pomcur.yaml
# PomCur config file -*- conf -*-
name: PomCur
long_name: Pombe community curation application
app_version: v71
authentication:
default_realm: 'members'
realms:
members:
credential:
class: 'Password'
password_field: 'password'
password_type: 'clear'
store:
class: DBIx::Class
user_class: TrackModel::Person
db_initial_data:
track:
cv:
- name: organismprop_types
cvterms:
- name: taxonId
dbxref:
accession: taxonId
db:
name: PomCur Track
- name: cvterm_property_type
cvterms:
- name: comment
dbxref:
accession: comment
db:
name: PomCur Track
- name: synonym_type
cvterms:
- name: broad
dbxref:
accession: broad
db:
name: PomCur Track
- name: narrow
dbxref:
accession: narrow
db:
name: PomCur Track
- name: exact
dbxref:
accession: exact
db:
name: PomCur Track
- name: related
dbxref:
accession: related
db:
name: PomCur Track
class_info:
cv:
class_display_name: controlled vocabulary
editable: 1
display_field: name
field_info_list:
- name: name
editable: 1
- name: definition
editable: 1
cvterm:
class_display_name: controlled vocabulary term
editable: 1
display_field: name
field_info_list:
- name: name
editable: 1
- name: definition
editable: 1
- name: cv_id
editable: 1
organism:
editable: 1
display_field: full_name
order_by:
- genus
- species
field_info_list:
- name: genus
editable: 1
- name: species
editable: 1
- name: ecotypes
editable: 1
person:
object_title_format: 'Details for @@DISPLAY_FIELD@@'
editable: 1
display_field: name
order_by: name
field_info_list:
- name: name
source: name
editable: 1
- name: Email address
source: networkaddress
editable: 1
- name: role
default_value: "'user'"
editable: 1
admin_only: 1
- name: password
editable: 1
admin_only: 1
- name: lab
editable: 1
lab:
editable: 1
display_field: name
order_by: name
field_info_list:
- name: name
editable: 1
- name: lab_head
editable: 1
- name: people
is_collection: 1
editable: 1
pub:
object_title_format: 'Details for PubMed ID: @@$object->pubmedid()@@'
class_display_name: publication
display_field: title
editable: 1
field_info_list:
- name: 'PubMed ID'
source: pubmedid
editable: 1
- name: title
editable: 1
- name: authors
editable: 1
- name: community_curator
editable: 1
- name: type
source: type_id
values_constraint: 'cv->name = "PomBase publication type"'
referenced_class: Cvterm
editable: 1
curs:
class_display_name: curation session
display_field: curs_key
editable: 1
field_info_list:
- name: community_curator
editable: 1
- name: publication
editable: 0
source: pub
- name: curs_key
editable: 0
# if the hook dies the creation fails
pre_create_hook: 'PomCur::Track::create_curs_db_hook'
gene:
editable: 1
display_field: primary_identifier
field_info_list:
- name: primary_identifier
editable: 1
- name: primary_name
editable: 1
- name: product
editable: 1
- name: genesynonyms
editable: 1
is_collection: 1
genesynonym:
editable: 1
display_field: identifier
field_info_list:
- name: identifier
editable: 1
- name: gene
editable: 1
export:
gene_association_fields:
db: "GeneDB_Spombe"
assigned_by: "GeneDB_Spombe"
db_object_type: gene
track_db_template_file: db_templates/track_db_template.sqlite3
curs_db_template_file: db_templates/curs_db_template.sqlite3
ontology_index_file: ontology_index
external_sources:
pubmed_query_url: 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&retmode=xml&id='
implementation_classes:
gene_lookup: PomCur::Track::GeneLookup
go_annotation_lookup: PomCur::Track::GOAnnotationLookup
go_lookup: PomCur::Track::OntologyLookup
evidence_types:
IMP:
name: Inferred from mutant phenotype
IDA:
name: Inferred from direct assay
IGI:
name: Inferred from genetic interaction
with_gene: 1
IPI:
name: Inferred from physical interaction
with_gene: 1
# each class needs to set up the stash for forwarding to a template
# page based on the module name, eg. go_function.html
annotation_type_list:
- name: molecular_function
abbreviation: F
display_name: 'GO molecular function'
class: 'PomCur::CurModules::GOModule'
constructor_args:
ontologies:
- function
evidence_codes:
- IMP
- IDA
- IGI
- IPI
- name: biological_process
abbreviation: P
display_name: 'GO biological process'
class: 'PomCur::CurModules::GOModule'
constructor_args:
ontologies:
- process
evidence_codes:
- IMP
- IDA
- IGI
- IPI
- name: cellular_component
abbreviation: C
display_name: 'GO cellular component or complex'
class: 'PomCur::CurModules::GOModule'
constructor_args:
ontologies:
- component
evidence_codes:
- IMP
- IDA
- IGI
- IPI
- name: phenotype
display_name: Phenotypes
class: 'PomCur::CurModules::PhenotypeModule'
disabled: 1
- name: post_translational_modifications
display_name: "Post translational modifications"
disabled: 1
- name: genetic_interactions
display_name: "Genetic Interactions"
disabled: 1
- name: physical_interactions
display_name: "Physical Interactions"
disabled: 1
messages:
gene_upload:
examples:
gene_identifier: 'SPCC1739.10'
gene_name: 'cdc11'
test_config_file: 't/test_config.yaml'
help_text:
inline:
molecular_function_hint: |
A molecular function is a molecular level activity usually, but not always
performed by a single gene product (catalytic activity, binding,
transporter)
biological_process_hint: |
A biological process is a series of events accomplished by one or more
ordered assemblies of molecular functions (cell cycle, transcription)
cellular_component_hint: |
A cellular component is a part of a cell (proteasome, nucleus)