Allow querying by annotations that don't have a given phenotype condition

[kimrutherford]

See #56

Is it useful to be able to query for eg. NOT high temperature?

[ValWood]

This will be useful because, for example, if you want all standard growth conditions or standard temperature, we do not always explicitly capture this. The best way to get the most accurate results would be by an exclusion query.

[kimrutherford]

The server-side code is done to support this. We just need to decide what the interface should look like.

The best way to get the most accurate results would be by an exclusion query.

I don't understand this bit.

[ValWood]

Probably what you have done.

When querying on phenotypes users might want to exclude all "high temperature" and "low temperature" for example, than to select all "standard temperature" because we often would not add the conditions explicitly if they are standard.

[kimrutherford]

We just need to decide what the interface should look like.

Would this be OK with improved wording?:

[ValWood]

Well having the text box is there by default would make the feature clearer, and probe boy encourage it's use..... Anyone?

[kimrutherford]

As discussed, I've released the changes so far into the dev version of the site. The main site is unchanged. The change in dev adds a "Exclude condition" option for phenotypes.

We should think about how to extend this to multiple conditions so users can do things like exclude "high temperature" and "low temperature" simultaneously.

[ValWood]

I tested this and it seems to work as I expected.

An example that might be useful to explain that this query/filter is annotation-based and not gene-based

40 | abnormal mitotic spindle elongation (FYPO:0000131) [single allele genotypes]

38 | abnormal mitotic spindle elongation (FYPO:0000131) [single allele genotypes - excluded conditions: low temperature (PECO:0000006)]

this query will exclude dis3 and scn1 which have low temperature ONLY

but will include dis1 which has

FYPO:0002688 | mitotic spindle collapse without elongation during prophase | dis1Δ | Microscopy | low temperature | Hsu KS et al. (2011)

and

FYPO:0007071 | increased rate of mitotic spindle elongation during anaphase A | dis1Δ | Microscopy |   | Pinder C et al. (2019)

(no temperature recorded)

--

[ValWood]

To make this really clear maybe the text could say

Constrain annotations with condition: Exclude annotations with condition:

A bit longer but probably worth it?

[ValWood]

AND Where we say Include genes from:

should this say Include genes with annotations from:

?

[ValWood]

Looks pretty good to me. I had quite a good play around and the behavior is as I expected ... Will wait for second opinion from @mah11 , and on the text tweaks.

[mah11]

Constrain annotations with condition: Exclude annotations with condition:

A bit longer but probably worth it?

Yes, although perhaps now that we can specify conditions to include OR exclude we could avoid saying "constrain":

Include annotations with condition: Exclude annotations with condition:

Include genes from:

should this say Include genes with annotations from:

I don't think we'd gain nearly as much by changing this bit.

[ValWood]

Action: implement text changes and release Action: Allow multiple conditions to be included or excluded, as per https://github.com/pombase/website/issues/1462 Action: Update documentation