Revision 1e99598442d3e078fc605a9788aece9efa498cba authored by Kim Rutherford on 27 June 2012, 01:10:13 UTC, committed by Kim Rutherford on 27 June 2012, 01:10:13 UTC
1 parent 184291e
pomcur.yaml
# PomCur config file -*- conf -*-
name: PomCur
long_name: Pombe community curation application
database_name: PomBase
header_image: logos/curation_tool.png
app_version: v390
schema_version: 0
# the path that the home link goes to
home_path: '/track/index_page'
# if zero, the user will need to log in before the links on the front page are
# visible
public_mode: 0
extra_css: ~
authentication:
default_realm: 'members'
realms:
members:
credential:
class: 'Password'
password_field: 'password'
password_type: 'clear'
store:
class: DBIx::Class
user_class: TrackModel::Person
view_options:
max_inline_results_length: 1000
# see PomCur::Meta::Util::initialise_core_data()
db_initial_data:
track:
cv:
- name: organismprop_types
cvterms:
- name: taxonId
dbxref:
accession: taxonId
db:
name: PomCur
- name: cvterm_property_type
cvterms:
- name: comment
dbxref:
accession: comment
db:
name: PomCur
- name: PomCur numeric priority
dbxref:
accession: numeric_priority
db:
name: PomCur
- name: synonym_type
cvterms:
- name: broad
dbxref:
accession: broad
db:
name: PomCur
- name: narrow
dbxref:
accession: narrow
db:
name: PomCur
- name: exact
dbxref:
accession: exact
db:
name: PomCur
- name: related
dbxref:
accession: related
db:
name: PomCur
- name: PomCur publication type
cvterms:
- name: unknown
dbxref:
accession: unknown
db:
name: PomCur
- name: PomCur cursprop types
cvterms:
- name: annotation_status
# The session status (eg. 'SESSION_CREATED', 'CURATION_IN_PROGRESS')
dbxref:
accession: annotation_status
db:
name: PomCur
- name: session_genes_count
# The number of genes the user has added to the session
dbxref:
accession: session_genes_count
db:
name: PomCur
- name: session_term_suggestions_count
# The number term suggestions made by the user in a session
dbxref:
accession: session_term_suggestions_count
db:
name: PomCur
- name: approver_name
# The name of the person approving the session (if it is in the
# APPROVAL_IN_PROGRESS state)
dbxref:
accession: approver_name
db:
name: PomCur
- name: PomCur publication triage status
cvterms:
- name: New
definition: Triage status for new papers.
dbxref:
accession: new
db:
name: PomCur
- name: Curatable
definition: Triage status for papers that can be curated.
dbxref:
accession: curatable
db:
name: PomCur
- name: Sequence feature or region
definition: >
Triage status for a paper that reports a sequence feature
with no other curatable information.
dbxref:
accession: sequence_feature_or_region
db:
name: PomCur
- name: Not English
definition: >
Triage status for a paper that will not be curated because
the text is not in English.
dbxref:
accession: not_english
db:
name: PomCur
- name: Method or reagent
definition: >
Triage status for a paper that will not be curated because it
is a methods paper.
dbxref:
accession: methods_paper
db:
name: PomCur
- name: Wrong organism
definition: >
Triage status for a paper that will not be curated because the
organism is not appropriate for this database.
dbxref:
accession: wrong_organism
db:
name: PomCur
- name: Review or comment
definition: >
Triage status for a review or comment.
dbxref:
accession: review
db:
name: PomCur
- name: Loaded in error
definition: >
Triage status for a publication that will not be curated for
a reason the is not covered by the other statuses.
dbxref:
accession: loaded_in_error
db:
name: PomCur
- name: Erratum
definition: >
Triage status for an erratum.
dbxref:
accession: erratum
db:
name: PomCur
- name: Mutagenicity or toxicity study
dbxref:
accession: mutagenicity_or_toxicity_study
db:
name: PomCur
- name: Not physically mapped
dbxref:
accession: not_physically_mapped
db:
name: PomCur
- name: Cell composition or WT feature
dbxref:
accession: cell_composition_or_wt_feature
db:
name: PomCur
- name: Phylogeny
dbxref:
accession: phylogeny_paper
db:
name: PomCur
- name: Other
definition: >
Triage status for a publication that will not be curated for
a reason the is not covered by the other statuses.
dbxref:
accession: other
db:
name: PomCur
- name: PomCur curation priorities
definition: Priorities assigned to papers
cvterms:
- name: low
dbxref:
accession: low_priority
db:
name: PomCur
cvtermprop_cvterms:
- type:
name: PomCur numeric priority
value: 100
- name: high
dbxref:
accession: high_priority
db:
name: PomCur
cvtermprop_cvterms:
- type:
name: PomCur numeric priority
value: 1000
- name: PomCur user types
cvterms:
- name: user
dbxref:
accession: user
db:
name: PomCur
- name: admin
dbxref:
accession: admin
db:
name: PomCur
- name: PomCur publication curation status
cvterms:
- name: not started
dbxref:
accession: admin
db:
name: PomCur
- name: complete
dbxref:
accession: admin
db:
name: PomCur
- name: PomCur publication experiment types
cvterms:
- name: Genome wide
dbxref:
accession: genome_wide
db:
name: PomCur
- name: High throughput
dbxref:
accession: high_throughput
db:
name: PomCur
- name: Computational analysis
dbxref:
accession: computational_analysis
db:
name: PomCur
# possibilities for the type_id of pubprops
- name: PomCur publication property types
cvterms:
- name: experiment_type
dbxref:
accession: experiment_type
db:
name: PomCur
- name: community_curatable
dbxref:
accession: community_curatable
db:
name: PomCur
- name: triage_comment
dbxref:
accession: triage_comment
db:
name: PomCur
- name: PomCur publication load types
definition: >
Publications can be added to database by the administrator or by user
actions such as going to /tools/pubmed_id_start. Types in this CV
record that information. A publication loaded by user actions can be
removed if no curation session refers to it.
cvterms:
- name: user_load
definition: Type used for a publication loaded by a user action.
dbxref:
accession: user_load
db:
name: PomCur
- name: admin_load
definition: Type used for a publication loaded by the administrator.
dbxref:
accession: user_load
db:
name: PomCur
- name: PomCur metadata types
definition: Types for the metadata table.
cvterms:
- name: schema_version
definition: >
Version number of the track schema, incremented when the schema
changes.
dbxref:
accession: schema_version
db:
name: PomCur
- name: PubMed publication types
definition: >
Publication types loaded from the PublicationType elements
of the PubMed XML.
cvterms:
- name: paper
dbxref:
accession: pubmed_paper
db:
name: PomCur
- name: review
dbxref:
accession: pubmed_review
db:
name: PomCur
class_info:
track:
cv:
class_display_name: controlled vocabulary
editable: 1
display_field: name
field_info_list:
- name: name
editable: 1
- name: definition
editable: 1
- name: "term count"
source:
sql: 'select count(*) from cvterm where cvterm.cv_id = me.cv_id'
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
db:
editable: 1
display_field: name
field_info_list:
- name: name
editable: 1
- name: description
editable: 1
- name: url
editable: 1
- name: "accessions stored"
source:
sql: 'select count(*) from dbxref where dbxref.db_id = me.db_id'
dbxref:
editable: 1
display_field: accession
field_info_list:
- name: db_id
editable: 1
- name: accession
editable: 1
- name: description
editable: 1
- name: cvterm_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
organism_report:
extends: organism
'+field_info_list':
- name: Number of genes
source:
sql: 'select count(*) from gene where gene.organism = me.organism_id'
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: email_address
editable: 1
- name: role
default_value: "'user'"
values_constraint: 'where me.cv_id = (SELECT cv_id FROM cv where cv.name = "PomCur user types")'
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 publication: @@$object->uniquename()@@'
class_display_name: publication
display_field: 'Publication ID'
editable: 1
# hack to order by pubmed id, or by doi number
order_by: "cast((case me.uniquename like 'PMID:%' WHEN 1 THEN substr(me.uniquename, 6) ELSE me.uniquename END) as integer)"
field_info_list:
- name: 'Publication ID'
source: uniquename
- name: title
- name: authors
- name: abstract
extra_field_class: non-important-attribute-field
hide_context:
- list
- inline_list
- name: citation
hide_context:
- list
- inline_list
- name: publication_date
hide_context:
- list
- inline_list
- name: affiliation
hide_context:
- list
- inline_list
- name: assigned_curator
editable: 1
# - name: type
# source: type_id
# values_constraint: 'where me.cv_id = (SELECT cv_id FROM cv where cv.name = "PomCur publication type")'
# referenced_class: Cvterm
# editable: 1
- name: session_status
source:
sql: "select value from curs, cursprop p, cvterm t where me.pub_id = curs.pub and curs.curs_id = p.curs and t.cvterm_id = p.type and t.name = 'annotation_status'"
editable: 0
- name: approver_name
source:
sql: "select value from curs, cursprop p, cvterm t where me.pub_id = curs.pub and curs.curs_id = p.curs and t.cvterm_id = p.type and t.name = 'approver_name'"
editable: 0
- name: community_curatable
source:
sql: "select value from pubprop p, cvterm t where me.pub_id = p.pub_id and t.cvterm_id = p.type_id and t.name = 'community_curatable'"
editable: 0
- name: load_type
source: load_type_id
values_constraint: 'where me.cv_id = (SELECT cv_id FROM cv where cv.name = "PomCur publication load types")'
referenced_class: Cvterm
editable: 1
hide_context:
- list
- inline_list
- name: triage_status
source: triage_status_id
values_constraint: 'where me.cv_id = (SELECT cv_id FROM cv where cv.name = "PomCur publication triage status")'
referenced_class: Cvterm
editable: 1
hide_context:
- inline_list
- name: curation_priority
source: curation_priority_id
values_constraint: 'where me.cv_id = (SELECT cv_id FROM cv where cv.name = "PomCur curation priorities")'
referenced_class: Cvterm
editable: 1
pub_curation_status:
class_display_name: publication curation status
display_field: status_id
editable: 1
field_info_list:
- name: publication
source: pub_id
editable: 1
- name: annotation_type
editable: 1
- name: status
source: status_id
values_constraint: 'where me.cv_id = (SELECT cv_id FROM cv where cv.name = "PomCur publication curation status")'
referenced_class: Cvterm
editable: 1
pubprop:
class_display_name: publication properties
display_field: value
editable: 1
field_info_list:
- name: publication
source: pub_id
editable: 1
- name: type_id
values_constraint: 'where me.cv_id = (SELECT cv_id FROM cv where cv.name = "PomCur publication experiment types")'
referenced_class: Cvterm
editable: 1
- name: value
editable: 1
curs:
class_display_name: curation session
display_field: curs_key
editable: 1
field_info_list:
- name: curs_key
editable: 0
- name: publication
editable: 0
source: pub
- name: assigned_curator
editable: 1
- name: status
source:
sql: "select value from cursprop p, cvterm t where me.curs_id = p.curs and t.cvterm_id = p.type and t.name = 'annotation_status'"
- name: approver_name
source:
sql: "select value from cursprop p, cvterm t where me.curs_id = p.curs and t.cvterm_id = p.type and t.name = 'approver_name'"
- name: genes_added
source:
sql: "cast((select value from cursprop p, cvterm t where me.curs_id = p.curs and t.cvterm_id = p.type and t.name = 'session_genes_count') as int)"
- name: term_suggestions
source:
sql: "cast((select value from cursprop p, cvterm t where me.curs_id = p.curs and t.cvterm_id = p.type and t.name = 'session_term_suggestions_count') as int)"
# if the hook dies the creation fails
pre_create_hook: 'PomCur::Track::create_curs_db_hook'
gene:
editable: 1
display_field: primary_identifier
search_fields:
- primary_identifier
- primary_name
- product
field_info_list:
- name: primary_identifier
editable: 1
- name: primary_name
editable: 1
- name: product
editable: 1
- name: genesynonyms
editable: 1
is_collection: 1
- name: organism
editable: 1
genesynonym:
editable: 1
display_field: identifier
field_info_list:
- name: identifier
editable: 1
- name: gene
editable: 1
all_publications:
extends: pub
untriged_publications:
class_display_name: un-triaged publications
extends: pub
constraint: "triage_status_id = (select cvterm_id from cvterm where name = 'New')"
triaged_publications:
extends: pub
constraint: "triage_status_id not in (select cvterm_id from cvterm where name = 'New')"
named_genes:
extends: gene
constraint: "primary_name is not null"
curatable_publications:
extends: pub
constraint: "triage_status_id in (select cvterm_id from cvterm where name = 'Curatable')"
uncuratable_publications:
extends: pub
constraint: "triage_status_id not in (select cvterm_id from cvterm where name ='Curatable' or name = 'New')"
high_priority_publications:
extends: pub
constraint: "curation_priority_id in (select cvterm_id from cvterm where name = 'high')"
community_curatable_publications:
extends: pub
constraint: "pub_id in (select pub_id from pubprop where type_id = (select cvterm_id from cvterm where name = 'community_curatable') and value = 'yes')"
triage_sequence_feature_or_region_publications:
class_display_name: Sequence feature or region
extends: pub
constraint: "triage_status_id in (select cvterm_id from cvterm where name = 'Sequence feature or region')"
triage_not_english_publications:
class_display_name: Not English
extends: pub
constraint: "triage_status_id in (select cvterm_id from cvterm where name = 'Not English')"
triage_wrong_organism_publications:
class_display_name: Wrong organism
extends: pub
constraint: "triage_status_id in (select cvterm_id from cvterm where name = 'Wrong organism')"
triage_method_or_reagent_publications:
class_display_name: Method or reagent
extends: pub
constraint: "triage_status_id in (select cvterm_id from cvterm where name = 'Method or reagent')"
triage_other_publications:
class_display_name: Other
extends: pub
constraint: "triage_status_id in (select cvterm_id from cvterm where name = 'Other')"
triage_review_or_comment_publications:
class_display_name: Review or comment
extends: pub
constraint: "triage_status_id in (select cvterm_id from cvterm where name = 'Review or comment')"
triage_erratum_publications:
class_display_name: Erratum
extends: pub
constraint: "triage_status_id in (select cvterm_id from cvterm where name = 'Erratum')"
triage_mutagenicity_or_toxicity_study_publications:
class_display_name: Mutagenicity or toxicity study
extends: pub
constraint: "triage_status_id in (select cvterm_id from cvterm where name = 'Mutagenicity or toxicity study')"
triage_not_physically_mapped_publications:
class_display_name: Not physically mapped
extends: pub
constraint: "triage_status_id in (select cvterm_id from cvterm where name = 'Not physically mapped')"
triage_cell_composition_or_wt_feature_publications:
class_display_name: Cell composition or WT feature
extends: pub
constraint: "triage_status_id in (select cvterm_id from cvterm where name = 'Cell composition or WT feature')"
triage_phylogeny_paper_publications:
class_display_name: Phylogeny
extends: pub
constraint: "triage_status_id in (select cvterm_id from cvterm where name = 'Phylogeny')"
triage_loaded_in_error_publications:
class_display_name: Loaded in error
extends: pub
constraint: "triage_status_id in (select cvterm_id from cvterm where name = 'Loaded in error')"
curatable_publications_with_sessions:
extends: pub
constraint: "pub_id in (select pub from curs) and triage_status_id in (select cvterm_id from cvterm where name = 'Curatable')"
curatable_publications_without_sessions:
extends: pub
constraint: "pub_id not in (select pub from curs) and triage_status_id in (select cvterm_id from cvterm where name = 'Curatable')"
publications_with_new_sessions:
extends: pub
constraint: "pub_id in (select pub from curs where curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and p.value = 'SESSION_CREATED')) and triage_status_id in (select cvterm_id from cvterm where name = 'Curatable')"
publications_with_active_sessions:
extends: pub
constraint: "pub_id in (select pub from curs where curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and (p.value = 'SESSION_ACCEPTED' or p.value = 'CURATION_IN_PROGRESS' or p.value = 'CURATION_PAUSED'))) and triage_status_id in (select cvterm_id from cvterm where name = 'Curatable')"
publications_with_session_needing_approval:
extends: pub
constraint: "pub_id in (select pub from curs where curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and (p.value = 'NEEDS_APPROVAL' or p.value = 'APPROVAL_IN_PROGRESS'))) and triage_status_id in (select cvterm_id from cvterm where name = 'Curatable')"
publications_with_approved_session:
extends: pub
constraint: "pub_id in (select pub from curs where curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and p.value = 'APPROVED')) and triage_status_id in (select cvterm_id from cvterm where name = 'Curatable')"
publications_with_unassigned_session:
extends: pub
constraint: "pub_id in (select pub from curs where assigned_curator is null)"
curatable_publications_with_no_annotatable_genes:
extends: pub
constraint: "pub_id in (select pub from curs where curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'annotation_status' and (p.value = 'NEEDS_APPROVAL' or p.value = 'APPROVAL_IN_PROGRESS')) and curs_id in (select curs from cursprop p, cvterm t where t.cvterm_id = p.type and t.name = 'session_genes_count' and p.value = 0)) and triage_status_id in (select cvterm_id from cvterm where name = 'Curatable')"
unassigned_publications:
extends: pub
constraint: "assigned_curator is null"
sessions_needing_approval:
extends: curs
constraint: "me.curs_id in (select curs from cursprop p, cvterm t where me.curs_id = p.curs and t.cvterm_id = p.type and t.name = 'annotation_status' and (p.value = 'NEEDS_APPROVAL' or p.value = 'APPROVAL_IN_PROGRESS'))"
sessions_with_term_requests:
extends: curs
constraint: "me.curs_id in (select curs from cursprop p, cvterm t where me.curs_id = p.curs and t.cvterm_id = p.type and t.name = 'annotation_status' and (p.value = 'CURATION_IN_PROGRESS' or p.value = 'CURATION_PAUSED' or p.value = 'NEEDS_APPROVAL' or p.value = 'APPROVAL_IN_PROGRESS') and cast((select value from cursprop p, cvterm t where me.curs_id = p.curs and t.cvterm_id = p.type and t.name = 'session_term_suggestions_count') as int) > 0)"
approved_sessions:
extends: curs
constraint: "me.curs_id in (select curs from cursprop p, cvterm t where me.curs_id = p.curs and t.cvterm_id = p.type and t.name = 'annotation_status' and p.value = 'APPROVED')"
unassigned_sessions:
extends: curs
constraint: "me.assigned_curator IS NULL"
all_sessions:
extends: curs
chado:
cv:
class_display_name: controlled vocabulary
editable: 1
display_field: name
field_info_list:
- name: name
editable: 1
- name: definition
editable: 1
- name: "terms in this CV"
source:
sql: 'select count(*) from cvterm where cvterm.cv_id = me.cv_id'
- name: "terms used"
source:
sql: 'select count(*) from cvterm c where c.cv_id = me.cv_id and c.cvterm_id in (select cvterm_id from feature_cvterm)'
- name: "annotation count"
source:
sql: 'select count(*) from feature_cvterm fc, cvterm c where fc.cvterm_id = c.cvterm_id and c.cv_id = me.cv_id'
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
source: cv_id
editable: 1
- name: dbxref_id
editable: 1
- name: "features annotated with this term"
source:
sql: 'select count(*) from feature_cvterm fc where fc.cvterm_id = me.cvterm_id'
organism:
editable: 1
display_field: full_name
order_by:
- genus
- species
field_info_list:
- name: genus
editable: 1
- name: species
editable: 1
pub:
object_title_format: 'Details for publication ID: @@$object->uniquename()@@'
class_display_name: publication
display_field: title
editable: 1
field_info_list:
- name: title
editable: 1
- name: uniquename
editable: 1
- name: type
source: type_id
values_constraint: 'where me.cv_id = (SELECT cv_id FROM cv where cv.name = "genedb_literature")'
referenced_class: Cvterm
editable: 1
feature:
editable: 1
display_field: uniquename
search_fields:
- uniquename
- name
field_info_list:
- name: uniquename
editable: 1
- name: name
editable: 1
- name: type
source: type_id
values_constraint: 'where me.cv_id = (SELECT cv_id FROM cv where cv.name = "sequence")'
referenced_class: Cvterm
editable: 1
- name: featureprops
is_collection: 1
editable: 1
featureprop:
editable: 1
display_field: value
field_info_list:
- name: type
source: type_id
referenced_class: Cvterm
- name: value
editable: 1
db:
editable: 1
display_field: name
field_info_list:
- name: name
editable: 1
- name: description
editable: 1
- name: url
editable: 1
- name: "accessions stored"
source:
sql: 'select count(*) from dbxref where dbxref.db_id = me.db_id'
dbxref:
editable: 1
display_field: accession
field_info_list:
- name: db
editable: 1
- name: accession
editable: 1
- name: description
editable: 1
- name: cvterm
editable: 1
genes:
extends: feature
constraint: "type_id = (select cvterm_id from cvterm, cv where cvterm.name = 'gene' and cvterm.cv_id = cv.cv_id and cv.name = 'sequence')"
pombe_genes:
class_display_name: S. pombe genes
extends: feature
constraint: "type_id = (select cvterm_id from cvterm, cv where cvterm.name = 'gene' and cvterm.cv_id = cv.cv_id and cv.name = 'sequence') and organism_id = (select organism_id from organism where genus = 'Schizosaccharomyces' and species = 'pombe')"
protein_and_domain_terms:
class_display_name: PomBase family or domain terms
extends: cvterm
constraint: "cv_id = (select cv_id from cv where cv.name = 'PomBase family or domain')"
types_and_counts:
class_display_name: SO DNA feature types and counts
constraint: "(select count(*) from feature where type_id = me.cvterm_id) > 0"
display_field: name
extends: cvterm
field_info_list:
- name: name
editable: 1
- name: cv
source: cv_id
editable: 1
- name: "features of this type"
as: count
source:
sql: 'select count(*) from feature where type_id = me.cvterm_id'
reports:
track:
- report: all_publications
children:
- report: untriged_publications
- report: triaged_publications
children:
- report: curatable_publications
children:
- report: curatable_publications_with_sessions
children:
- report: publications_with_new_sessions
- report: publications_with_active_sessions
- report: publications_with_session_needing_approval
- report: publications_with_approved_session
- report: publications_with_unassigned_session
- report: curatable_publications_without_sessions
- report: curatable_publications_with_no_annotatable_genes
- report: high_priority_publications
- report: community_curatable_publications
- report: uncuratable_publications
children:
- report: triage_sequence_feature_or_region_publications
- report: triage_not_english_publications
- report: triage_method_or_reagent_publications
- report: triage_wrong_organism_publications
- report: triage_review_or_comment_publications
- report: triage_erratum_publications
- report: triage_mutagenicity_or_toxicity_study_publications
- report: triage_not_physically_mapped_publications
- report: triage_cell_composition_or_wt_feature_publications
- report: triage_phylogeny_paper_publications
- report: triage_loaded_in_error_publications
- report: triage_other_publications
- report: unassigned_publications
- report: all_sessions
children:
- report: approved_sessions
- report: sessions_with_term_requests
# - report: sessions_needing_approval
# - report: unassigned_sessions
# - report: named_genes
chado:
- report: protein_and_domain_terms
- report: types_and_counts
export:
gene_association_fields:
db: "GeneDB_Spombe"
assigned_by: "GeneDB_Spombe"
db_object_type: gene
load:
ontology:
synonym_types:
- exact
- narrow
- broad
- related
track_db_template_file: db_templates/track_db_template.sqlite3
curs_db_template_file: db_templates/curs_db_template.sqlite3
ontology_index_dir: ontology_index
external_sources:
pubmed_efetch_url: 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&retmode=xml&retmax=99999&id='
pubmed_esearch_url: 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&remode=xml&retmax=99999&term='
implementation_classes:
gene_adaptor: PomCur::Track::GeneLookup
ontology_adaptor: PomCur::Track::OntologyLookup
status_adaptor: PomCur::Track::StatusStorage
allele_type_list:
- name: wild type
description_required: 0
allele_name_required: 1
allow_expression_change: 1
autopopulate_name: '@@gene_name@@+'
- name: deletion
description_required: 0
allele_name_required: 1
allow_expression_change: 0
autopopulate_name: '@@gene_name@@delta'
- name: unknown
description_required: 0
allele_name_required: 1
allow_expression_change: 1
- name: mutation of single amino acid residue
description_required: 1
allele_name_required: 0
allow_expression_change: 1
placeholder: eg. K132A
- name: mutation of multiple non-consecutive amino acid residues
description_required: 1
allele_name_required: 0
allow_expression_change: 1
placeholder: eg. K132A,K144A
- name: mutation of multiple consecutive amino acid residues
description_required: 1
allele_name_required: 0
allow_expression_change: 1
placeholder: eg. KEN26AAA
- name: partial deletion, amino acid
description_required: 1
allele_name_required: 0
allow_expression_change: 1
placeholder: eg. 100-200
- name: partial deletion, nucleotide
description_required: 1
allele_name_required: 0
allow_expression_change: 1
placeholder: eg. 100-200
- name: mutation of a single nucleotide
description_required: 1
allele_name_required: 0
allow_expression_change: 1
placeholder: eg. A25G
- name: other
description_required: 1
allele_name_required: 0
allow_expression_change: 1
placeholder: Please provide a description
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
EXP:
name: Inferred from Experiment
IEP:
name: Inferred from Expression Pattern
ISS:
name: Inferred from Sequence or Structural Similarity
ISO:
name: Inferred from Sequence Orthology
ISA:
name: Inferred from Sequence Alignment
ISM:
name: Inferred from Sequence Model
IGC:
name: Inferred from Genomic Context
IBA:
name: Inferred from Biological aspect of Ancestor
IBD:
name: Inferred from Biological aspect of Descendant
IKR:
name: Inferred from Key Residues
IRD:
name: Inferred from Rapid Divergence
RCA:
name: inferred from Reviewed Computational Analysis
NAS:
name: Non-traceable Author Statement
IC:
name: Inferred by Curator
ND:
name: No biological Data available
IEA:
name: Inferred from Electronic Annotation
NR:
name: Not Recorded
TAS:
name: Traceable Author Statement
UNK:
name: Unknown
Microscopy: ~
'Cell growth assay': ~
'Other': ~
'Affinity Capture-Luminescence':
name: 'Affinity Capture-Luminescence (affinity captures)'
'Affinity Capture-MS':
name: 'Affinity Capture-MS (affinity captures)'
'Affinity Capture-RNA':
name: 'Affinity Capture-RNA (affinity captures)'
'Affinity Capture-Western':
name: 'Affinity Capture-Western (affinity captures)'
'Biochemical Activity': ~
'Chromatography evidence': ~
'Co-crystal Structure': ~
'Co-fractionation': ~
'Co-localization': ~
'Co-purification': ~
'Dosage Growth Defect':
name: 'Dosage Growth Defect (growth defect in presence of overexpressed)'
'Dosage Lethality':
name: 'Dosage Lethality (inviable in presence of overexpressed)'
'Dosage Rescue':
name: 'Dosage Rescue (rescued by overexpression of)'
'FRET':
name: 'FRET (fluorescence resonance energy donor to)'
'Far Western':
name: 'Far Western (captures)'
'Microarray RNA expression level data': ~
'Negative Genetic': ~
'PCA':
name: 'PCA (interacts with)'
'Phenotypic Enhancement':
name: 'Phenotypic Enhancement (phenotype enhanced by)'
'Phenotypic Suppression':
name: 'Phenotypic Suppression (rescued by)'
'Positive Genetic': ~
'Protein-RNA':
name: 'Protein-RNA (binds to RNA)'
'Protein-peptide':
name: 'Protein-peptide (binds to peptide)'
'Reconstituted Complex': ~
'Synthetic Growth Defect': ~
'Synthetic Haploinsufficiency': ~
'Synthetic Lethality': ~
'Synthetic Rescue':
name: 'Synthetic Rescue (synthetically rescued by)'
'Two-hybrid':
name: 'Two-hybrid (binds activation domain construct with)'
'Reporter gene assay': ~
'Enzyme assay data': ~
'Flow cytometry data': ~
'Chromatin immunoprecipitation experiment': ~
'Quantitative PCR': ~
'Fusion protein localization experiment': ~
'Immunolocalization experiment data': ~
'Epitope-tagged protein immunolocalization experiment data': ~
'Protein localization experiment': ~
'Co-immunoprecipitation experiment': ~
'Electrophoretic mobility shift assay data': ~
'Northern assay evidence': ~
'Western blot assay': ~
annotation_type_list:
- name: molecular_function
category: ontology
abbreviation: F
very_short_display_name: 'function'
short_display_name: 'molecular function'
display_name: 'GO molecular function'
evidence_codes:
- IDA
- IGI
- IMP
- IPI
- EXP
broad_term_suggestions: >
transporter, transferase activity
specific_term_examples: >
adenylate cyclase activity or biotin transporter activity
help_text: >
A molecular function is an activity, such as a catalytic or binding
activitiy, that occurs at the molecular level. GO molecular function
terms represent activities that perform the actions (protein
serine/threonine kinase activity, pyruvate carboxylase activity),
rather than the entities (gene products or complexes).
more_help_text: >
As a general rule, molecular functions correspond to single step
activities performed by individual gene products.
- name: biological_process
category: ontology
abbreviation: P
very_short_display_name: 'process'
short_display_name: 'biological process'
display_name: 'GO biological process'
evidence_codes:
- IMP
- IDA
- IGI
- IPI
- EXP
broad_term_suggestions: >
cell cycle, transport
specific_term_examples: >
pyrimidine metabolic process or alpha-glucoside transport
help_text: >
A biological process is series of events accomplished by one or more
ordered assemblies of molecular functions.
more_help_text: >
It can be difficult to distinguish between a biological process
and a molecular function, but the general rule is that a process must
have more than one distinct steps (eg. cell cycle, transport, signal
transduction).
suggest_term_help_text: >
A new term should be differentiated from the parent as a "sub term" by
the mechanism of action, or the genes which are required to perform the
action. It should not be differentiated only by its target gene
products. For example, histone H2A-S121 phosphorylation
is a valid term request because it is performed by a set of genes
specific for this process, translation of histone H2a is not a valid
term request because there is no translation machinery specifically for
histone H2a.
- name: cellular_component
category: ontology
abbreviation: C
very_short_display_name: 'component'
short_display_name: 'cellular component'
display_name: 'GO cellular component'
evidence_codes:
- IDA
- IGI
- IMP
- IPI
- EXP
broad_term_suggestions: >
rough endoplasmic reticulum, nucleus, ribosome
specific_term_examples: >
condensed nuclear chromosome, inner kinetochore and GET complex
help_text: >
Cellular component describes locations, at the levels of
subcellular structures and macromolecular complexes. Examples of
cellular components include nucleus, nuclear inner membrane, nuclear
pore, and proteasome complex.
more_help_text: >
Generally, a gene product is located in or is a subcomponent of a
particular cellular component. The cellular component ontology includes
multi-subunit enzymes and other protein complexes, but not individual
proteins or nucleic acids. Cellular component also does not include
multicellular anatomical terms.
- name: phenotype
needs_allele: 1
gene_cardinality: one_or_more # default is "one"
category: ontology
namespace: fission_yeast_phenotype
very_short_display_name: 'phenotype'
short_display_name: 'phenotype'
display_name: 'phenotype'
evidence_codes:
- Cell growth assay
- Chromatin immunoprecipitation experiment
- Chromatography evidence
- Co-immunoprecipitation experiment
- Electrophoretic mobility shift assay data
- Enzyme assay data
- Epitope-tagged protein immunolocalization experiment data
- Flow cytometry data
- Fusion protein localization experiment
- Immunolocalization experiment data
- Microscopy
- Northern assay evidence
- Western blot assay
- Protein localization experiment
- Quantitative PCR
- Reporter gene assay
- Other
broad_term_suggestions: >
multinucleate, abnormal spindle, inviable
specific_term_examples: >
growth auxotrophic for arginine, abnormal cytokinetic cell separation
help_text: >
A phenotype is any observable characteristic or trait of an organism;
such as its morphology, development, biochemical or physiological
properties, behavior, and products of behaviour.
more_help_text: >
Phenotypes result from the expression of the genes of an organism as well
as the influence of environmental factors and the interactions between
the two.
extra_help_text: >
You can also annotate normal and abnormal phenotypes, such as normal
flocculation or absent flocculation.
- name: post_translational_modification
category: ontology
namespace: PSI-MOD
display_name: 'protein modification'
broad_term_suggestions: >
phosphorylated, methylated, lysine
specific_term_examples: >
O-phospho-L-serine, monomethylated L-lysine
help_text: >
A protein modification is a covalent modification or other change that
alters the measured molecular mass of a peptide or protein amino acid
residue
more_help_text: ~
evidence_codes:
- IDA
- name: genetic_interaction
category: interaction
display_name: 'genetic interaction'
evidence_codes:
- Dosage Growth Defect
- Dosage Lethality
- Dosage Rescue
- Negative Genetic
- Phenotypic Enhancement
- Phenotypic Suppression
- Positive Genetic
- Synthetic Growth Defect
- Synthetic Haploinsufficiency
- Synthetic Lethality
- Synthetic Rescue
- name: physical_interaction
category: interaction
display_name: 'physical interaction'
evidence_codes:
- Affinity Capture-Luminescence
- Affinity Capture-MS
- Affinity Capture-RNA
- Affinity Capture-Western
- Co-crystal Structure
- Co-fractionation
- Co-purification
- Far Western
- FRET
- PCA
- Protein-peptide
- Protein-RNA
- Reconstituted Complex
- Two-hybrid
default_curation_priority_name: low
messages:
gene_upload:
systematic_identifier_desc: systematic identifier
primary_name_desc: primary identifier
examples:
gene_identifier: 'SPCC1739.10'
gene_name: 'cdc11'
test_config_file: 't/test_config.yaml'
test_gene_identifiers:
- SPAC22F3.13
- SPBC12C2.02c
- SPAC23H3.03c
- SPAC458.03
- SPAC57A7.11
- SPAC630.13c
- SPAPYUG7.02c
- SPBC12C2.02c
- SPBC16A3.08c
- SPBC216.07c
- SPBC21B10.05c
- SPBC30D10.10c
- SPBC543.04
- SPBP18G5.03
- SPCC162.12
- SPCC24B10.07
- SPCC4B3.16
- SPCC63.05
- SPCC777.08c
test_publication_uniquename: 'PMID:10467002'
help_text:
choose_gene:
inline: >
Once you have selected a gene to annotate you will be presented with a
set of annotation options
genetic_interaction_evidence:
url: "http://wiki.thebiogrid.org/doku.php/experimental_systems#genetic_interactions"
physical_interaction_evidence:
url: "http://wiki.thebiogrid.org/doku.php/experimental_systems#physical_interactions"
contact_email:
address: "set_me@localhost"
external_links:
gene:
generic:
- name: AmiGO
icon: amigo.png
url: 'http://amigo.geneontology.org/cgi-bin/amigo/gp-assoc.cgi?gp=@@primary_identifier@@'
- name: PomBase
icon: pombase_logo_small.png
url: 'http://www.pombase.org/spombe/result/@@primary_identifier@@'
- name: BioGRID
icon: biogrid_logo_small.png
url: 'http://thebiogrid.org/275721/summary/schizosaccharomyces-pombe/@@primary_identifier@@.html'
organism:
Schizosaccharomyces pombe:
- name: GeneDB
icon: genedb.gif
url: 'http://old.genedb.org/genedb/Search?organism=pombe&name=@@primary_identifier@@'
pub:
- name: PubMed
icon: PubMed_logo_small.png
url: 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=@@uniquename@@'
webservices:
uniprot_batch_lookup_url: 'http://www.uniprot.org/batch/'
quickgo_annotation_lookup_url: 'http://www.ebi.ac.uk/QuickGO/GAnnotation?format=gaf&ref='
ontology_external_links:
cellular_component:
- name: AmiGO
icon: amigo.png
url: 'http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=@@term_ont_id@@'
- name: QuickGO
icon: quickgo.png
url: 'http://www.ebi.ac.uk/QuickGO/GTerm?id=@@term_ont_id@@#term=ancchart'
molecular_function:
- name: AmiGO
icon: amigo.png
url: 'http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=@@term_ont_id@@'
- name: QuickGO
icon: quickgo.png
url: 'http://www.ebi.ac.uk/QuickGO/GTerm?id=@@term_ont_id@@#term=ancchart'
biological_process:
- name: AmiGO
icon: amigo.png
url: 'http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=@@term_ont_id@@'
- name: QuickGO
icon: quickgo.png
url: 'http://www.ebi.ac.uk/QuickGO/GTerm?id=@@term_ont_id@@#term=ancchart'
chado:
ontology_cv_names:
post_translational_modification: PSI-MOD
phenotype: fission_yeast_phenotype
annotation_extension: PomBase annotation extension terms
Computing file changes ...
