Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Adding qudt QuantityKind mappings. #563

Merged
merged 4 commits into from
Aug 10, 2024
Merged

Adding qudt QuantityKind mappings. #563

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
c70ad16
Adding qudt QuantityKind mappings.
cmungall Aug 9, 2024
ee24c8c
Undo import refresh, will be done in another context
matentzn Aug 10, 2024
48cb964
Register PATO to QUDT mapping in config
matentzn Aug 10, 2024
8b8360c
Refresh ODK (includes 1.5.2 migration)
matentzn Aug 10, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 3 additions & 3 deletions .github/workflows/qc.yml
View file
Open in desktop
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
Open in desktop
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
Open in desktop
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
Open in desktop
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
Loading