canto_deploy.yaml

---
Model::TrackModel:
  connect_info:
    - dbi:SQLite:dbname=/data/track.sqlite3
  schema_class: Canto::TrackDB
data_directory: /data

name: PHI-Canto
database_name: PHI-base
long_name: Curation application for PHI-base, the Pathogen-Host Interactions database

email:
  from_address:    curation@phi-base.org
  admin_address:   curation@phi-base.org
  noreply_address: curation@phi-base.org

contact_email:
  address: curation@phi-base.org

demo_mode: 0

canto_demo_url: "http://demo-canto.phi-base.org"

google_tag_manager_id: G-CSERKLNF4N

oauth:
  authenticator: ORCID
  grant_uri: 'https://orcid.org/oauth/authorize'
  token_uri: 'https://orcid.org/oauth/token'
  client_id: 'ORCID_CLIENT_ID'
  client_secret: 'ORCID_CLIENT_SECRET'
  scope: '/authenticate'

strains_mode: 1
diploid_mode: 1
allow_single_wildtype_allele: 1
show_quick_wild_type_buttons: 1

implementation_classes:
  gene_adaptor:     Canto::UniProt::GeneLookup
  ontology_adaptor: Canto::Track::OntologyLookup
  status_adaptor:   Canto::Track::StatusStorage
  person_adaptor:   Canto::Track::PersonLookup
  pubs_adaptor:     Canto::Track::PubsLookup
  ontology_annotation_adaptor: Canto::UniProt::OntologyAnnotationLookup

allele_type_list:
  - name: wild type
    export_type: wild_type
    show_description: false
    description_required: false
    allele_name_required: true
    allow_expression_change: true
    expression_required: true
  - name: deletion
    export_type: deletion
    show_description: false
    description_required: false
    allele_name_required: true
    allow_expression_change: false
  - name: disruption
    name_hint: "e.g. pom1::ura4+"
    export_type: disruption
    show_description: true
    description_required: false
    allele_name_required: true
    allow_expression_change: true
  - name: unknown
    export_type: unknown
    show_description: false
    description_required: false
    allele_name_required: true
    allow_expression_change: true
    expression_required: true
  - name: amino acid insertion
    export_type: amino_acid_insertion
    show_description: true
    description_required: true
    allele_name_required: false
    allow_expression_change: true
    expression_required: true
    placeholder: e.g. 858-MKGYP
  - name: "amino acid substitution(s)"
    export_type: amino_acid_mutation
    show_description: true
    description_required: true
    allele_name_required: false
    allow_expression_change: true
    expression_required: true
    placeholder: eg. K132A
  - name: amino acid insertion and substitution
    export_type: amino_acid_insertion_and_mutation
    show_description: true
    description_required: true
    allele_name_required: false
    allow_expression_change: true
    expression_required: true
    placeholder: e.g. 858-MKGYP,F124D
  - name: amino acid insertion and deletion
    export_type: amino_acid_insertion_and_deletion
    show_description: true
    description_required: true
    allele_name_required: false
    allow_expression_change: true
    expression_required: true
    placeholder: e.g. 858-MKGYP,100-200
  - name: partial deletion and amino acid change
    export_type: amino_acid_deletion_and_mutation
    show_description: true
    description_required: true
    allele_name_required: false
    allow_expression_change: true
    expression_required: true
    placeholder: e.g. 100-200,F124D
  - name: partial deletion, amino acid
    export_type: partial_amino_acid_deletion
    show_description: true
    description_required: true
    allele_name_required: false
    allow_expression_change: true
    expression_required: true
    placeholder: "Please specify deleted residues - eg. 100-200 OR 10-20,40-50"
  - name: nucleotide insertion
    export_type: nucleotide_insertion
    show_description: true
    description_required: true
    allele_name_required: false
    allow_expression_change: true
    expression_required: true
    placeholder: e.g. 132-AATTT
  - name: "nucleotide substitution(s)"
    export_type: nucleotide_mutation
    show_description: true
    description_required: true
    allele_name_required: false
    allow_expression_change: true
    expression_required: true
    placeholder: eg. A25G, OR A-25G (for promoter region)
  - name: partial deletion, nucleotide
    export_type: partial_nucleotide_deletion
    show_description: true
    description_required: true
    allele_name_required: false
    allow_expression_change: true
    expression_required: true
    placeholder: "Please specify deleted residues - eg. 100-200 OR -20--30 (for promoter region)"
  - name: nonsense mutation
    export_type: nonsense_mutation
    show_description: true
    description_required: true
    allow_expression_change: true
    expression_required: true
    allele_name_required: false
    placeholder: 'e.g. aa123->stop, aa1299->amber'
  - name: transformant
    export_type: transformant
    show_description: true
    description_required: true
    allow_expression_change: true
    expression_required: true
    allele_name_required: false
    placeholder: 'transformed (strain-gene) e.g. (sn100-Tox1A1)'
  - name: other
    export_type: other
    show_description: true
    description_required: true
    allele_name_required: false
    allow_expression_change: true
    expression_required: true
    placeholder: Please provide a description

available_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'
    feature_type: 'gene'
    can_have_with: 1
    allow_annotation_transfer: 1
    evidence_codes:
      - IDA
      - IGI
      - IMP
      - IPI
      - EXP
      - TAS
    admin_evidence_codes: []
    broad_term_suggestions: "transporter, transferase activity"
    specific_term_examples: "adenylate cyclase activity or biotin transporter activity"
    help_text: >
      A molecular function is a catalytic (e.g. protein
      serine/threonine kinase activity, pyruvate carboxylase activity)
      or binding activity, or any other activity that occurs at the
      molecular level.
    more_help_text: >
      GO molecular function terms represent activities, rather than
      the things that perform the actions (gene products or
      complexes). As a general rule, molecular functions correspond to
      single step activities performed by individual gene products.
    detailed_help_path: /docs/go_annotation
  - name: biological_process
    category: ontology
    abbreviation: P
    very_short_display_name: 'process'
    short_display_name: 'biological process'
    display_name: 'GO biological process'
    feature_type: 'gene'
    can_have_with: 1
    allow_annotation_transfer: 1
    evidence_codes:
      - IMP
      - IDA
      - IGI
      - IPI
      - EXP
      - TAS
    admin_evidence_codes: []
    broad_term_suggestions: "effector-mediated modulation of host process by symbiont, 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, such as cell cycle regulation,
      ion transport, or signal transduction.
    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 step.
    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.
    detailed_help_path: /docs/go_annotation
  - name: cellular_component
    category: ontology
    abbreviation: C
    very_short_display_name: 'component'
    short_display_name: 'cellular component'
    display_name: 'GO cellular component'
    feature_type: 'gene'
    can_have_with: 1
    allow_annotation_transfer: 1
    evidence_codes:
      - IDA
      - IGI
      - IMP
      - IPI
      - EXP
      - TAS
    admin_evidence_codes: []
    broad_term_suggestions: "rough endoplasmic reticulum, nucleus, ribosome"
    specific_term_examples: "condensed nuclear chromosome, inner kinetochore and GET complex"
    help_text: >
      Cellular components include subcellular structures and
      macromolecular complexes, such as 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.
    detailed_help_path: /docs/go_annotation
  - name: host_phenotype
    category: ontology
    namespace: 'single_species_phenotype'
    very_short_display_name: 'host phenotype'
    short_display_name: 'host phenotype'
    display_name: 'host phenotype'
    synonyms_to_display:
      - exact
    feature_type: 'genotype'
    feature_subtype: 'host'
    can_have_conditions: 1
    allow_annotation_transfer: 1
    evidence_codes:
      - Cell growth assay
      - Electrophysiology assay
      - Enzyme assay data
      - Epitope-tagged protein immunolocalization experiment data
      - Flow cytometry data
      - Gel electrophoresis evidence
      - Immunolocalization experiment data
      - Macroscopic observation (qualitative observation)
      - Macroscopic observation (quantitative observation)
      - Microscopy
      - Other
      - Particle size and count assay
      - Quantitative PCR
      - Reporter gene assay
      - Substance quantification evidence
      - Transcript expression level evidence
      - Western blot assay
    broad_term_suggestions: "inviable population, chemical phenotype (sensitivity or resistance), reproductive phenotype"
    specific_term_examples: "normal transporter activity, abnormal cell wall organization"
    help_text: >
      Annotate normal or abnormal phenotypes of host organisms with this genotype.
    more_help_text: >
      A host phenotype is any observable characteristic or trait of a host organism; observable characteristics include morphology, development, biochemical or physiological properties, behaviour, and products of behaviour of the organism. 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: >
      Alleles may be annotated with multiple phenotype terms, including both normal and abnormal phenotypes for one allele.
    detailed_help_path: /docs/phipo_annotation
  - name: pathogen_phenotype
    category: ontology
    namespace: 'single_species_phenotype'
    very_short_display_name: 'pathogen phenotype'
    short_display_name: 'pathogen phenotype'
    display_name: 'pathogen phenotype'
    synonyms_to_display:
      - exact
    feature_type: 'genotype'
    feature_subtype: 'pathogen'
    can_have_conditions: 1
    allow_annotation_transfer: 1
    evidence_codes:
      - Asexual sporulation assay
      - Cell growth assay
      - Competitive growth assay evidence
      - Electrophysiology assay
      - Enzyme assay data
      - Epitope-tagged protein immunolocalization experiment data
      - Flow cytometry data
      - Gel electrophoresis evidence
      - Immunolocalization experiment data
      - Macroscopic observation (qualitative observation)
      - Macroscopic observation (quantitative observation)
      - Microscopy
      - Particle size and count assay
      - Penetration assay
      - Quantitative PCR
      - Reporter gene assay
      - Sexual sporulation assay
      - Substance quantification evidence
      - Transcript expression level evidence
      - Western blot assay
      - Other
    broad_term_suggestions: "inviable population, chemical phenotype (sensitivity or resistance), hyphal growth phenotype, reproductive phenotype"
    specific_term_examples: "decreased protein phosphorylation, increased level of pyocyanin, abolished chitinase activity"
    help_text: >
      Annotate normal or abnormal phenotypes of pathogen organisms with this genotype.
    more_help_text: >
      A pathogen phenotype is any observable characteristic or trait of a pathogen organism; observable characteristics include morphology, development, biochemical or physiological properties, behaviour, and products of behaviour of the organism. 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: >
      Alleles may be annotated with multiple phenotype terms, including both normal and abnormal phenotypes for one allele.
    detailed_help_path: /docs/phipo_annotation
  - name: pathogen_host_interaction_phenotype
    category: ontology
    namespace: pathogen_host_interaction_phenotype
    very_short_display_name: 'PHI phenotype'
    short_display_name: 'PHI phenotype'
    display_name: 'pathogen-host interaction phenotype'
    synonyms_to_display:
      - exact
    feature_type: 'metagenotype'
    can_have_conditions: 1
    evidence_codes:
      - Asexual sporulation assay
      - Cell growth assay
      - Chromatin immunoprecipitation experiment
      - Chromatography evidence
      - Coimmunoprecipitation
      - Competitive growth assay evidence
      - Electrophoretic mobility shift assay data
      - Electrophysiology assay
      - Enzyme assay data
      - Epitope-tagged protein immunolocalization experiment data
      - Flow cytometry data
      - Gel electrophoresis evidence
      - Immunolocalization experiment data
      - Macroscopic observation (qualitative observation)
      - Macroscopic observation (quantitative observation)
      - Microscopy
      - Particle size and count assay
      - Penetration assay
      - Quantitative PCR
      - Reporter gene assay
      - Sexual sporulation assay
      - Substance quantification evidence
      - Transcript expression level evidence
      - Western blot assay
      - Other
    broad_term_suggestions: "pathogen colonization of host phenotype, binding, effector, host lesion"
    specific_term_examples: "pathogen toxin within host absent, normal pathogen protein localization to host chloroplast"
    help_text: >
      Annotate normal or abnormal phenotypes of organisms within this pathogen-host interaction (metagenotype).
    more_help_text: >
      A pathogen-host interaction phenotype is any observable characteristic or trait of an interaction between a pathogen organism and a host organism; observable characteristics include morphology, development, biochemical or physiological properties, behaviour, and products of behaviour of the organisms. Pathogen-host interaction phenotypes result from the expression of the genes of any of these organisms, as well as the influence of environmental factors (or the interaction between genes and environmental factors).
    extra_help_text: >
      Alleles may be annotated with multiple phenotype terms, including both normal and abnormal phenotypes for one allele.
    detailed_help_path: /docs/phipo_annotation
  - name: gene_for_gene_phenotype
    category: ontology
    namespace: pathogen_host_interaction_phenotype
    very_short_display_name: 'GFG phenotype'
    short_display_name: 'gene-for-gene phenotype'
    display_name: 'gene-for-gene phenotype'
    synonyms_to_display:
      - exact
    feature_type: 'metagenotype'
    can_have_conditions: 1
    evidence_codes:
      - Asexual sporulation assay
      - Cell growth assay
      - Chromatin immunoprecipitation experiment
      - Chromatography evidence
      - Coimmunoprecipitation
      - Competitive growth assay evidence
      - Electrophoretic mobility shift assay data
      - Electrophysiology assay
      - Enzyme assay data
      - Epitope-tagged protein immunolocalization experiment data
      - Flow cytometry data
      - Gel electrophoresis evidence
      - Immunolocalization experiment data
      - Macroscopic observation (qualitative observation)
      - Macroscopic observation (quantitative observation)
      - Microscopy
      - Particle size and count assay
      - Penetration assay
      - Quantitative PCR
      - Reporter gene assay
      - Sexual sporulation assay
      - Substance quantification evidence
      - Transcript expression level evidence
      - Western blot assay
      - Other
    broad_term_suggestions: "absence of pathogen-associated host lesions, presence of pathogen-associated host lesions"
    specific_term_examples: "absence of pathogen host protein-protein interaction, presence of pathogen host protein-protein interaction"
    help_text: >
      Annotate normal or abnormal gene-for-gene phenotypes of organisms within this pathogen-host interaction (metagenotype).
    extra_help_text: >
      Alleles may be annotated with multiple phenotype terms, including both normal and abnormal phenotypes for one allele.
    detailed_help_path: /docs/phipo_annotation
  - name: post_translational_modification
    category: ontology
    namespace: PSI-MOD
    display_name: 'protein modification'
    feature_type: 'gene'
    allow_annotation_transfer: 1
    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
    detailed_help_path: /docs/modification_annotation
  - name: physical_interaction
    category: interaction
    display_name: 'physical interaction'
    feature_type: 'gene'
    allow_annotation_transfer: 1
    second_feature_organism_selector: 1
    help_text: 'Examples: co-purification, two-hybrid, affinity capture'
    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
    detailed_help_path: /docs/physical_interaction_annotation
  - name: wt_rna_expression
    category: ontology
    ontology_size: small
    namespace: PomGeneExRNA
    display_name: 'Wild-type RNA level'
    feature_type: 'gene'
    broad_term_suggestions: ~
    specific_term_examples: ~
    help_text: >
      Qualitative descriptions of presence, absence, increase, decrease, etc.
      of the RNA transcribed from a gene. Note: if you need to capture changes
      in RNA level observed in a mutant in a single species, please use the
      single-species 'RNA level' phenotypes, or for changes in RNA level in a
      pathogen-host interaction, please use the pathogen-host interaction
      'altered RNA level' phenotypes.
    more_help_text: ~
    annotation_table_columns_to_hide: [term_ontid]
    evidence_codes:
      - Microarray
      - Northern blot
      - Quantitative PCR
      - Reporter gene assay
  - name: wt_protein_expression
    category: ontology
    ontology_size: small
    namespace: PomGeneExProt
    display_name: 'Wild-type protein level'
    feature_type: 'gene'
    broad_term_suggestions: ~
    specific_term_examples: ~
    help_text: >
      Qualitative descriptions of presence, absence, increase, decrease, etc.
      of the protein translated from a gene. Note: if you need to capture
      changes in protein level observed in a mutant in a single species, please
      use the single-species 'protein level' phenotypes, or for changes in
      protein level in a pathogen-host interaction, please use the pathogen-host
      interaction 'level of pathogen protein' or 'level of host protein'
      phenotypes.
    more_help_text: ~
    annotation_table_columns_to_hide: [term_ontid]
    evidence_codes:
      - Reporter gene assay
      - Western blot
  - name: disease_name
    category: ontology
    namespace: phido
    very_short_display_name: 'disease'
    short_display_name: 'disease'
    display_name: 'disease name'
    synonyms_to_display:
      - exact
    feature_type: 'metagenotype'
    can_have_conditions: 0
    broad_term_suggestions: ""
    specific_term_examples: ""
    help_text:
      Annotate the expected disease for this pathogen-host interaction, where 'expected' refers to the case of a pathogen strain interacting with a host strain with no experimentally-induced mutations, and where the interaction between the pathogen and the host is compatible (i.e. the interaction results in disease).
    more_help_text: ~
    extra_help_text: ~
    detailed_help_path: /docs/disease_annotation

enabled_annotation_type_list:
  - pathogen_phenotype
  - host_phenotype
  - pathogen_host_interaction_phenotype
  - gene_for_gene_phenotype
  - molecular_function
  - biological_process
  - cellular_component
  - post_translational_modification
  - physical_interaction
  - wt_rna_expression
  - wt_protein_expression
  - disease_name

extension_conf_files:
  - /import_export/phipo_extensions.tsv
  - /import_export/phibase_go_extensions.tsv
  - /import_export/GO_BP_A_E_config.tsv
  - /import_export/GO_CC_A_E_config.tsv
  - /import_export/GO_MF_A_E_config.tsv
  - /import_export/PomGeneEx_A_E_config.tsv
  - /import_export/PSI-MOD_A_E_config.tsv
  - /import_export/phido_extensions.tsv

ontology_namespace_config:
  subsets_to_ignore:
    primary_autocomplete:
      - "is_a(Grouping_terms)"
      - "is_a(qc_do_not_annotate)"
      - "is_a(qc_extension_only)"
    primary_select:
      - "is_a(Grouping_terms)"
      - "is_a(qc_do_not_annotate)"
      - "is_a(qc_extension_only)"
    extension:
      - "is_a(canto_root_subset)"
      - "is_a(qc_do_not_annotate)"
  do_not_annotate_subsets:
    - "is_a(canto_root_subset)"
    - "is_a(qc_do_not_annotate)"
    - "is_a(gocheck_do_not_annotate)"
    - "is_a(gocheck_do_not_manually_annotate)"

phenotype_condition_namespace: phenotype_condition

load:
  ontology:
    term_boosts:
      "PHIPO:0000022": 2.0
      "PHIPO:0000021": 2.0
      "PHIPO:0001308": 2.0

export:
  canto_json:
    set_deletion_names_from_gene: 0
  gene_association_fields:
    db: "UniProtKB"
    assigned_by: "PHI-base"

instance_front_mhtml: /phi_base_docs/phibase_instance_front.mhtml
instance_front_subtitle: Currently curating fungal, protist, and bacterial pathogens
base_docs_path: phi_base_docs

messages:
  gene_upload:
    systematic_identifier_desc: UniProt identifier
    primary_name_desc: ~
    examples:
      gene_identifier: 'Q00909'
      gene_name: ~

email_signature: "Kim Hammond-Kosack and the PHI-base team"

curs_config:
  gene_page_top_message: >
    <p><b>Note:</b> PHI-Canto groups UniProt identifiers by their nearest corresponding NCBI Taxonomy identifier (at the rank of species), so the organism name may not match what is shown in UniProt. Please use the 'experimental strains' field to specify lower taxonomic ranks (such as strains, subspecies, and pathovars).</p>
    <p><b>Note:</b> Do not add species here if their only use is as a delivery mechanism. Information about delivery mechanisms should be added later, as an experimental condition.</p>
  experimental_conditions_help_text: >
    Please add experimental conditions (including delivery mechanism). Conditions are the aspects of the experimental setup that are independent of what cells (strain, genotype, constructs, etc.) are used.
  finish_form:
    extra_text_gene_information: >
      <p>
        Examples include:
        <ul>
        <li> protein domain data or other protein sequence features
        <li> missing gene names (synonyms)
        <li> transcriptional regulation (of the wild-type allele - transcriptional changes due to mutations can be captured in Canto)
        <li> complementation data (whether the gene complements a homologue in a different organism or vice versa; complementation may be full, partial or absent)
        <li> gene product name updates
        </ul>
        Most of these annotation types will be handled in future releases of the
        curation tool.
      </p>

privacy_policy_url: "https://github.com/PHI-base/PHI5_web_display/wiki/Privacy-Policy"

extra_sponsors:
  - link_url: "https://bbsrc.ukri.org/"
    logo_url: "/logos/bbsrc_logo.png"
  - link_url: "http://www.elixiruknode.org/"
    logo_url: "/logos/elixir_uk_logo.png"
  - link_url: "http://www.phi-base.org/"
    logo_url: "/logos/phi-base_logo.png"
  - link_url: "http://www.phytopathdb.org/"
    logo_url: "/logos/phytopath_logo.png"
  - link_url: "https://www.rothamsted.ac.uk/"
    logo_url: "/logos/rres_logo.png"

extra_config_files:
  - /import_export/host_organism_taxon_ids.yaml
  - /import_export/species_strain_map.yaml