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Config file
The config file is in Git: https://github.com/pombase/pombase-config/blob/master/website/pombase_v2_config.json
The following setting are available:
To appear in the "Target of" part of the gene page the annotation must have a extension relation that matches a "rel_name" in this section. Some items have a "if_descendent_of" setting. If that is present then the term in the annotation must be a descendent of the configured term.
eg.
{
"rel_name": "has_input",
"if_descendent_of": "GO:0003824",
"display_name": "has substrate",
"reciprocal_display": "substrate of"
},
This will match any annotation where the term is a descendent of "GO:0003824" and has "has_direct_input" as a extension relation.
The string in the "reciprocal_display" field is used in the "Relationship" column of the target of gene page section.
The first matching configuration (via if_descendent_of) will be used.
Preconfigured links to the query builder and "Canned queries" in the query builder are configured here.
The format is:
"<QUERY_NAME>": {
"name": "<USER_FRIENDLY_NAME>",
"constraints": "<QUERY_CONSTRAINTS>"
}The <QUERY_NAME> can be any string as long it's unique.
The <USER_FRIENDLY_NAME> is a short title or description of the query that can be shown to users. For canned queries (see canned_query_ids below) this friendly name is shown in the "Canned queries" section of the query builder. For other predefined queries the name is currently not used.
The <QUERY_CONSTRAINTS> is the internal JSON representation of the query. This text is available via a hidden menu to the right of each query.
example:
"physical_interactors_of_wee1": {
"constraints":{
"interactors":{
"gene_uniquename": "SPCC18B5.03",
"interaction_type": "physical"
}
}
}Whitespace outside of the quotes isn't significant and the newlines are optional.
This can be used in a query in the documentation like this. The <QUERY_NAME> from predefined_queries is the predefinedQueryName in the query-link, e.g.
<app-query-link [goToResults]="true" [linkText]="'Physical interactors of wee1'"
[predefinedQueryName]="'physical_interactors_of_wee1'">
</app-query-link> See Links to the query builder for more on query links.
Extra links to show on reference page. The format is:
"PMID:...": [
{
"link": "SOME_URL",
"text": "LINK_LABEL"
},
...
],
...
A list of settings for the front page panels. The configuration for each panel is chosen randomly from this list on each visit to the front page.
The text to include in the title of the panel. Required.
Optional external link URL.
One of "explore", "community" or "spotlight". Required.
A list of images for the top of this panel. The image will be chosen at random from this list on each visit to the front page. Required.
Markdown content for this panel. Required.
A link for the bottom of the panel. Optional.
The text to use for the link, required when link is configured.
If true, this panel config is a candidate for the front page. If false the panel is only visible in the archive. Required.
See also "Adding a new external reference".
Sub-fields of external_gene_references:
The string to appear in the first column of the external references table
This reference will only appear on gene page with these types. Some be an array with the values "mRNA gene" and/or "pseudogene". It can also be "ALL" so it will appear on all pages including RNA gene pages.
The string to appear in column 2.
Column 4 contents.
The field of the gene to substitute into the configured URL.
Possibilities:
-
uniquename: the systematic ID -
name: the gene name uniprot_identifierorfeome_identifier
and the special case: NCBI_ALL_IDS which will create a string containing name, uniquename and synonyms suitable for a link to PubMed.
The URL of the external site. The <<IDENTIFIER>> in the string will be replaced with the value of the field set with the field_name setting.
Instead of providing a url you can provide a database abbreviation that matches an entry in GO.xrf_abbs
There is a configuration item here for each ontology annotation section on the gene pages.
Attributes:
This defaults to "gene" and is set to "genotype" for the phenotype annotation sections.
The title to use at the top of the section. eg. "Single allele phenotype"
The filters item is a list of the configuration for the filters that should shown for this section.
Attributes:
The name for the filter that is shown to the user.
A unique identifier for this filter. eg. "evidence"
Should be "true" for filters the should only be shown in the detail (non-summary) view
For term type filters this is used to group the annotation by ancestor term. Each category has:
- a
display_namelike "Normal process" - an ancestors list with the ancestor term ID and the relation to follow to get to the ancestor
There can be multiple ancestors per category. The category will contain all terms that have any of the configured ancestors.
Each has:
- a
display_namelike "Western blot" - an
evidence_codeslist
The evidence codes can be any case. They shouldn't have the word "evidence" at the end. eg. use "Western blot" not "Western blot evidence". That's because we have both versions in Chado (needs fixing) so the web code checks for annotations with and without the " evidence" at the end as the evidence code.
Config for abbreviations in the "modified residue" relation on modification extensions.
See: https://github.com/pombase/pombase-chado/issues/1141#issuecomment-1972530354
This map contains aliases for databases that aren't available in GO.xrf_abbs. These aliases are also used for fixing the database names for output in ProteinFeatures.tsv.
The keys should be lower case and the code will then check for any case. eg. for the configuration "amigo": "GO" the code will look for "amigo", "AMIGO" or "AmiGO" and map it to "GO".
This is a map from slim name to slim config. The keys are something like pombe_mondo_slim and the config details are:
Something like "Disease slim" to show as a user friendly name for the slim on the website.
The path to the documentation for this slim.
The path in the website for this overview path of this slim
Used when a bit more detail is needed.
Text to added at the top of the results page when a gene set is slimmed. Example: https://www.pombase.org/slim:bp_goslim_pombe/from/id/ae2c8f19-6d8c-43bb-a2ac-dc81665b7292
The name of the ontology that underlies this slim.
This is a list of the top level terms / slim categories. Each element is a term name (name) and a term ID (termid).
A map from term name to a tidier name for display purposes. Currently used for the misc. sequence feature table. See: https://github.com/pombase/website/issues/37#issuecomment-765301311
A list of term prefixes (like "CHEBI") for terms that should be external links rather than links to term details pages. The prefixes need to be added to the "ABBREVS" variable in update_generated_files.sh. The IDs in ABBREVS must be in the GO db-xref file - add a pull request for any missing databases.
Configuration for the sequence feature page. See: https://github.com/pombase/website/issues/37
The SO type names to show on the sequence feature page.
Configuration for the "Target of" section on the gene pages.
The text to use in the "Ontology" column of the "Target of" table.
These relation priorities determine the order of rows in the table. Rows with an extension relation with a higher priority will appear closer to the top. If a priority isn't configured it defaults to 0.
Configuration for files exported at the end of the nightly load. These files mostly end up in the "misc" directory.
We create a sitemap.txt for Google. Only pages for terms starting with these term prefixes are written to that file.
References with these IDs are written to sitemap.txt.
Config for writing Complex_annotation.tsv
Only annotation for terms that are descendants of this are written.
Terms that aren't written, even if they are descendants of parent_complex_termid.
Config for writing rnacentral.json
Only details for genes with these SO types (RNA terms) are written to rnacentral.json
The exporter has basic support for writing annotation files where the subset and columns to write can be configured. The output files are TSV format.
Constrains the term IDs of the annotation. Only annotation with one of these terms as the parent will be written.
Name of the file written to the misc directory. eg. "increased_sensitivity_to_chemical.tsv"
Write only the annotation from "single" or "multi" allele genotypes.
The column names and types to write to the TSV file, retrieved from the annotation data. name can be "gene_uniquename", "gene_name", "allele", "termid" or "term_name".
The display_name is the column heading written to the TSV file.
Configuration for the protein feature viewer (eg. https://www.pombase.org/gene_protein_features/SPBC28F2.12)
A list of extension relation types that should be shown when the user moves the mouse over a modification in the protein feature viewer.
The names of the tracks in the feature viewer.
Each of these groups will get a different colour in the feature viewer. The colours are currently hard coded here: https://github.com/pombase/pombase-python-web/blob/master/protein_feature_view/templates/protein_feature_view/index.html
PomBase is funded by the Wellcome Trust