cl-odk.yaml

id: cl
title: "Cell Ontology"
github_org: obophenotype
git_main_branch: master
repo: cell-ontology
#report_fail_on: ERROR
report_fail_on: None
use_dosdps: TRUE
export_formats:
  - owl
  - obo
  - json
namespaces: 
  - http://purl.obolibrary.org/obo/CP_
  - http://purl.obolibrary.org/obo/CL_
  - http://purl.obolibrary.org/obo/cl_
primary_release: full
release_artefacts: 
  - base
  - full
  - simple
  - basic
  - non-classified
documentation:
  documentation_system: mkdocs
subset_group:
  products:
    - id: BDS_subset
import_group:
  use_base_merging: TRUE
  slme_individuals: exclude
  exclude_iri_patterns:
    - <http://www.informatics.jax.org/marker/MGI:*>
    - <http://purl.obolibrary.org/obo/OBA_*>
    - <http://purl.obolibrary.org/obo/ENVO_*>
    - <http://purl.obolibrary.org/obo/OBI_*>
    - <http://purl.obolibrary.org/obo/GOCHE_*>
    - <http://purl.obolibrary.org/obo/CLO_*>
    - <http://www.genenames.org/cgi-bin/gene_symbol_report*>
  products:
    - id: pr
      make_base: TRUE
      mirror_from: https://raw.githubusercontent.com/obophenotype/pro_obo_slim/master/pr_slim.owl
      is_large: TRUE
    - id: go
      use_base: TRUE
      base_iris:
        - http://purl.obolibrary.org/obo/GO_
        - http://purl.obolibrary.org/obo/GOREL_
        - http://purl.obolibrary.org/obo/GOCHE_
    - id: caro
      use_base: TRUE
    - id: uberon 
      use_base: TRUE
    - id: ro
      use_base: TRUE
    - id: chebi
      make_base: TRUE
      use_gzipped: TRUE
      is_large: TRUE
    - id: pato
      use_base: TRUE
    - id: ncbitaxon
      mirror_from: http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl
pattern_pipelines_group:
  products:
    - id: clustering
      dosdp_tools_options: "--obo-prefixes=true"
robot_java_args: '-Xmx16G'
allow_equivalents: asserted-only
robot_report:
  release_reports: False
  fail_on : ERROR
  use_labels : False
  custom_profile : False
  report_on :
    - edit
  custom_sparql_checks :
    - equivalent-classes
    - owldef-self-reference
    - nolabels
    - pmid-not-dbxref
    - obsolete-replaced_by
  custom_sparql_exports :
    - basic-report
components:
  products:
    - filename: mappings.owl