SGD chemical phenotypes

[matentzn]

The alliance SGD records have many entries like:

{
            "conditionRelations": [
                {
                    "conditionRelationType": "has_condition",
                    "conditions": [
                        {
                            "chemicalOntologyId": "CHEBI:78661",
                            "conditionClassId": "ZECO:0000111",
                            "conditionStatement": "chemical:borrelidin"
                        }
                    ]
                }
            ],
            "dateAssigned": "2006-05-05T00:05:00-00:00",
            "evidence": {
                "publicationId": "PMID:785224"
            },
            "objectId": "SGD:S000000854",
            "phenotypeStatement": "decreased resistance to chemicals",
            "phenotypeTermIdentifiers": [
                {
                    "termId": "APO:0000003",
                    "termOrder": 1
                },
                {
                    "termId": "APO:0000087",
                    "termOrder": 2
                }
            ]
        },

You can find the corresponding SGD record here:

https://www.yeastgenome.org/chemical/CHEBI:78661#phenotype

To extract our g2p faithfully, I think we need to do not only take into account the phenotype statement, but also the experimental conditions. So, we do not just do what we usually do:

SGD:S000000854 --[has phenotype]--> APO:0000087 (resistance to chemicals) and 'has modifier' some APO:0000003 (decreased)

but we do the following:

SGD:S000000854 --[has phenotype]--> APO:0000087 (resistance to chemicals) and 'characteristic of' some CHEBI:78661 and 'has modifier' some APO:0000003 (decreased)

Please confirm.

[srengel]

Hi @matentzn, is it true that the CHEBI ID does need to be included in the 'resistance to chemicals' phenotypes for them to be accurately represented.

is that what you are asking?

i don't have input regarding format of your statement (SGD:S000000854 --[has phenotype]--> APO:0000087 (resistance to chemicals) and 'characteristic of' some CHEBI:78661 and 'has modifier' some APO:0000003 (decreased)) because i don't know the usage/formatting rules.

[matentzn]

@srengel thanks, that is what we thought! Great, thank you! Thats all we needed to know!

[matentzn]

cc @kevinschaper!

[kevinschaper]

Hi @srengel!

I think we’re trying to tease out how the chemical is involved. Is it that HOM3 has a decreased chemical resistance phenotype in the context of environmental exposure to borrelidin, or that HOM3 has a decreased resistance to borrelidin phenotype?

[matentzn]

I was hoping the meaning is: HOM3 expression
Causes increased resistance to borrelidin.

[srengel]

I was hoping the meaning is: HOM3 expression Causes increased resistance to borrelidin.

No, this is not correct, it does not mean this.

SGD phenotypes are always MUTANT phenotypes. the type of mutant must also be indicated. the Alliance phenotype records are incomplete for yeast because they do not accommodate the mutant_type information.

in the example in this ticket, @kevinschaper the [some mutant_type] of HOM3 has decreased resistance to borrelidin relative to wild-type

the mutant_types are these:

APO:0000007 misexpression
APO:0000008 overexpression
APO:0000009 activation
APO:0000010 gain of function
APO:0000011 null
APO:0000012 repressible
APO:0000013 reduction of function
APO:0000014 conditional
APO:0000015 unspecified

[kevinschaper]

Oh! that's super helpful, thank you @srengel! Are the gene to phenotype associations with mutant type downloadable directly from SGD?

[srengel]

oh yes!, the entire set of phenotype data can be accessed via YeastMine:

https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Phenotype_Tab_New&scope=all

[kevinschaper]

Hi @srengel, just picking this back up again. It looks like yeast mine.yeastgenome.org isn't responding anymore. Do you have an updated url?

[srengel]

Hi @kevinschaper we had to shut down YeastMine due to funding cuts. the entire set of SGD phenotype data can be accessed via the SGD downloads site at this url:

http://sgd-archive.yeastgenome.org/curation/literature/phenotype_data.tab

the file is updated weekly on Friday nights.

[kevinschaper]

Hi @srengel, would you consider adding APO & CHEBI identifiers to that file? I think my pipeline is likely to be a bit error prone if I have to extract names to convert them to identifiers.