Skip to content

Commit a5ff665

Browse files
jgrewejgrewe
authored
Merge pull request #328 from mpsonntag/templates
Add odML templates support
2 parents 15bb570 + e627e76 commit a5ff665

17 files changed

+237
-38
lines changed

‎doc/example_odMLs/THGTTG.odml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@
22
<?xml-stylesheet type="text/xsl" href="odmlTerms.xsl"?>
33
<?xml-stylesheet type="text/xsl" href="odml.xsl"?>
44
<odML version="1.1">
5-
<repository>http://portal.g-node.org/odml/terminologies/v1.1/terminologies.xml</repository>
5+
<repository>https://terminologies.g-node.org/v1.1/terminologies.xml</repository>
66
<version>42</version>
77
<section>
88
<name>TheCrew</name>

‎doc/example_odMLs/sample_odml.odml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@
33
<?xml-stylesheet type="text/xsl" href="odml.xsl"?>
44
<odML version="1.1">
55
<author>D. N. Adams</author>
6-
<repository>http://portal.g-node.org/odml/terminologies/v1.1/terminologies.xml</repository>
6+
<repository>https://terminologies.g-node.org/v1.1/terminologies.xml</repository>
77
<section>
88
<property>
99
<type>person</type>

‎doc/example_odMLs/sample_odml.rdf‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -83,5 +83,5 @@ odml:d98afe9b-3982-44bf-9373-12aaa4798628 a rdf:Bag ;
8383
"Tricia Marie McMillan",
8484
"Zaphod Beeblebrox" .
8585

86-
<https://g-node.org/projects/odml-rdf#7e0e07c7-7501-454e-88e7-cfa072db94c1> a <http://portal.g-node.org/odml/terminologies/v1.1/terminologies.xml> .
86+
<https://g-node.org/projects/odml-rdf#7e0e07c7-7501-454e-88e7-cfa072db94c1> a <https://terminologies.g-node.org/v1.1/terminologies.xml> .
8787

‎doc/example_odMLs/thgttg.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -25,7 +25,7 @@
2525
save_to = os.path.join(output_directory, "THGTTG.odml")
2626

2727

28-
odmlrepo = 'http://portal.g-node.org/odml/terminologies/v1.1/terminologies.xml'
28+
odmlrepo = 'https://terminologies.g-node.org/v1.1/terminologies.xml'
2929

3030
# CREATE A DOCUMENT
3131
doc = odml.Document(author="D. N. Adams",

‎doc/example_rdfs/example_data/drosophila_2.ttl‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -643,5 +643,5 @@ odml:fadffec7-6b23-454e-bfd1-9d5884802abb a odml:Property ;
643643
odml:ff5fb5e5-5104-41c8-ab45-9d8787e7fbdc a rdf:Bag ;
644644
rdf:li "simpleErg" .
645645

646-
<https://g-node.org/projects/odml-rdf#7517fc3b-a12c-47b3-bfc5-96cc98fefa8a> a <http://portal.g-node.org/odml/terminologies/v1.0/terminologies.xml> .
646+
<https://g-node.org/projects/odml-rdf#7517fc3b-a12c-47b3-bfc5-96cc98fefa8a> a <https://terminologies.g-node.org/v1.0/terminologies.xml> .
647647

‎doc/example_rdfs/example_data/drosophila_4.ttl‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1352,5 +1352,5 @@ odml:fedefe26-0f36-433f-993d-ad827dcb0a50 a odml:Property ;
13521352
odml:hasUnit "ms" ;
13531353
odml:hasValue <https://g-node.org/projects/odml-rdf#7fe2ea64-262c-4cdd-acd2-4d59c42cd4aa> .
13541354

1355-
<https://g-node.org/projects/odml-rdf#9cf7f270-eb40-4406-a78b-d5de29fe5879> a <http://portal.g-node.org/odml/terminologies/v1.0/terminologies.xml> .
1355+
<https://g-node.org/projects/odml-rdf#9cf7f270-eb40-4406-a78b-d5de29fe5879> a <https://terminologies.g-node.org/v1.0/terminologies.xml> .
13561356

‎doc/example_rdfs/example_data/drosophila_8.ttl‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1351,5 +1351,5 @@ odml:fe6a8363-a5f4-46ed-8eea-b57257d4823b a odml:Property ;
13511351
odml:ff532446-ca25-4092-8abb-302e12344b3b a rdf:Bag ;
13521352
rdf:li "1.0" .
13531353

1354-
odml:b0d95b14-a12f-4057-aed3-fdd3a6ea5f82 a <http://portal.g-node.org/odml/terminologies/v1.0/terminologies.xml> .
1354+
odml:b0d95b14-a12f-4057-aed3-fdd3a6ea5f82 a <https://terminologies.g-node.org/v1.0/terminologies.xml> .
13551355

‎doc/odml_ontology/root-ontology.ttl‎

Lines changed: 11 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -227,7 +227,7 @@ rdf:Seq rdf:type owl:Class ;
227227
rdfs:subClassOf :Section ;
228228
rdfs:comment "Description"^^xsd:string ;
229229
rdfs:label "Cell" ;
230-
rdfs:seeAlso <http://portal.g-node.org/odml/terminologies/v1.0/cell/cell.xml> .
230+
rdfs:seeAlso <https://terminologies.g-node.org/v1.0/cell/cell.xml> .
231231

232232

233233
### https://g-node.org/projects/odml-rdf#CellProperties
@@ -242,15 +242,15 @@ rdf:Seq rdf:type owl:Class ;
242242
rdfs:subClassOf :Section ;
243243
rdfs:comment "Description"^^xsd:string ;
244244
rdfs:label "DataAcquisition" ;
245-
rdfs:seeAlso <http://portal.g-node.org/odml/terminologies/v1.0/hardware/daq.xml> .
245+
rdfs:seeAlso <https://terminologies.g-node.org/v1.0/hardware/daq.xml> .
246246

247247

248248
### https://g-node.org/projects/odml-rdf#Dataset
249249
:Dataset rdf:type owl:Class ;
250250
rdfs:subClassOf :Section ;
251251
rdfs:comment "Description"^^xsd:string ;
252252
rdfs:label "Dataset" ;
253-
rdfs:seeAlso <http://portal.g-node.org/odml/terminologies/v1.0/dataset/dataset.xml> .
253+
rdfs:seeAlso <https://terminologies.g-node.org/v1.0/dataset/dataset.xml> .
254254

255255

256256
### https://g-node.org/projects/odml-rdf#Document
@@ -298,23 +298,23 @@ rdf:Seq rdf:type owl:Class ;
298298
rdfs:subClassOf :Section ;
299299
rdfs:comment "Description"^^xsd:string ;
300300
rdfs:label "Electrode" ;
301-
rdfs:seeAlso <http://portal.g-node.org/odml/terminologies/v1.0/electrode/electrode.xml> .
301+
rdfs:seeAlso <https://terminologies.g-node.org/v1.0/electrode/electrode.xml> .
302302

303303

304304
### https://g-node.org/projects/odml-rdf#Hardware
305305
:Hardware rdf:type owl:Class ;
306306
rdfs:subClassOf :Section ;
307307
rdfs:comment "Description"^^xsd:string ;
308308
rdfs:label "Hardware" ;
309-
rdfs:seeAlso <http://portal.g-node.org/odml/terminologies/v1.0/hardware/hardware.xml> .
309+
rdfs:seeAlso <https://terminologies.g-node.org/v1.0/hardware/hardware.xml> .
310310

311311

312312
### https://g-node.org/projects/odml-rdf#HardwareSettings
313313
:HardwareSettings rdf:type owl:Class ;
314314
rdfs:subClassOf :Section ;
315315
rdfs:comment "Description"^^xsd:string ;
316316
rdfs:label "HardwareSettings" ;
317-
rdfs:seeAlso <http://portal.g-node.org/odml/terminologies/v1.0/collection/hardware_settings.xml> .
317+
rdfs:seeAlso <https://terminologies.g-node.org/v1.0/collection/hardware_settings.xml> .
318318

319319

320320
### https://g-node.org/projects/odml-rdf#Hub
@@ -338,7 +338,7 @@ rdf:Seq rdf:type owl:Class ;
338338
rdfs:subClassOf :Section ;
339339
rdfs:comment "Description"^^xsd:string ;
340340
rdfs:label "Preparation" ;
341-
rdfs:seeAlso <http://portal.g-node.org/odml/terminologies/v1.0/preparation/preparation.xml> .
341+
rdfs:seeAlso <https://terminologies.g-node.org/v1.0/preparation/preparation.xml> .
342342

343343

344344
### https://g-node.org/projects/odml-rdf#Property
@@ -394,7 +394,7 @@ rdf:Seq rdf:type owl:Class ;
394394
rdfs:subClassOf :Section ;
395395
rdfs:comment "Description"^^xsd:string ;
396396
rdfs:label "Recording" ;
397-
rdfs:seeAlso <http://portal.g-node.org/odml/terminologies/v1.0/recording/recording.xml> .
397+
rdfs:seeAlso <https://terminologies.g-node.org/v1.0/recording/recording.xml> .
398398

399399

400400
### https://g-node.org/projects/odml-rdf#Section
@@ -457,23 +457,23 @@ rdf:Seq rdf:type owl:Class ;
457457
rdfs:subClassOf :Section ;
458458
rdfs:comment "Description"^^xsd:string ;
459459
rdfs:label "Setup" ;
460-
rdfs:seeAlso <http://portal.g-node.org/odml/terminologies/v1.0/setup/setup.xml> .
460+
rdfs:seeAlso <https://terminologies.g-node.org/v1.0/setup/setup.xml> .
461461

462462

463463
### https://g-node.org/projects/odml-rdf#Stimulus
464464
:Stimulus rdf:type owl:Class ;
465465
rdfs:subClassOf :Section ;
466466
rdfs:comment "Description of the Stimulus."^^xsd:string ;
467467
rdfs:label "Stimulus" ;
468-
rdfs:seeAlso <http://portal.g-node.org/odml/terminologies/v1.0/stimulus/stimulus.xml> .
468+
rdfs:seeAlso <https://terminologies.g-node.org/v1.0/stimulus/stimulus.xml> .
469469

470470

471471
### https://g-node.org/projects/odml-rdf#Subject
472472
:Subject rdf:type owl:Class ;
473473
rdfs:subClassOf :Section ;
474474
rdfs:comment "Description"^^xsd:string ;
475475
rdfs:label "Subject" ;
476-
rdfs:seeAlso <http://portal.g-node.org/odml/terminologies/v1.0/subject/subject.xml> .
476+
rdfs:seeAlso <https://terminologies.g-node.org/v1.0/subject/subject.xml> .
477477

478478

479479
### https://g-node.org/projects/odml-rdf#Terminology

‎doc/tutorial.rst‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -71,7 +71,7 @@ The code for the example odML files, which we use within this tutorial is part
7171
of the documentation package (see doc/example_odMLs/).
7272

7373
A summary of available odML terminologies and templates can be found `here
74-
<http://portal.g-node.org/odml/terminologies/v1.1/terminologies.xml>`_.
74+
<https://terminologies.g-node.org/v1.1/terminologies.xml>`_.
7575

7676
-------------------------------------------------------------------------------
7777

@@ -221,7 +221,7 @@ them to build your own metadata odML file will be described in later chapters.
221221
Further advanced functions you can use to navigate through your odML files, or to
222222
create an odML template file, or to make use of common odML terminologies
223223
provided via `the G-Node repository
224-
<http://portal.g-node.org/odml/terminologies/v1.1/terminologies.xml>`_ can also
224+
<https://terminologies.g-node.org/v1.1/terminologies.xml>`_ can also
225225
be found later on in this tutorial.
226226

227227
But now, let us first have a look at the example odML file (THGTTG.odml)!
@@ -289,7 +289,7 @@ Let's check out all attributes with the following commands::
289289
>>> print(odmlEX.parent)
290290
None
291291
>>> print(odmlEX.repository)
292-
http://portal.g-node.org/odml/terminologies/v1.1/terminologies.xml
292+
https://terminologies.g-node.org/v1.1/terminologies.xml
293293
>>> print(odmlEX.version)
294294
42
295295

‎docs/data_model.md‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -1,19 +1,19 @@
1-
# odml data model
1+
# The odML data model
22

3-
Data exchange requires that also annoations, metadata, are
4-
exchanged. In oder to allow interoperability we need both a common
3+
Data exchange requires that annotations, metadata, are also
4+
shared. In order to allow interoperability both a common
55
(meta) data model, the format in which the metadata are exchanged, and
6-
a common terminology.
6+
a common terminology are required.
77

88
Here, we briefly describe the *odML* data model. It is based on
99
the idea of key-value pairs like ``temperature = 26°C``.
1010

1111
The model is as simple as possible while being flexible, allowing
12-
interoperability, and being customizable. The model defines four
13-
entities (Property, Section, Value, RootSection) whose relations and
12+
interoperability, and being customizable. The model defines three
13+
entities (Property, Section, Document) whose relations and
1414
elements are shown in the figure below.
1515

16-
![odml_logo](images/erModel.png "odml data model")
16+
![odml_logo](images/erModel.png "odML data model")
1717

1818
Property and Section are the core entities. A Section contains
1919
Properties and can further have subsection thus building a tree-like

0 commit comments

Comments
 (0)