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gene2go associations will only be populated for active taxa (new in 1.5.8).
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## Gene Tiers
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Users' genes are categorized in tiers based on their familiarity and experience with the gene. This is explained in
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Every time new model systems are added to the application, they will have to be activated in this manner.
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## GO term recommendation
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Users can receive recommended terms based on the TIER1 and TIER2 genes they have added to their profiles.
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The recommendation algorithm works as follows:
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1. Retrieve GO terms associated to all TIER1 and TIER2 genes
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2. Retrieve all the descendants of these terms
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3. For each term, compute how many TIER1 or TIER2 genes they are associated either directly or indirectly via their
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descendants
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4. Keep terms that are not already on the user profile and that mention at least 2 TIER1 or TIER2 genes
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5. Exclude terms with more than 50 associated genes
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6. Retain terms that have at least one novel gene that is not on the user's profile
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7. Retain most specific terms if a given term and its descendant is recommended
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You can adjust the number of overlapping TIER1 or TIER2 genes and the maximum size of a GO term by setting the
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following:
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```ini
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rdp.settings.go-term-min-overlap=2 # new in 1.5.8
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rdp.settings.go-term-size-limit=50
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```
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### Customizing taxon appearance (new in 1.5.5)
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By default, taxon are rendered using the common name in title case. The only exception is for *Homo sapiens* which
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- "Deactivate" (or "Deactivate All Terms" in the case of an ontology category): this will remove the category from the Profile and Search pages. This action is reversible, as the category can be easily re-activated. This action is recommended in cases where a category cannot be deleted because it has already been used by some users.
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- "Deactivate" (or "Deactivate All Terms" in the case of an ontology category): this will remove the category from the
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Profile and Search pages. This action is reversible, as the category can be easily re-activated. This action is
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recommended in cases where a category cannot be deleted because it has already been used by some users.
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- Update from "source": Update the ontology category using the original URL (if available)
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- Download as OBO: Download the category as an OBO file
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The number of used terms indicate how many terms in the ontology have been associated with associated with users.
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In the Edit window on the Manage Profile Category page, you can add a definition/description of the category, which
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is used in a tooltip on the Profile Page. You can also specify if this category will be used as a filter on the Gene
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Search page. While all active categories will be available on the Researcher Search page, only categories that have "Available for gene search?" checked will be displayed on the Gene Search page.
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Search page. While all active categories will be available on the Researcher Search page, only categories that have "
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Available for gene search?" checked will be displayed on the Gene Search page.
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@@ -346,8 +419,6 @@ values. A warning will be displayed in the admin section if this is the case.
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Read more about configuring messages in [Customizing the application messages](#customizing-the-applications-messages)
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section of this page.
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### Resolving external URLs
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By default, ontologies and terms are resolved from [OLS](https://www.ebi.ac.uk/ols/index). Reactome pathways get a
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#this setting relates only to gene info files. Files for all taxons will be stord under gene/
The provided default file can be found in [faq.properties](https://github.com/PavlidisLab/rdp/tree/{{ config.extra.git_ref }}/src/main/resources/faq.properties).
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The provided default file can be found in [faq.properties](https://github.com/PavlidisLab/rdp/tree/{{
log.warn( "The refresh delay for reading " + allowedEmailDomainsFile + " is set to zero: the file will be re-read for every email domain validation." );
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