Canto v1253
Community curation
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Configuration settings

canto.yaml

The default configuration is stored in canto.yaml in the top level directory. Any installation specific settings can be added to canto_deploy.yaml, and will override the defaults. The canto_deploy.yaml will be created automatically by the canto_start start script when it is run with the --initialise option.

The configuration files are YAML format.

name

A one word name for the site. default: Canto

long_name

A longer description of the site. e.g. The SlugBase community annotation tool

database_name

The destination database name. This is used whenever we need to refer to the destination of the annotations while curating.

database_url

The URL of the database that this instance is installed for. e.g. http://www.pombase.org/

header_image

A path (relative to root/static) of the logo to put in the header.

instance_organism

Canto has two modes: single or multi organism. Single organism mode is activated by setting an "instance organism". That organism will be assumed throughout the interface. Only genes from that single organism can be annotated and the user will not be shown the organism name.

In multi organism mode, genes from any number of organisms can be annotated in each session. In this mode after uploading a list of gene identifiers, the user will be shown the organism name as well as the names, synonyms and products. The organism is shown so the user can confirm that the identifier they gave matched the gene from the right organism. Generally an external gene adaptor should be configured using the instance_organism setting in the multi-organism case.

Example:

instance_organism:
  taxonid: 4896

canto_url

The link for the main Canto web site.

app_version

The software version, automatically updated each release.

schema_version

The version of the schema. This is incremented when the schema changes in an incompatible way.

authentication

Configuration for the Catalyst authentication code. This shouldn't need changing.

view_options

Configuration for the admin view pages.

max_inline_results_length

The maximum number of lines of results to show in a table on an object page.

db_initial_data

Data needed to initialise a Canto instance.

class_info

Descriptions of table in the database used by the interface. This information is used for rendering the view and object pages.

reports

A list of report names to show on the front page.

export

Configuration for exporting.

load

Configuration for loading data.

track_db_template_file

The template database to use when creating a new Canto instance.

curs_db_template_file

The template database to use when creating a new curation session.

ontology_index_dir

The name of the directory used for the ontology Lucene index. This index is used to do autocompeletion in the interface.

external_sources

URLs of external services.

implementation_classes

Names of classes used to implement database query and storage. This allows the implementations to be swapped from the defaults.

gene_adaptor

Used to look up gene identifier, name, synonyms and products. The default is to use the internal Canto database ("track").

evidence_types

Short name (codes) and long names of evidence types. Any evidence type configured with the option "with_gene" set to true will cause the interface to ask for a gene for later storage in the "with/from" column of a GAF file.

Evidence codes must also be configured for in available_annotation_type_list. See evidence_codes in the Configuring annotation types section.

Example:

evidence_types:
  IMP:
    name: Inferred from Mutant Phenotype
  IDA:
    name: Inferred from Direct Assay
  IGI:
    name: Inferred from Genetic Interaction
    with_gene: 1
  Microscopy: ~

In this case "Microscopy" is treated as an evidence code and an evience description.

available_annotation_type_list

List of possible annotation type and their configuration details.

See Configuring annotation types for details.

enabled_annotation_type_list

The names of the types that are enabled in this Canto instance. If not set all annotation types from available_annotation_type_list will be enabled.

name

The identifier for this annotation type, used internally and in URLs.

category

One of: "ontology" or "interaction", used to select which Perl package should be used for rendering and storing these annotation type.

messages

test_config_file

The path to the extra configuration file needed while testing.

help_text

The keys under help_text identify a page in Canto and under the key is one or both of inline or url. The help text and link is rendered by the inline_help.mhtml template. If a url is given, the text under inline will be title attribute of a link with that URL. Without a url a help link (a "?" icon) will be shown and the inline text will be displayed in a pop-up DIV.

contact_email

This email address is shown anytime a contact address is needed. See the contact.mhtml template.

Each external link configuration has three possible parameters:

There are two possible types of external link on the gene pages:

The external links are implemented in the linkouts.html template.

Configuring annotation types

The possible annotation type are set with the available_annotation_type_list configuration. It should be set to a YAML list of maps. An example is provided in the canto.yaml but can be overridden in the instance specific canto_deploy.yaml.

In canto_deploy.yaml you can add an optional enabled_annotation_type_list. If set only the listed types will be enabled.

For example this would enable just two annotation types:

enabled_annotation_type_list:
  - molecular_function
  - cellular_component

enabled_annotation_type_list exists so that one available_annotation_type_list configuration in canto.yaml can be used in several Canto instances. It is optional. If not set, all available types are enabled.

Each annotation type in available_annotation_type_list has the following settings:

name

A short internal name or key for this type. (Required)

category

This setting selects which code to use for the interface for this type. There are currently two possibilities: ontology and interaction. (Required)

display_name

The long name to display in the user for this type. eg. for molecular_function PomBase displays GO molecular function. (Required)

short_display_name

A shorter name for this type. eg molecular function (Optional)

very_short_display_name

A very short name for this type. eg F for GO molecular function. (Optional)

abbreviation

Currently used only for types from GO (molecular_function, cellular_component, and biological_process), the abbreviation is used from exporting annotation to GAF files. Required only if GO ontologies are enabled.

evidence_codes

Possible evidence codes for this annotation type. Each evidence code must appear in the evidence_types list. (Required)

broad_term_suggestions

A few comma separated high level or broad term names for use in help text. eg. for molecular function: "transporter, transferase activity" (Required only for ontology annotation types)

specific_term_examples:

Comma separated specific term name examples. eg. "adenylate cyclase activity or biotin transporter activity" (Required only for ontology annotation types)

help_text

Short help to be soon initially to users when they begin an annotation of this type. (Required)

more_help_text

A longer help text shown when the user clicks "more ..." under the help_text. (Optional)

detailed_help_path

A path in the documentation directory (root/docs/) to link to for detailed help about this type of annotation.

annotation_comment_help_text

Help text to show once the user finishes annotating a paper, after "Submit to curators". (Optional)

host_organism_taxonids

A list of taxon IDs for the organisms that are treated as host species in pathogen-host mode. All the list taxon IDs need to match organisms in the organism table. The organisms are loaded using using canto_add.pl --organism. See the Canto setup documentation for details.

If this list has any elements, Canto will start in pathogen-host mode and the internal config setting pathogen_host_mode will be automatically set to 1. Also host_organisms will be set to a list the Organism objects. multi_organism_mode is also set to 1/true.

Note that when pathogen_host_mode is enabled, every organism that is in the organism table but not in host_organism_taxonids will be assumed to be a pathogen organism.