Making protein features more visible

[ValWood]

• 1. Change tab label in query builder to "protein features" (from protein motifs)

2. Add TM domains to the Examples help text (under search box)

• 3. Add a commonly user query for ALL protein features (motifs, signal sequences and TM domains)

[kimrutherford]

Add a commonly user query for ALL protein features (motifs, signal sequences and TM domains)

Do we want everything with a SO term?: https://www.pombase.org/term/SO:0000001

[kimrutherford]

Change tab label in query builder to "protein features" (from protein motifs)

Done

Add TM domains to the Examples help text (under search box)

Done. I added "TM domains, " but if you search for that string it doesn't found anything useful. Maybe we should change the text to "transmembrane helix"?

[kimrutherford]

can we make it like this?
https://www.pombase.org/term_genes/SO:0000839

Linking to that page from the commonly used queries will take a bit of work because it's not a standard results page.

But if we add the SO term ID to the query description, it will be clickable link to that page:

It that enough?

[kimrutherford]

Actually linking directly to
https://www.pombase.org/term/SO:0000839
would be even better (i.e shows the subsets)

Perhaps we could have that link in a different list? It feels wrong to have it in the list of commonly used queries since it's not a query - it's just a link to a term page.

[ValWood]

That's true. Let's chat about it on Tuesday.

[ValWood]

Thoughts

1. I'm not sure how useful this list is if it can't be used to access the subsets, so maybe we don't require this (because its such a heterogenous bin)"commonly query".

• 2. It seems slightly odd to have 2 separate ways to search fro TM domains (under TM domains or with the SO term), but maybe this is OK

resolve by removing "transmembrane domain" prompts from the SO search

• 3. should "signal sequence" in the prompts be "signal peptide" (name)

• 4. should we add "transit peptide" to the under the box prompt

• 5. Actually when I search on "transit peptide" or "transit_peptide" in "protein features" I don't locate
  SO:0000725 , and although SO:0000725 is recognised by the search it give no results?
  (resolved by providing exact term name for searching)

• 6. Examples: short motifs such as TM domains, NLS or KEN box, signal sequence, cleaved region, helix
  -> Examples: NLS or KEN box, signal sequence, cleaved region, transit peptide helix (I don't think helix is in here)

[ValWood]

OK (Re point 5 and 6) we used mitochondrial_targeting_signal (SO:0001808)
because we thought it would be a more meaningful label so the prompt would need to be
"mitochondrial targeting signal"

[kimrutherford]

We have "TM domains" and "helix" separately in the help text. Perhaps we can combine those to just "TM helix"?

[ValWood]

so
"transmembrane domain" (I don't think we need to distinguish the subtype at this juncture - but if we can import additional non redundant transmembrane domains from Uniprot we should (they should probably be completely non overlapping with the existing)

[kimrutherford]

I'll do that now.

After the change it's:

Examples: short motifs such as NLS or KEN box, signal peptide, mitochondrial targeting signal,
cleaved region

Are there any other important features we could mention? There's plenty of space if we need a longer list.

[kimrutherford]

That change is on pombase.org now. Can we close this?

[ValWood]

Yep, thanks!