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Merging hack24 mappings into omemap.obda.
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Carsten Fortmann-Grote committed Dec 19, 2024
1 parent bb9bc6e commit 9b3c2e7
Showing 1 changed file with 102 additions and 52 deletions.
154 changes: 102 additions & 52 deletions ontop/omemap.obda
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Original file line number Diff line number Diff line change
Expand Up @@ -15,63 +15,113 @@ ome_marshal: http://www.openmicroscopy.org/Schemas/OME/2015-01/
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} .
mappingId MAPID-project(1)
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,
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;
_project.id as project_id,
_project.name as project_name,
_project.description as project_description
from project as _project

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} .
mappingId MAPID-project(2)
target ome_instance:Project/{project_id} a ome_core:Project ; ome_core:dataset ome_instance:Dataset/{dataset_id} .
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;
_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-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 .
mappingId MAPID-project(3)
target ome_instance:Project/{project_id} a ome_core:Project ; <{map_key}> {map_value} .
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( regexp_replace(
regexp_replace(
case
when annotation.ns is null then 'www.openmicroscopy.org/ns/default'
else annotation.ns
end,
'^([^h])',
'http://\1'),
'([^\/,#])$',
'\1/'
),
annotation_mapvalue.name) as map_key,
annotation_mapvalue.value as map_value
from image
join imageannotationlink on imageannotationlink.parent = image.id
join annotation on imageannotationlink.child = annotation.id
join annotation_mapvalue on annotation.id = annotation_mapvalue.annotation_id;
_project.id as project_id,
concat( regexp_replace(
regexp_replace(
case
when _annotation.ns is null then 'www.openmicroscopy.org/ns/default'
else _annotation.ns
end,
'^([^h])',
'http://\1'),
'([^\/,#])$',
'\1/'
),
_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

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( regexp_replace(
regexp_replace(
case
when _annotation.ns is null then 'www.openmicroscopy.org/ns/default'
else _annotation.ns
end,
'^([^h])',
'http://\1'),
'([^\/,#])$',
'\1/'
),
_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( regexp_replace(
regexp_replace(
case
when _annotation.ns is null then 'www.openmicroscopy.org/ns/default'
else _annotation.ns
end,
'^([^h])',
'http://\1'),
'([^\/,#])$',
'\1/'
),
_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 .
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