id: upheno
title: "Unified Phenotype Ontology"
github_org: obophenotype
git_main_branch: master
repo: upheno
report_fail_on: none
use_dosdps: TRUE
dosdp_tools_options: "--obo-prefixes=true --restrict-axioms-to=logical"
robot_opts: -vv
robot_java_args: -Xmx10G
timeout_external_processes: 36000
working_directory: /work/src
overwrite_matches: False
skip_pattern_download: True
max_upheno_id: 9999999
min_upheno_id: 500
overwrite_ontologies: False
overwrite_upheno_intermediate: True
match_owl_thing: False
allow_non_upheno_eq: False
upheno_axiom_blacklist: ../ontology/components/upheno-removed-axioms.owl
clean: False
upheno_intermediate_layer_depth: 0
namespaces: 
  - http://purl.obolibrary.org/obo/UPHENO_
legal_fillers:
  - http://purl.obolibrary.org/obo/GO_
  - http://purl.obolibrary.org/obo/UBERON_
  - http://purl.obolibrary.org/obo/NBO_
  - http://purl.obolibrary.org/obo/PR_
  - http://purl.obolibrary.org/obo/CHEBI_
  - http://purl.obolibrary.org/obo/PATO_
remove_disjoints:
  - http://purl.obolibrary.org/obo/BFO_0000002
  - http://purl.obolibrary.org/obo/BFO_0000003
  - http://purl.obolibrary.org/obo/BFO_0000004
  - http://purl.obolibrary.org/obo/UBERON_0000466
  - http://purl.obolibrary.org/obo/BFO_0000040
  - http://purl.obolibrary.org/obo/BFO_0000050
  - http://purl.obolibrary.org/obo/GO_0003674
  - http://purl.obolibrary.org/obo/GO_0005575
  - http://purl.obolibrary.org/obo/GO_0008150
  - http://purl.obolibrary.org/obo/CL_0000000
  - http://purl.obolibrary.org/obo/GO_0043226
  - http://purl.obolibrary.org/obo/GO_0005623
  - http://purl.obolibrary.org/obo/UBERON_0004367
  - http://purl.obolibrary.org/obo/UBERON_0001135
  - http://purl.obolibrary.org/obo/UBERON_0000476
blacklisted_upheno_iris:
  - http://purl.obolibrary.org/obo/UPHENO_0000001
  - http://purl.obolibrary.org/obo/UPHENO_0000501
  - http://purl.obolibrary.org/obo/UPHENO_0000502
  - http://purl.obolibrary.org/obo/UPHENO_0000503
  - http://purl.obolibrary.org/obo/UPHENO_0000504
  - http://purl.obolibrary.org/obo/UPHENO_0000505
  - http://purl.obolibrary.org/obo/UPHENO_0000506
  - http://purl.obolibrary.org/obo/UPHENO_0001001
  - http://purl.obolibrary.org/obo/UPHENO_0001002
  - http://purl.obolibrary.org/obo/UPHENO_0001003
  - http://purl.obolibrary.org/obo/UPHENO_9000001
  - http://purl.obolibrary.org/obo/UPHENO_9000002
  - http://purl.obolibrary.org/obo/UPHENO_9000003
  - http://purl.obolibrary.org/obo/UPHENO_9000004
instantiate_superclasses_pattern_vars:
  - anatomical_entity
  - biological_process
sources:
  - id: fbbt
    mirror_from: http://purl.obolibrary.org/obo/fbbt/fbbt-base.owl
  - id: fbdv
    mirror_from: http://purl.obolibrary.org/obo/fbdv/fbdv-base.owl
  - id: nbo
    mirror_from: http://purl.obolibrary.org/obo/nbo/nbo-base.owl
  - id: pr
    mirror_from: http://purl.obolibrary.org/obo/pr.owl.gz
  - id: go
    mirror_from: http://purl.obolibrary.org/obo/go/go-base.owl
  - id: uberon 
    mirror_from: http://purl.obolibrary.org/obo/uberon/uberon-base.owl
  - id: ro
    mirror_from: http://purl.obolibrary.org/obo/ro.owl
  - id: chebi
    mirror_from: http://purl.obolibrary.org/obo/chebi.owl
  - id: hsapdv
    mirror_from: http://purl.obolibrary.org/obo/hsapdv.owl
  - id: pato
    mirror_from: http://purl.obolibrary.org/obo/pato.owl
  - id: cl
    mirror_from: http://purl.obolibrary.org/obo/cl/cl-base.owl
  - id: mpath
    mirror_from: http://purl.obolibrary.org/obo/mpath.owl
  - id: iao
    mirror_from: http://purl.obolibrary.org/obo/iao.owl
  - id: bspo
    mirror_from: http://purl.obolibrary.org/obo/bspo.owl
  - id: hsapdv
    mirror_from: http://purl.obolibrary.org/obo/hsapdv.owl
  - id: wbls
    mirror_from: http://purl.obolibrary.org/obo/wbls.owl
  - id: wbbt
    mirror_from: http://purl.obolibrary.org/obo/wbbt.owl
  - id: ncbitaxon
    mirror_from: http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl
  - id: plana
    mirror_from: http://purl.obolibrary.org/obo/plana.owl
  - id: bfo
    mirror_from: http://purl.obolibrary.org/obo/bfo.owl
  - id: zfa
    mirror_from: http://purl.obolibrary.org/obo/zfa.owl
  - id: ncit
    mirror_from: http://purl.obolibrary.org/obo/ncit.owl
  - id: xao
    mirror_from: http://purl.obolibrary.org/obo/xao.owl
  - id: zfa-uberon
    mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-zfa.owl
  - id: bspo-uberon
    mirror_from: https://raw.githubusercontent.com/obophenotype/uberon/master/bridge/uberon-bridge-to-bspo.obo
  - id: caro-uberon
    mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-caro.owl
  - id: xao-uberon
    mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-xao.owl
  - id: wbbt-uberon
    mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-wbbt.owl
  #- id: plana-uberon
  #  mirror_from: xref
  - id: mp
    mirror_from: http://purl.obolibrary.org/obo/mp/mp-base.owl
    taxon: http://purl.obolibrary.org/obo/MP
    taxon_label: MPO
    modifier: PATO:0000460
    root: http://purl.obolibrary.org/obo/MP_0000001
    prefix_iri: http://purl.obolibrary.org/obo/MP_
    class_hierarchy: asserted
    dependencies:
      - nbo
      - pr
      - chebi
      - cl
      - mpath
  - id: hp
    taxon: http://purl.obolibrary.org/obo/HP
    taxon_label: HPO
    root: http://purl.obolibrary.org/obo/HP_0000118
    prefix_iri: http://purl.obolibrary.org/obo/HP_
    mirror_from: http://purl.obolibrary.org/obo/hp.owl
    modifier: PATO:0000460
    dependencies:
      - nbo
      - pr
      - chebi
      - hsapdv
      - cl
      - mpath
  - id: wbphenotype
    mirror_from: http://purl.obolibrary.org/obo/wbphenotype/wbphenotype-base.owl
    root: http://purl.obolibrary.org/obo/WBPhenotype_0000886
    prefix_iri: http://purl.obolibrary.org/obo/WBPhenotype_
    taxon: http://purl.obolibrary.org/obo/WBPhenotype
    taxon_label: WBP
    modifier: PATO:0000460
    dependencies:
      - bfo
      - wbbt
      - wbls
      - chebi
      - cl
      - wbbt-uberon
  - id: xpo
    mirror_from: http://purl.obolibrary.org/obo/xpo/xpo-base.owl
    root: http://purl.obolibrary.org/obo/XPO_00000000
    prefix_iri: http://purl.obolibrary.org/obo/XPO_
    taxon: http://purl.obolibrary.org/obo/XPO
    taxon_label: XPO
    modifier: PATO:0000460
    dependencies:
      - chebi
      - bfo
      - xao
      - xao-uberon
      - bspo-uberon
      - caro-uberon
  - id: planp
    mirror_from: http://purl.obolibrary.org/obo/planp/planp-base.owl
    root: http://purl.obolibrary.org/obo/PLANP_00000000
    prefix_iri: http://purl.obolibrary.org/obo/PLANP_
    taxon: http://purl.obolibrary.org/obo/PLANP
    taxon_label: PLANP
    modifier: PATO:0000460
    anatomy: plana
    dependencies:
      - plana
      #- plana-uberon
      - bspo-uberon
      - caro-uberon
      #- ncit
  - id: zp
    mirror_from: http://purl.obolibrary.org/obo/zp/zp-base.owl
    root: http://purl.obolibrary.org/obo/ZP_00000000
    prefix_iri: http://purl.obolibrary.org/obo/ZP_
    taxon: http://purl.obolibrary.org/obo/ZP
    taxon_label: ZPO
    modifier: PATO:0000460
    dependencies:
      - zfa
      - chebi
      - bspo
      - mpath
      - bfo
      - zfa-uberon
      - bspo-uberon
      - caro-uberon
  - id: dpo
    mirror_from: http://purl.obolibrary.org/obo/dpo/dpo-base.owl
    root: http://purl.obolibrary.org/obo/FBcv_0001347
    prefix_iri: http://purl.obolibrary.org/obo/FBcv_
    taxon: http://purl.obolibrary.org/obo/DPO
    taxon_label: DPO
    modifier: PATO:0000460
    dependencies:
      - fbdv
      - fbbt
      - cl
      - chebi
common_dependencies:
  - go
  - uberon
  - pato
  - ro
  - iao
  - ncbitaxon
species_modules:
  - mp
  - hp
  - wbphenotype
  - xpo
  - dpo
  - planp
  - zp
upheno_profiles:
  - id: mp-hp
    species_modules:
    - mp
    - hp
  - id: mp-hp-dpo
    species_modules:
    - mp
    - hp
    - dpo
  - id: all
    species_modules:
    - mp
    - hp
    - dpo
    - xpo
    - planp
    - wbphenotype
pattern_repos:
  - obophenotype/upheno/contents/src/patterns/dosdp-dev
  - obophenotype/upheno/contents/src/patterns/dosdp-patterns
release_artefacts: 
  - base
  - simple-non-classified
  - full
primary_release: full
export_formats:
  - owl
  - obo
  - json
import_group:
  products:
    - id: nbo
    - id: pr
    - id: go
    - id: uberon 
    - id: ro
    - id: chebi
    - id: hsapdv
    - id: pato
    - id: cl
    - id: mpath
documentation:
  documentation_system: mkdocs