Adding ontop artifacts for hackathon.

hack24/catalog-v001.xml

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+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
+    <uri id="Imports Wizard Entry" name="http://www.openmicroscopy.org/rdf/2016-06/ome_core/" uri="file:/home/ubuntu/repos/omero-ontop-mappings/ome-owl/ontology/owl/ome_core/ome_core.owl.ttl"/>
+    <group id="Folder Repository, directory=, recursive=true, Auto-Update=true, version=2" prefer="public" xml:base=""/>
+</catalog>

hack24/omemap.obda

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+[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://example.org/site/
+
+[MappingDeclaration] @collection [[
+mappingId	MAPID-project
+target		ome_instance:Project/{project_id} a ome_core:Project ; rdfs:label {project_name} ; rdfs:comment {project_description} ; ome_core:dataset ome_instance:Dataset/{dataset_id} ; <{map_key}> {map_value} . 
+source		select
+			project.id as project_id,
+			projectannotationlink.child as annotation_id,
+			projectdatasetlink.child as dataset_id,
+			project.name as project_name,
+			project.description as project_description,
+			concat(annotation.ns, annotation_mapvalue.name) as map_key,
+			annotation_mapvalue.value as map_value
+			from project
+			join projectannotationlink on projectannotationlink.parent = project.id
+			join annotation on projectannotationlink.child = annotation.id
+			join annotation_mapvalue on annotation.id = annotation_mapvalue.annotation_id
+			join projectdatasetlink on project.id = projectdatasetlink.parent;
+
+mappingId	MAPID-dataset
+target		ome_instance:Dataset/{dataset_id} a ome_core:Dataset ; rdfs:label {dataset_name} ; rdfs:comment {dataset_description} ; ome_core:image ome_instance:Image/{image_id} ; <{map_key}> {map_value} . 
+source		select
+			dataset.id as dataset_id,
+			datasetannotationlink.child as annotation_id,
+			datasetimagelink.child as image_id,
+			dataset.name as dataset_name,
+			dataset.description as dataset_description,
+			concat(annotation.ns, annotation_mapvalue.name) as map_key,
+			annotation_mapvalue.value as map_value,
+			annotation.textvalue as tag_text
+			from dataset
+			join datasetannotationlink on datasetannotationlink.parent = dataset.id
+			join annotation on datasetannotationlink.child = annotation.id
+			join annotation_mapvalue on annotation.id = annotation_mapvalue.annotation_id join datasetimagelink on dataset.id = datasetimagelink.parent;
+
+mappingId	MAPID-Image
+target		ome_instance:Image/{image_id} a ome_core:Image ; rdfs:label {image_name} ; rdfs:comment {image_description} ; <{map_key}> {map_value} ; 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,
+			imageannotationlink.child as annotation_id,
+			image.name as image_name,
+			image.description as image_description,
+			concat(annotation.ns, annotation_mapvalue.name) as map_key,
+			annotation_mapvalue.value as map_value
+			from image
+			join imageannotationlink on imageannotationlink.parent = image.id
+			join annotation on imageannotationlink.child = annotation.id
+			join 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} . 
+source		select
+			dataset.id as dataset_id,
+			annotation.textvalue as tag_text
+			from dataset
+			join datasetannotationlink on datasetannotationlink.parent = dataset.id
+			join 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} . 
+source		select
+			image.id as image_id,
+			annotation.textvalue as tag_text
+			from image
+			join imageannotationlink on imageannotationlink.parent = image.id
+			join 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} . 
+source		select
+			project.id as project_id,
+			annotation.textvalue as tag_text
+			from project
+			join projectannotationlink on projectannotationlink.parent = project.id
+			join 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 ;
+]]
+

hack24/omemap.properties

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+#Thu Nov 14 21:58:37 CET 2024
+jdbc.password=omero_db
+jdbc.user=omero_db
+jdbc.url=jdbc\:postgresql\://localhost\:5432/postgres
+jdbc.driver=org.postgresql.Driver

hack24/omemap.ttl

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+@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://example.org/site/> .
+@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 4.5.25.2023-02-15T19:15:49Z) https://github.com/owlcs/owlapi

hack24/run_ontop.sh

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