Skip to content

Commit

Permalink
Adding mapping and ontology geared towards mpieb.
Browse files Browse the repository at this point in the history
  • Loading branch information
Carsten committed Dec 6, 2024
1 parent 9f58e6e commit 2385015
Show file tree
Hide file tree
Showing 3 changed files with 247 additions and 0 deletions.
159 changes: 159 additions & 0 deletions mpieb/omemap.obda
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,159 @@
[PrefixDeclaration]
: https://www.openmicroscopy.org/omemap/
dc: http://purl.org/dc/elements/1.1/
owl: http://www.w3.org/2002/07/owl#
rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
xml: http://www.w3.org/XML/1998/namespace
xsd: http://www.w3.org/2001/XMLSchema#
foaf: http://xmlns.com/foaf/0.1/
obda: https://w3id.org/obda/vocabulary#
rdfs: http://www.w3.org/2000/01/rdf-schema#
vcard: http://www.w3.org/2006/vcard/ns#
omemap: https://www.openmicroscopy.org/omemap#
ome_core: http://www.openmicroscopy.org/rdf/2016-06/ome_core/
ome_instance: https://ome.evolbio.mpg.de/

[MappingDeclaration] @collection [[
mappingId MAPID-project
target ome_instance:Project/{project_id} a ome_core:Project ; rdfs:label {project_name} ; rdfs:comment {project_description} .
source select
_project.id as project_id,
_project.name as project_name,
_project.description as project_description
from project as _project

mappingId MAPID-dataset-0
target ome_instance:Dataset/{dataset_id} a ome_core:Dataset ; rdfs:label {dataset_name} ; rdfs:comment {dataset_description}.
source select
_dataset.id as dataset_id,
_dataset.name as dataset_name,
_dataset.description as dataset_description
from dataset as _dataset

mappingId MAPID-dataset-1
target ome_instance:Dataset/{dataset_id} ome_core:image ome_instance:Image/{image_id}.
source select
_dataset.id as dataset_id,
_datasetimagelink.child as image_id
from dataset as _dataset
left join datasetimagelink as _datasetimagelink on _dataset.id = _datasetimagelink.parent

mappingId MAPID-dataset-2
target ome_instance:Dataset/{dataset_id} <{map_key}> {map_value} .
source select
_dataset.id as dataset_id,
_datasetannotationlink.child as annotation_id,
concat('http://',_annotation.ns,'#', _annotation_mapvalue.name) as map_key,
_annotation_mapvalue.value as map_value
from dataset as _dataset
join datasetannotationlink as _datasetannotationlink on _datasetannotationlink.parent = _dataset.id
join annotation as _annotation on _datasetannotationlink.child = _annotation.id
join annotation_mapvalue as _annotation_mapvalue on _annotation.id = _annotation_mapvalue.annotation_id


mappingId MAPID-Image-0
target ome_instance:Image/{image_id} a ome_core:Image ; rdfs:label {image_name} ; rdfs:comment {image_description} ; ome_core:acquisitionDate {image_acquisitiondate}^^xsd:dateTime ; dc:identifier {image_id}^^xsd:string .
source select
_image.id as image_id,
_image.acquisitiondate as image_acquisitiondate,
_image.name as image_name,
_image.description as image_description
from image as _image

mappingId MAPID-Image-1
target ome_instance:Image/{image_id} a ome_core:Image; <{map_key}> {map_value} .
source select
_image.id as image_id,
concat('http://',_annotation.ns,'#', _annotation_mapvalue.name) as map_key,
_annotation_mapvalue.value as map_value
from image as _image
join imageannotationlink as _imageannotationlink on _imageannotationlink.parent = _image.id
join annotation as _annotation on _imageannotationlink.child = _annotation.id
join annotation_mapvalue as _annotation_mapvalue on _annotation.id = _annotation_mapvalue.annotation_id


mappingId MAPID-experimentergroup
target ome_instance:ExperimenterGroup/{experimentergroup_id} a ome_core:ExperimenterGroup .
source select
experimentergroup.id as experimentergroup_id
from experimentergroup

mappingId MAPID-experiment
target ome_instance:Experiment/{experiment_id} a ome_core:Experiment .
source select
experiment.id as experiment_id
from experiment

mappingId MAPID-well
target ome_instance:Well/{well_id} a ome_core:Well .
source select
well.id as well_id
from well

mappingId MAPID-wellsample
target ome_instance:WellSample/{wellsample_id} a ome_core:WellSample .
source select
wellsample.id as wellsample_id
from wellsample

mappingId MAPID-reagentset
target ome_instance:ReagentSet/{reagentset_id} a ome_core:ReagentSet .
source select
reagent.id as reagentset_id
from reagent

mappingId MAPID-dataset_tag
target ome_instance:Dataset/{dataset_id} ome_core:tagAnnotationValue {tag_text}^^xsd:string .
source select
_dataset.id as dataset_id,
_annotation.textvalue as tag_text
from dataset as _dataset
left join datasetannotationlink as _datasetannotationlink on _datasetannotationlink.parent = _dataset.id
join annotation as _annotation on _datasetannotationlink.child = _annotation.id where _annotation.textvalue is not NULL

mappingId MAPID-image_tag
target ome_instance:Image/{image_id} ome_core:tagAnnotationValue {tag_text}^^xsd:string .
source select
_image.id as image_id,
_annotation.textvalue as tag_text
from image as _image
left join imageannotationlink as _imageannotationlink on _imageannotationlink.parent = _image.id
left join annotation as _annotation on _imageannotationlink.child = _annotation.id where _annotation.textvalue is not NULL

mappingId MAPID-project_tag
target ome_instance:Project/{project_id} ome_core:tagAnnotationValue {tag_text}^^xsd:string .
source select
_project.id as project_id,
_annotation.textvalue as tag_text
from project as _project
left join projectannotationlink as _projectannotationlink on _projectannotationlink.parent = _project.id
left join annotation as _annotation on _projectannotationlink.child = _annotation.id where _annotation.textvalue is not NULL

mappingId MAPID-a5bdd29d4c994a6bbb3acdc666403abd
target ome_instance:RegionOfInterest/{roi_id} a ome_core:RegionOfInterest ; dc:identifier {roi_id}^^xsd:string .
source select id as roi_id from roi

mappingId MAPID-roi
target ome_instance:RegionOfInterest/{roi_id} a ome_core:RegionOfInterest ; ome_core:image ome_instance:Image/{roi_image_id} ; dc:identifier {roi_id}^^xsd:string .
source select id as roi_id, image as roi_image_id from roi

mappingId MAPID-project(0)
target ome_instance:Project/{project_id} a ome_core:Project ; ome_core:dataset ome_instance:Dataset/{dataset_id} .
source select
_project.id as project_id,
_projectdatasetlink.child as dataset_id
from project as _project
left join projectdatasetlink as _projectdatasetlink on _project.id = _projectdatasetlink.parent

mappingId MAPID-project(1)
target ome_instance:Project/{project_id} a ome_core:Project ; <{map_key}> {map_value} .
source select
_project.id as project_id,
concat('http://',_annotation.ns,'#', _annotation_mapvalue.name) as map_key,
_annotation_mapvalue.value as map_value
from project as _project
join projectannotationlink as _projectannotationlink on _projectannotationlink.parent = _project.id
join annotation as _annotation on _projectannotationlink.child = _annotation.id
join annotation_mapvalue as _annotation_mapvalue on _annotation.id = _annotation_mapvalue.annotation_id
]]

78 changes: 78 additions & 0 deletions mpieb/omemap.ttl
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,78 @@
@prefix : <https://www.openmicroscopy.org/omemap/> .
@prefix dc: <http://purl.org/dc/elements/1.1/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix obda: <https://w3id.org/obda/vocabulary#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix vcard: <http://www.w3.org/2006/vcard/ns#> .
@prefix omemap: <https://www.openmicroscopy.org/omemap#> .
@prefix ome_core: <http://www.openmicroscopy.org/rdf/2016-06/ome_core/> .
@prefix ome_instance: <https://ome.evolbio.mpg.de/> .
@base <https://www.openmicroscopy.org/omemap/> .

<https://www.openmicroscopy.org/omemap> rdf:type owl:Ontology ;
owl:imports ome_core: .

#################################################################
# Annotation properties
#################################################################

### http://www.openmicroscopy.org/rdf/2016-06/ome_core/annotation
ome_core:annotation rdf:type owl:AnnotationProperty .


### http://www.openmicroscopy.org/rdf/2016-06/ome_core/mapAnnotationValue
ome_core:mapAnnotationValue rdf:type owl:AnnotationProperty .


### http://www.openmicroscopy.org/rdf/2016-06/ome_core/nameSpace
ome_core:nameSpace rdf:type owl:AnnotationProperty .


#################################################################
# Object Properties
#################################################################

### http://www.openmicroscopy.org/rdf/2016-06/ome_core/mapAnnotationValue
ome_core:mapAnnotationValue rdfs:domain ome_core:Annotation ,
ome_core:LongAnnotation ,
ome_core:StructuredAnnotation .


#################################################################
# Data properties
#################################################################

### http://www.openmicroscopy.org/rdf/2016-06/ome_core/nameSpace
ome_core:nameSpace rdfs:domain ome_core:Annotation ,
ome_core:MapAnnotation .


### http://www.openmicroscopy.org/rdf/2016-06/ome_core/tagAnnotationValue
ome_core:tagAnnotationValue rdf:type owl:DatatypeProperty .


#################################################################
# Classes
#################################################################

### http://www.openmicroscopy.org/rdf/2016-06/ome_core/Dataset
ome_core:Dataset owl:disjointWith ome_core:Image .


### http://www.openmicroscopy.org/rdf/2016-06/ome_core/Folder
ome_core:Folder rdfs:subClassOf owl:Thing .


### http://www.openmicroscopy.org/rdf/2016-06/ome_core/Image
ome_core:Image owl:disjointWith ome_core:Project .


### http://www.openmicroscopy.org/rdf/2016-06/ome_core/StructuredAnnotation
ome_core:StructuredAnnotation rdfs:subClassOf ome_core:Annotation .


### Generated by the OWL API (version 4.5.29.2024-05-13T12:11:03Z) https://github.com/owlcs/owlapi
10 changes: 10 additions & 0 deletions mpieb/run_ontop.sh
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
#! /bin/bash

# Spin up ontop
ontop endpoint \
-t omemap.ttl \
-m omemap.obda \
-p omemap.properties \
-x catalog-v001.xml \
--dev

0 comments on commit 2385015

Please sign in to comment.