qualifier= field

[pombase-admin]

These are the remaining qualifiers:

c | value | name
-----+--------------------------+------------------------------------

Need to decide what to do with these:

219 | required | biological_process 79 | same_pathway | biological_process 53 | region | sequence 47 | different_pathway | biological_process
~33 | cancer_census | disease_associated~ 21 | predominantly | cellular_component 18 | acts_downstream_of | biological_process 18 | redundant_with | biological_process 17 | acts_upstream_of | biological_process ~13 | activates | biological_process~ 11 | constitutive | cellular_component 7 | partially_redundant | biological_process ~4 | antagonistic_interaction | biological_process~ 4 | major | molecular_function 4 | minor | molecular_function 3 | partially_redundant | molecular_function
~2 | constitutive | molecular_function~ ~2 | weak | fission_yeast_phenotype~ ~1 | inhibits | PSI-MOD~

We should keep these

49 | heterologous_system | cellular_component 69 | heterologous_system | molecular_function 100 | heterologous_system | biological_process

We need these until there is a way to split these genes into their constiuent peptides:

8 | N_term | molecular_function 7 | N_term | cellular_component 18 | C_term | molecular_function 6 | C_term | biological_process 6 | N_term | biological_process 4 | C_term | cellular_component

Allowed for GO 263 | contributes_to | molecular_function 40 | colocalizes_with | cellular_component

Documented for gene expression: 2 | present | gene_ex 4 | decreased | gene_ex 24 | increased | gene_ex

Documented for complementation 9 | full | complementation 9 | partial | complementation

These are attached to the extension rather than the term?? There is a SF chado load tracker item about this, follow up with Kim 9 | decreased | PomBase annotation extension terms 11 | contributes_to | PomBase annotation extension terms 7 | required | PomBase annotation extension terms 6 | inhibits | PomBase annotation extension terms 68 | increased | PomBase annotation extension terms 25 | present | PomBase annotation extension terms 10 | absent | PomBase annotation extension terms 10 | unchanged | PomBase annotation extension terms 2 | constitutive | PomBase annotation extension terms 2 | same_pathway | PomBase annotation extension terms 3 | activates | PomBase annotation extension terms

Original comment by: ValWood

[pombase-admin]

these are now sorted (updated) 8 | N_term | molecular_function 7 | N_term | cellular_component 18 | C_term | molecular_function 6 | C_term | biological_process 6 | N_term | biological_process 4 | C_term | cellular_component

Original comment by: ValWood

[ValWood]

@kimrutherford do we have a list of qualifers used currently somewhere?

[kimrutherford]

Is this what you need?: https://curation.pombase.org/dumps/builds/pombase-build-2019-11-24/logs/log.2019-11-24-21-56-54.qualifier_counts_by_cv

[ValWood]

Yes thanks. We have dealt with some already.

For GO we will keep 74 | heterologous_system | biological_process 60 | heterologous_system | molecular_function 42 | heterologous_system | cellular_component (don't do any harm, used with IGI and other organism)

9 | C_term | molecular_function 7 | C_term | biological_process 7 | N_term | molecular_function 4 | N_term | cellular_component 4 | N_term | biological_process 3 | C_term | cellular_component (until we have IDs for parts)

These might be useful for epistasis 50 | same_pathway | biological_process 7 | different_pathway | biological_process 10 | redundant_with | biological_process 3 | partially_redundant | biological_process 6 | acts_downstream_of | biological_process 6 | acts_upstream_of | biological_process

Some of these can probably go but they aren't doing any harm 65 | required | biological_process 11 | predominantly | cellular_component 4 | major | molecular_function 3 | minor | molecular_function ~1 | activates | biological_process~

[ValWood]

These aren't doing any harm. I made notes in "future doc" where things might be useful later.