Skip to content

Commit

Permalink
Merge pull request #563 from pato-ontology/adding-qudt-kind-mappings
Browse files Browse the repository at this point in the history 
Adding qudt QuantityKind mappings.
  • Loading branch information
@matentzn
matentzn authored Aug 10, 2024
2 parents 19dc7ac + 8b8360c commit 38ceca9
Show file tree
Hide file tree
Showing 10 changed files with 225 additions and 60 deletions.
6 changes: 3 additions & 3 deletions .github/workflows/qc.yml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -19,15 +19,15 @@ jobs:
ontology_qc:
# The type of runner that the job will run on
runs-on: ubuntu-latest
container: obolibrary/odkfull:v1.3.0
container: obolibrary/odkfull:v1.5.2

# Steps represent a sequence of tasks that will be executed as part of the job
steps:
# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
- uses: actions/checkout@v2
- uses: actions/checkout@v3

- name: Run ontology QC checks
env:
DEFAULT_BRANCH: master
run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false
run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false MIR=false

1 change: 1 addition & 0 deletions docs/odk-workflows/ManageDocumentation.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -44,3 +44,4 @@ The documentation is _not_ automatically updated from the Markdown, and needs to
Just make sure you give GitHub 2-5 minutes to build the pages!



2 changes: 1 addition & 1 deletion docs/odk-workflows/RepoManagement.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@

## Updating your ODK repository

Your ODK repositories configuration is managed in `src/ontology/pato-odk.yaml`. Once you have made your changes, you can run the following to apply your changes to the repository:
Your ODK repositories configuration is managed in `src/ontology/pato-odk.yaml`. The [ODK Project Configuration Schema](https://github.com/INCATools/ontology-development-kit/blob/master/docs/project-schema.md) defines all possible parameters that can be used in this config YAML. Once you have made your changes, you can run the following to apply your changes to the repository:


```
Expand Down
57 changes: 57 additions & 0 deletions src/mappings/pato-to-qudt-quantitykind.sssom.tsv
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,57 @@
#curie_map:
# PATO: http://purl.obolibrary.org/obo/PATO_
# oio: http://www.geneontology.org/formats/oboInOwl#
# owl: http://www.w3.org/2002/07/owl#
# quantitykind: http://w3id.org/sssom/unknown_prefix/quantitykind/
# rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
# rdfs: http://www.w3.org/2000/01/rdf-schema#
# semapv: https://w3id.org/semapv/vocab/
# skos: http://www.w3.org/2004/02/skos/core#
# sssom: https://w3id.org/sssom/
# ORCID: "https://orcid.org/"
#creator_id:
# - "ORCID:0000-0002-6601-2165"
#license: https://w3id.org/sssom/license/unspecified
#mapping_set_id: http://purl.obolibrary.org/obo/pato/mappings/pato-to-qudt-quantitykind.sssom.tsv
#mapping_set_description: "Mappings between PATO and qudt QuantityKind types. Seeded using lexmatch then curated"
#license: "https://creativecommons.org/licenses/by/4.0/"
#subject_source: "obo:pato.owl"
#object_source: "quantitykind:"
#mapping_date: "2024-08-09"
subject_id subject_label predicate_id object_id object_label mapping_justification mapping_tool confidence subject_match_field object_match_field match_string
PATO:0000008 speed skos:exactMatch quantitykind:Speed Speed semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label speed
PATO:0000033 concentration of skos:exactMatch quantitykind:Concentration Concentration semapv:ManualMappingCuration oaklib 1.0 oio:hasExactSynonym rdfs:label concentration
PATO:0000057 occurrence skos:exactMatch quantitykind:Incidence Incidence semapv:ManualMappingCuration oaklib 1.0 oio:hasExactSynonym rdfs:label incidence
PATO:0000133 orientation skos:exactMatch quantitykind:Angle Angle semapv:ManualMappingCuration oaklib 1.0 oio:hasRelatedSynonym rdfs:label angle
PATO:0000146 temperature skos:exactMatch quantitykind:Temperature Temperature semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label temperature
PATO:0000915 thickness skos:exactMatch quantitykind:Thickness Thickness semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label thickness
PATO:0000918 volume skos:exactMatch quantitykind:Volume Volume semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label volume
PATO:0000921 width skos:exactMatch quantitykind:Width Width semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label width
PATO:0000970 permeability skos:exactMatch quantitykind:Permeability Permeability semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label permeability
PATO:0000992 viscosity skos:exactMatch quantitykind:Viscosity Viscosity semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label viscosity
PATO:0001019 mass density skos:exactMatch quantitykind:Density Density semapv:ManualMappingCuration oaklib 1.0 oio:hasRelatedSynonym rdfs:label density
PATO:0001022 impulse skos:exactMatch quantitykind:Impulse impulse semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label impulse
PATO:0001030 flux skos:exactMatch quantitykind:Flux Flux semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label flux
PATO:0001034 strain skos:exactMatch quantitykind:Strain Strain semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label strain
PATO:0001046 resistance to skos:exactMatch quantitykind:Resistance Resistance semapv:ManualMappingCuration oaklib 1.0 oio:hasExactSynonym rdfs:label resistance
PATO:0001297 reflectivity skos:exactMatch quantitykind:Reflectivity Reflectivity semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label reflectivity
PATO:0001309 duration skos:exactMatch quantitykind:Period Period semapv:ManualMappingCuration oaklib 1.0 oio:hasExactSynonym rdfs:label period
PATO:0001352 linear density skos:exactMatch quantitykind:LinearDensity Linear Density semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label linear density
PATO:0001414 catalytic activity skos:exactMatch quantitykind:CatalyticActivity Catalytic Activity semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label catalytic activity
PATO:0001470 ratio skos:exactMatch quantitykind:Ratio ratio semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label ratio
PATO:0001521 sound amplitude skos:exactMatch quantitykind:Loudness loudness semapv:ManualMappingCuration oaklib 1.0 oio:hasBroadSynonym rdfs:label loudness
PATO:0001585 conductivity skos:exactMatch quantitykind:Conductivity Conductivity semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label conductivity
PATO:0001591 curvature skos:exactMatch quantitykind:Curvature Curvature semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label curvature
PATO:0001595 depth skos:exactMatch quantitykind:Depth Depth semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label depth
PATO:0001679 specific volume skos:exactMatch quantitykind:SpecificVolume Specific Volume semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label specific volume
PATO:0001718 luminance skos:exactMatch quantitykind:Luminance Luminance semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label luminance
PATO:0001740 activity (of a radionuclide) skos:exactMatch quantitykind:Radioactivity radioactivity semapv:ManualMappingCuration oaklib 1.0 oio:hasExactSynonym rdfs:label radioactivity
PATO:0001842 acidity skos:exactMatch quantitykind:Acidity Acidity semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label acidity
PATO:0002205 capacitance skos:exactMatch quantitykind:Capacitance Capacitance semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label capacitance
PATO:0002243 fluid flow rate skos:exactMatch quantitykind:VolumeFlowRate Volume Flow Rate semapv:ManualMappingCuration oaklib 1.0 oio:hasExactSynonym rdfs:label volume flow rate
PATO:0002244 mass flow rate skos:exactMatch quantitykind:MassFlowRate Mass Flow Rate semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label mass flow rate
PATO:0002284 tension skos:exactMatch quantitykind:Tension Tension semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label tension
PATO:0002326 angle skos:exactMatch quantitykind:Angle Angle semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label angle
PATO:0002390 radius skos:exactMatch quantitykind:Radius Radius semapv:ManualMappingCuration oaklib 1.0 rdfs:label rdfs:label radius


Loading

0 comments on commit 38ceca9

Please sign in to comment.