phenotype score / Phenotype score units
  • use Severity column
    • currently: FYPO_EXT:0000003 etc.
    • add:
      • fitness_log2(0.123)
      • normalised_difference(-0.4234)
      • store as properties in Chado (feature_cvtermprop)

• FYECO -> Glucose present (CHEBI)
• CHEBI,concentration
• FYECO (UV) -> FYECO:X(mJ)

[manulera]

Related to pombase/curation#3465

[manulera]

@kimrutherford I am almost done with the file, would just have to figure out those exceptional systematic ids and what the alleles should be called. Going swimming now but will check tomorrow 🏊

https://github.com/manulera/phenomics_paper_HTP/blob/master/results/pombase_dataset.tsv

[kimrutherford]

Thanks Manu. I've changed the loading code to handle the changes to the severity and condition columns.

[kimrutherford]

I've changed the PHAF loader to store the allele_variant and the phenotype score in Chado. I'm still trying to think of a good way to store the new condition details.

We need to think about how and where to display the new information on the website.

[kimrutherford]

Ploidy - needs to be mandatory

I've changed my mind on that. It can continue to be optional in the cases where there is no allele variant.

[manulera]

I've changed my mind on that.

I guess the assumption is haploid unless otherwise stated, but why does this have to do with the allele variant present or absent?

[kimrutherford]

I guess the assumption is haploid unless otherwise stated, but why does this have to do with the allele variant present or absent?

I was thinking that we would need to put something in the "Ploidy" column only if we have an allele variant column. If there is no allele variant column, we won't need a "Ploidy" column.

[manulera]

I am looking at the PHAF headers and I think I see what you mean, but I don't think this problem is restricted to the allele variant column. The headers are clearly meant to describe either haploids or homozygous diploids, but it is not clear how you would describe a heterozygous diploid. Separating allele names, expression levels and all with a spacer? Two lines for the same phenotype, but then what would be the unique identifier of the pair?

You can call me on skype if you want to quickly discuss this.

[kimrutherford]

but it is not clear how you would describe a heterozygous diploid.

There isn't a way to store these in the PHAF file. The "Ploidy" column is a hack to allow loading the commonest diploids ("homozygous diploid"). That format doesn't support anything more complicated.

We have plans for a new PHAF format to handle this problem (see #496) but we haven't implemented it yet. Stable allele identifiers will make this problem easier.

[kimrutherford]

Hi @manulera

Sorry to come back to this after 2 weeks.

In the new PHAF file (pombe-embl/external_data/phaf_files/chado_load/htp_phafs/PMID_34984977_phaf.tsv), some of the FYECO conditions have empty brackets, like: FYECO:0000211(). Does that need fixing?

Also should we include the unit ("C") after temperatures in conditions? Or is the unit obvious in that case?

Here an example line that has examples of both questions:

Gene systematic ID	FYPO ID	Allele description	Expression	Parental strain	Background strain name	Background genotype description	Gene name	Allele name	Allele synonym	Allele type	Evidence	Condition	Penetrance	Severity	Extension	Reference	taxon	Date	Ploidy	Allele variant
SPNCRNA.1130	FYPO:0000725	deletion	null	972 h-						deletion	ECO:0001563	FYECO:0000138,FYECO:0000211(),FYECO:0000334,FYECO:0000005(32)		fitness_log2(0.11)		PMID:34984977	4896	2023-02-23	haploid	III:g.319210_319876del

Thanks!

[manulera]

Hi @kimrutherford, fixed here and updated on revision 8824 of svn

manulera/phenomics_paper_HTP@ae5baa3

[kimrutherford]

Hi @kimrutherford, fixed here and updated on revision 8824 of svn

Thanks! I've finished the changes needed to load the conditions with temperatures and quantities into Chado. The new PHAF file loads perfectly now.

I think this in done now.

We now need to think about how to show this new information:

• Display extra details from new PHAF file website#2029