A question for the review I'm writing

[ValWood]

How many unique annotations does cdc2 have (and how many total)

also what is the number for our most annotated gene (is that sty1 I can't remember?)

[kimrutherford]

How many unique annotations does cdc2 have

Aren't all annotations unique?

[ValWood]

Sorry, detail! I mean unique at the term level (can have different source and evidence)

[kimrutherford]

also what is the number for our most annotated gene (is that sty1 I can't remember?)

Do you just want to count ontology annotations and ignore interactions and orthologs for finding the most annotated gene?

Sorry, detail! I mean unique at the term level (can have different source and evidence)

Should we include annotations from non-PomBase sources?

Do you want to include all of these CVs?:

• PSI-MOD
• PomBase gene characterisation status
• PomGeneExProt
• PomGeneExRNA
• biological_process
• cellular_component
• complementation
• molecular_function
• name_description
• pombase_family_or_domain
• species_dist

And count any phenotype terms where an allele of cdc2 is part of the genotype?

[ValWood]

yes for this question everything because it is to illustrate what needs to be summarized (I.e it's source independent)

[kimrutherford]

I mean unique at the term level (can have different source and evidence)

How should that work for interactions and orthologs?

[ValWood]

each interaction, and each ortholog annotation can be counted because it is potentially something that could be referred to in the summary depending how the summary is crafted

[kimrutherford]

cdc2 has 427 ontology annotations. 88 distinct terms.

genotypes with cdc2 have 972 annotations. 242 distinct terms.

cdc2 has 282 interactions and 5 ortholog annotations

So 1686 total annotations and 617 unique annotations if we ignore the details for ontology annotations.

[ValWood]

wow! I don't even think that's our highest

[kimrutherford]

Do you need any other numbers?

[ValWood]

Out of curiosity, do we know which gene has the most? If it takes more than 10 mins I don't need to know (just wondering if the number is much higher, but I don't think it is). This example will do just fine,

[kimrutherford]

Out of curiosity, do we know which gene has the most?

From quick look it's probably fft3 / SPAC25A8.01c because of a zillion genetic interactions.

[ValWood]

oh yeah, not so useful . I think cdc2 is close to the top. it's fine.

[ValWood]

So 1686 total annotations and 617 unique annotations if we ignore the details for ontology annotations.

What do you mean by "details" here? Doe this include extensions making different annotations?

[kimrutherford]

Sorry that was unclear. I meant ignore the details so they are unique at the term level.

[ValWood]

i.e publication and evidence?

[kimrutherford]

I followed what you said here:

Sorry, detail! I mean unique at the term level (can have different source and evidence)

So I counted the annotations that were unique at the term level, ignoring the other details. Should an annotation count as unique if the extension is different? Sorry, I didn't think about that.

When counting I also ignored conditions.

[ValWood]

It should count as unique if the extension is different.

probably for conditions not

[ValWood]

Hi @kimrutherford no hurry but could you provide this number classing different extensions and different annotations (essentially they are unique annotations because the extension extends the term

[kimrutherford]

Hi @kimrutherford no hurry but could you provide this number classing different extensions and different annotations (essentially they are unique annotations because the extension extends the term

That's in this comment: https://github.com/pombase/pombase-chado/issues/1207#issuecomment-2297703945

So 1686 total annotations and 617 unique annotations if we ignore the details for ontology annotations.

[ValWood]

Ah ok so "if we ignore the details for ontology annotations." means you observe extensions but ignore different source/evidence (if so this is perfect)

[kimrutherford]

"if we ignore the details for ontology annotations." means you observe extensions but ignore different source/evidence (if so this is perfect)

There are 617 unique annotations if we ignore the extensions. The are 1686 annotations if we include the extensions.