Create intermediary search pages that use pre-canned queries

[goldturtle]

@vanaukenk commented on Mar 2, 2016

It would be useful to have some intermediary search pages that allow users to search the Textpresso corpus using pre-canned queries that correspond to specific biological questions.

For example,
What proteins have experimentally determined kinase activity?
With what proteins does my protein of interest interact?

These searches would allow users to interrogate the literature without necessarily having to know which categories to use, thus hopefully making searching easier.

An intermediary search page is planned for the Noctua-TPC communication; exact specs still need to be worked out.

Chris Grove please add to this ticket as needed.

[goldturtle]

vanaukenk commented on Mar 7, 2016

Some thoughts on what kinds of Texptresso searches I'd like to have available for curators from within annotons:

If a gene product is entered, curators would be able to search using the gene product name as a keyword and a combination of categories for identifying experimental evidence for:
MF - enzymatic activities
MF - macromolecular interactions
MF - union of one or more types (i.e., enzymatic activities AND macromolecular interactions)
CC - subcellular localization
Case sensitivity, or other differences between gene and gene product names, can be critical for getting decent precision so we may need to make it easy for curators to toggle between upper and lower cases wrt keyword, or devise some other rules for how to populate genes vs gene products as keywords (rules seem harder than toggles, though).

If gene product is not known, could perform search with entire category of gene and/or protein names for a given species using the same categories as above.
Best source of entity names and synonyms? UniProt?

Other types of MF categories, e.g. transporters, will be included in the future.

[goldturtle]

vanaukenk commented on Mar 7, 2016

See also:

geneontology/noctua#282

[goldturtle]

vanaukenk commented on Apr 5, 2016

From email yesterday:

Here are the categories that each specific search would use:

Cellular Component - match all
Localization assay terms
Localization cellular components
Localization verbs

Molecular Function - Physical Interactions - match all
MFINT assay terms
MFINT verbs

Molecular Function - Enzymatic Activity - match all
MFEA assay terms
MFEA verbs

Biological Process - match any
involvement (old Textpresso)
regulation (old Textpresso)