A query BioGRID types

[ValWood]

BIOGRID are changing the way that genetic interactions are described

I'm trying to make a plan (no hurry to implement, might take 2 years, but there might be small changes we could make to curation procedures now, to makes the eventual transition easier).

I will address the existing "types" one by one on the curation tracker first and curators can make a plan.

So for now I have a question. Could you let me know how many annotations we have to each GI term (synthetic lethal etc) (Is there anywhere I can look this up? I think there might be but I can't remember where it is)

[ValWood]

first part of this, getting the numbers, I put at high priority so we can see what we have

[kimrutherford]

It's easy to query Chado to get all the legacy interactions, but harder to query the genotype-genotype interactions.

Are these the numbers you were after?:

Old style genetic interactions:

interaction_type	evidence	count
interacts_genetically	Dosage Growth Defect	98
interacts_genetically	Dosage Lethality	94
interacts_genetically	Dosage Rescue	1164
interacts_genetically	Negative Genetic	67112
interacts_genetically	Phenotypic Enhancement	1586
interacts_genetically	Phenotypic Suppression	1890
interacts_genetically	Positive Genetic	29482
interacts_genetically	Synthetic Growth Defect	5422
interacts_genetically	Synthetic Lethality	3241
interacts_genetically	Synthetic Rescue	1612

Physical interactions:

interaction_type	evidence	count
interacts_physically	Affinity Capture-Luminescence	3
interacts_physically	Affinity Capture-MS	8618
interacts_physically	Affinity Capture-RNA	456
interacts_physically	Affinity Capture-Western	2637
interacts_physically	Biochemical Activity	586
interacts_physically	Co-crystal Structure	190
interacts_physically	Co-fractionation	143
interacts_physically	Co-localization	35
interacts_physically	Co-purification	880
interacts_physically	FRET	9
interacts_physically	Far Western	35
interacts_physically	PCA	1401
interacts_physically	Protein-RNA	23
interacts_physically	Protein-peptide	84
interacts_physically	Proximity Label-MS	303
interacts_physically	Reconstituted Complex	1559
interacts_physically	Two-hybrid	3762

Note to self:

select p.value as evidence, rel_t.name as interaction_type, count(rel.feature_relationship_id)  from feature_relationship rel join feature_relationshipprop p on rel.feature_relationship_id = p.feature_relationship_id join cvterm pt on pt.cvterm_id = p.type_id join cvterm rel_t on rel.type_id = rel_t.cvterm_id where rel_t.name like '%interact%' and pt.name = 'evidence' group by p.value, rel_t.name order by rel_t.name, p.value;

[ValWood]

OK, thanks. I wondered if we used them all consistently thats all, it seems all are fairly well used. I'm going to close this ticket, until prompted by BIOGRID, because I can't remember what the pending changes were, maybe they never happened?