Skip to content

Commit be21cf8

Browse files
committed
update: computational module
1 parent 5ed5a42 commit be21cf8

5 files changed

Lines changed: 313 additions & 342 deletions

File tree

CQs/v_3_0/CQs.md

Lines changed: 6 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -74,13 +74,13 @@ SELECT ?project ?user WHERE {
7474
}
7575
```
7676

77-
**CQ2 — studies a researcher performed** (was `prov:wasAttributedTo`; now `ro:0002211` has agent)
77+
**CQ2 — studies a researcher performed**
7878
```sparql
7979
PREFIX core: <https://purls.helmholtz-metadaten.de/prima/core#>
8080
PREFIX ro: <http://purl.obolibrary.org/obo/RO_>
8181
8282
SELECT ?study ?user WHERE {
83-
?study a core:Study ; ro:0002211 ?user .
83+
?study a core:Study ; ro:0000057 ?user . #has participant
8484
?user a core:ResearchUser .
8585
}
8686
```
@@ -92,7 +92,7 @@ PREFIX ro: <http://purl.obolibrary.org/obo/RO_>
9292
9393
SELECT ?process ?user WHERE {
9494
VALUES ?type { core:DataAcquisition core:DataAnalysis }
95-
?process a ?type ; ro:0002211 ?user .
95+
?process a ?type ; ro:0000057 ?user .
9696
?user a core:ResearchUser .
9797
}
9898
```
@@ -155,7 +155,7 @@ SELECT ?study ?process ?processType WHERE {
155155
}
156156
```
157157

158-
**CQ9 — data used and produced in a data analysis / data processing** (was `pmd:input/output`)
158+
**CQ9 — data used and produced in a data analysis / data processing**
159159
```sparql
160160
PREFIX core: <https://purls.helmholtz-metadaten.de/prima/core#>
161161
PREFIX dal: <https://purls.helmholtz-metadaten.de/prima/dal#>
@@ -188,7 +188,7 @@ PREFIX ro: <http://purl.obolibrary.org/obo/RO_>
188188
189189
SELECT ?process ?user WHERE {
190190
VALUES ?type { core:DataAnalysis dal:DataProcessing }
191-
?process a ?type ; ro:0002211 ?user .
191+
?process a ?type ; ro:0000057 ?user .
192192
?user a core:ResearchUser .
193193
}
194194
```
@@ -298,7 +298,7 @@ PREFIX ro: <http://purl.obolibrary.org/obo/RO_>
298298
299299
SELECT ?process ?user WHERE {
300300
VALUES ?type { exp:Measurement exp:ProcessingAndTreatment }
301-
?process a ?type ; ro:0002211 ?user .
301+
?process a ?type ; ro:0000057 ?user .
302302
?user a core:ResearchUser .
303303
}
304304
```
@@ -382,17 +382,3 @@ SELECT ?prep ?model ?input WHERE {
382382
```
383383

384384
---
385-
386-
## Gaps surfaced (v2 CQ concepts without a v3 class/property yet)
387-
388-
Resolve during the rewrite (reformulate or extend the ontology):
389-
390-
- **DataAnalysisLifecycle aggregator** (v2 CQ5–8, 12): v3 has `core:DataAnalysis` and
391-
`dal:DataProcessing` but **no `DataAnalysisLifecycle` class** linking them — CQs reformulated
392-
around the individual processes / `core:Study`.
393-
- **DataInterpretation** (v2 CQ8–12): class removed in v3 — dropped from the CQs.
394-
- **Project-level attribution** (CQ12): `prov:wasAttributedTo` ranges over `core:ResearchUser` only.
395-
- **Data derivation** (v2 "which dataset was the publication data derived from"): v3 has no
396-
`prov:wasDerivedFrom`; only `dcterms:references` / `dcterms:hasPart`. Consider re-introducing a
397-
derivation property for the lineage facet.
398-
- **When** (CQ20): `prov:startedAtTime`/`endedAtTime` declared but not attached to processes.

PRIMA/computational/ver_3_0/index.html

Lines changed: 31 additions & 39 deletions
Original file line numberDiff line numberDiff line change
@@ -459,14 +459,14 @@ <h3>Calculation
459459
<span>
460460
<span>
461461
<span>
462-
<a href="http://purl.obolibrary.org/obo/RO_0002233">has input</a>
462+
<a href="http://purl.obolibrary.org/obo/RO_0002234">has output</a>
463463
<sup class="sup-op" title="OWL Object Property">op</sup>
464464
</span>
465465
<span>
466466
<span class="cardinality">some</span>
467467
<span>
468468
<span>
469-
<a href="#Model">Model</a>
469+
<a href="https://purls.helmholtz-metadaten.de/prima/dataset#RawData">https://purls.helmholtz-metadaten.de/prima/dataset#RawData</a>
470470
<sup class="sup-c" title="OWL/RDFS Class">c</sup>
471471
</span>
472472
</span>
@@ -478,14 +478,14 @@ <h3>Calculation
478478
<span>
479479
<span>
480480
<span>
481-
<a href="http://purl.obolibrary.org/obo/RO_0002234">has output</a>
481+
<a href="https://purls.helmholtz-metadaten.de/prima/core#hasSetting">core:hasSetting</a>
482482
<sup class="sup-op" title="OWL Object Property">op</sup>
483483
</span>
484484
<span>
485485
<span class="cardinality">some</span>
486486
<span>
487487
<span>
488-
<a href="https://purls.helmholtz-metadaten.de/prima/dataset#RawData">https://purls.helmholtz-metadaten.de/prima/dataset#RawData</a>
488+
<a href="https://purls.helmholtz-metadaten.de/prima/core#Settings">core:Settings</a>
489489
<sup class="sup-c" title="OWL/RDFS Class">c</sup>
490490
</span>
491491
</span>
@@ -497,14 +497,14 @@ <h3>Calculation
497497
<span>
498498
<span>
499499
<span>
500-
<a href="https://purls.helmholtz-metadaten.de/prima/core#hasSetting">core:hasSetting</a>
500+
<a href="http://purl.obolibrary.org/obo/RO_0002233">has input</a>
501501
<sup class="sup-op" title="OWL Object Property">op</sup>
502502
</span>
503503
<span>
504504
<span class="cardinality">some</span>
505505
<span>
506506
<span>
507-
<a href="https://purls.helmholtz-metadaten.de/prima/core#Settings">core:Settings</a>
507+
<a href="https://purls.helmholtz-metadaten.de/prima/core#ResearchData">core:ResearchData</a>
508508
<sup class="sup-c" title="OWL/RDFS Class">c</sup>
509509
</span>
510510
</span>
@@ -523,7 +523,7 @@ <h3>Calculation
523523
<span class="cardinality">some</span>
524524
<span>
525525
<span>
526-
<a href="https://purls.helmholtz-metadaten.de/prima/core#ResearchData">core:ResearchData</a>
526+
<a href="#Model">Model</a>
527527
<sup class="sup-c" title="OWL/RDFS Class">c</sup>
528528
</span>
529529
</span>
@@ -579,14 +579,14 @@ <h3>Model Preparation
579579
<span>
580580
<span>
581581
<span>
582-
<a href="http://www.w3.org/ns/prov#atLocation">atLocation</a>
582+
<a href="http://purl.obolibrary.org/obo/RO_0002233">has input</a>
583583
<sup class="sup-op" title="OWL Object Property">op</sup>
584584
</span>
585585
<span>
586586
<span class="cardinality">some</span>
587587
<span>
588588
<span>
589-
<a href="https://purls.helmholtz-metadaten.de/prima/experiment#Laboratory">https://purls.helmholtz-metadaten.de/prima/experiment#Laboratory</a>
589+
<a href="https://purls.helmholtz-metadaten.de/prima/core#ResearchData">core:ResearchData</a>
590590
<sup class="sup-c" title="OWL/RDFS Class">c</sup>
591591
</span>
592592
</span>
@@ -598,14 +598,14 @@ <h3>Model Preparation
598598
<span>
599599
<span>
600600
<span>
601-
<a href="http://purl.obolibrary.org/obo/RO_0000057">has participant</a>
601+
<a href="http://www.w3.org/ns/prov#atLocation">atLocation</a>
602602
<sup class="sup-op" title="OWL Object Property">op</sup>
603603
</span>
604604
<span>
605605
<span class="cardinality">some</span>
606606
<span>
607607
<span>
608-
<a href="https://purls.helmholtz-metadaten.de/prima/core#ResearchUser">core:ResearchUser</a>
608+
<a href="https://purls.helmholtz-metadaten.de/prima/experiment#Laboratory">https://purls.helmholtz-metadaten.de/prima/experiment#Laboratory</a>
609609
<sup class="sup-c" title="OWL/RDFS Class">c</sup>
610610
</span>
611611
</span>
@@ -617,14 +617,14 @@ <h3>Model Preparation
617617
<span>
618618
<span>
619619
<span>
620-
<a href="https://purls.helmholtz-metadaten.de/prima/core#hasTechnique">core:hasTechnique</a>
620+
<a href="http://purl.obolibrary.org/obo/RO_0002234">has output</a>
621621
<sup class="sup-op" title="OWL Object Property">op</sup>
622622
</span>
623623
<span>
624624
<span class="cardinality">some</span>
625625
<span>
626626
<span>
627-
<a href="https://purls.helmholtz-metadaten.de/prima/core#Technique">core:Technique</a>
627+
<a href="#Model">Model</a>
628628
<sup class="sup-c" title="OWL/RDFS Class">c</sup>
629629
</span>
630630
</span>
@@ -636,14 +636,14 @@ <h3>Model Preparation
636636
<span>
637637
<span>
638638
<span>
639-
<a href="https://purls.helmholtz-metadaten.de/prima/core#usesEquipment">core:usesEquipment</a>
639+
<a href="http://purl.obolibrary.org/obo/RO_0000057">has participant</a>
640640
<sup class="sup-op" title="OWL Object Property">op</sup>
641641
</span>
642642
<span>
643643
<span class="cardinality">some</span>
644644
<span>
645645
<span>
646-
<a href="https://purls.helmholtz-metadaten.de/prima/core#Equipment">core:Equipment</a>
646+
<a href="https://purls.helmholtz-metadaten.de/prima/core#ResearchUser">core:ResearchUser</a>
647647
<sup class="sup-c" title="OWL/RDFS Class">c</sup>
648648
</span>
649649
</span>
@@ -655,14 +655,14 @@ <h3>Model Preparation
655655
<span>
656656
<span>
657657
<span>
658-
<a href="https://purls.helmholtz-metadaten.de/prima/core#usesResearchSoftware">core:usesResearchSoftware</a>
658+
<a href="https://purls.helmholtz-metadaten.de/prima/core#hasTechnique">core:hasTechnique</a>
659659
<sup class="sup-op" title="OWL Object Property">op</sup>
660660
</span>
661661
<span>
662662
<span class="cardinality">some</span>
663663
<span>
664664
<span>
665-
<a href="https://purls.helmholtz-metadaten.de/prima/core#ResearchSoftware">core:ResearchSoftware</a>
665+
<a href="https://purls.helmholtz-metadaten.de/prima/core#Technique">core:Technique</a>
666666
<sup class="sup-c" title="OWL/RDFS Class">c</sup>
667667
</span>
668668
</span>
@@ -674,14 +674,14 @@ <h3>Model Preparation
674674
<span>
675675
<span>
676676
<span>
677-
<a href="http://purl.obolibrary.org/obo/RO_0002233">has input</a>
677+
<a href="https://purls.helmholtz-metadaten.de/prima/core#usesEquipment">core:usesEquipment</a>
678678
<sup class="sup-op" title="OWL Object Property">op</sup>
679679
</span>
680680
<span>
681681
<span class="cardinality">some</span>
682682
<span>
683683
<span>
684-
<a href="https://purls.helmholtz-metadaten.de/prima/core#ResearchData">core:ResearchData</a>
684+
<a href="https://purls.helmholtz-metadaten.de/prima/core#Equipment">core:Equipment</a>
685685
<sup class="sup-c" title="OWL/RDFS Class">c</sup>
686686
</span>
687687
</span>
@@ -693,14 +693,14 @@ <h3>Model Preparation
693693
<span>
694694
<span>
695695
<span>
696-
<a href="http://purl.obolibrary.org/obo/RO_0002234">has output</a>
696+
<a href="https://purls.helmholtz-metadaten.de/prima/core#usesResearchSoftware">core:usesResearchSoftware</a>
697697
<sup class="sup-op" title="OWL Object Property">op</sup>
698698
</span>
699699
<span>
700700
<span class="cardinality">some</span>
701701
<span>
702702
<span>
703-
<a href="#Model">Model</a>
703+
<a href="https://purls.helmholtz-metadaten.de/prima/core#ResearchSoftware">core:ResearchSoftware</a>
704704
<sup class="sup-c" title="OWL/RDFS Class">c</sup>
705705
</span>
706706
</span>
@@ -756,14 +756,6 @@ <h3>Simulation
756756
</ul>
757757
</td>
758758
</tr>
759-
<tr>
760-
<th>
761-
<a class="hover_property" href="http://www.w3.org/2002/07/owl#equivalentClass" title="The property that determines that two given classes are equivalent, and that is used to specify datatype definitions. Defined in The OWL 2 Schema vocabulary (OWL 2)">Equivalentclass</a>
762-
</th>
763-
<td>
764-
<a href="https://w3id.org/pmd/co/PMD_0000933">pmd:PMD_0000933</a>
765-
</td>
766-
</tr>
767759
<tr>
768760
<th>
769761
<a class="hover_property" href="https://w3id.org/profile/ontdoc/restriction" title="Convenience property for things that subclass owl:Restriction. Defined in Ontology Documentation Profile">Restriction</a>
@@ -774,14 +766,14 @@ <h3>Simulation
774766
<span>
775767
<span>
776768
<span>
777-
<a href="http://purl.obolibrary.org/obo/RO_0002233">has input</a>
769+
<a href="http://purl.obolibrary.org/obo/RO_0002234">has output</a>
778770
<sup class="sup-op" title="OWL Object Property">op</sup>
779771
</span>
780772
<span>
781773
<span class="cardinality">some</span>
782774
<span>
783775
<span>
784-
<a href="https://purls.helmholtz-metadaten.de/prima/core#ResearchData">core:ResearchData</a>
776+
<a href="#Model">Model</a>
785777
<sup class="sup-c" title="OWL/RDFS Class">c</sup>
786778
</span>
787779
</span>
@@ -793,14 +785,14 @@ <h3>Simulation
793785
<span>
794786
<span>
795787
<span>
796-
<a href="http://purl.obolibrary.org/obo/RO_0002234">has output</a>
788+
<a href="https://purls.helmholtz-metadaten.de/prima/core#hasSetting">core:hasSetting</a>
797789
<sup class="sup-op" title="OWL Object Property">op</sup>
798790
</span>
799791
<span>
800792
<span class="cardinality">some</span>
801793
<span>
802794
<span>
803-
<a href="#Model">Model</a>
795+
<a href="https://purls.helmholtz-metadaten.de/prima/core#Settings">core:Settings</a>
804796
<sup class="sup-c" title="OWL/RDFS Class">c</sup>
805797
</span>
806798
</span>
@@ -831,14 +823,14 @@ <h3>Simulation
831823
<span>
832824
<span>
833825
<span>
834-
<a href="http://purl.obolibrary.org/obo/RO_0002234">has output</a>
826+
<a href="http://purl.obolibrary.org/obo/RO_0002233">has input</a>
835827
<sup class="sup-op" title="OWL Object Property">op</sup>
836828
</span>
837829
<span>
838830
<span class="cardinality">some</span>
839831
<span>
840832
<span>
841-
<a href="https://purls.helmholtz-metadaten.de/prima/dataset#RawData">https://purls.helmholtz-metadaten.de/prima/dataset#RawData</a>
833+
<a href="#Model">Model</a>
842834
<sup class="sup-c" title="OWL/RDFS Class">c</sup>
843835
</span>
844836
</span>
@@ -850,14 +842,14 @@ <h3>Simulation
850842
<span>
851843
<span>
852844
<span>
853-
<a href="http://purl.obolibrary.org/obo/RO_0002233">has input</a>
845+
<a href="http://purl.obolibrary.org/obo/RO_0002234">has output</a>
854846
<sup class="sup-op" title="OWL Object Property">op</sup>
855847
</span>
856848
<span>
857849
<span class="cardinality">some</span>
858850
<span>
859851
<span>
860-
<a href="#Model">Model</a>
852+
<a href="https://purls.helmholtz-metadaten.de/prima/dataset#RawData">https://purls.helmholtz-metadaten.de/prima/dataset#RawData</a>
861853
<sup class="sup-c" title="OWL/RDFS Class">c</sup>
862854
</span>
863855
</span>
@@ -869,14 +861,14 @@ <h3>Simulation
869861
<span>
870862
<span>
871863
<span>
872-
<a href="https://purls.helmholtz-metadaten.de/prima/core#hasSetting">core:hasSetting</a>
864+
<a href="http://purl.obolibrary.org/obo/RO_0002233">has input</a>
873865
<sup class="sup-op" title="OWL Object Property">op</sup>
874866
</span>
875867
<span>
876868
<span class="cardinality">some</span>
877869
<span>
878870
<span>
879-
<a href="https://purls.helmholtz-metadaten.de/prima/core#Settings">core:Settings</a>
871+
<a href="https://purls.helmholtz-metadaten.de/prima/core#ResearchData">core:ResearchData</a>
880872
<sup class="sup-c" title="OWL/RDFS Class">c</sup>
881873
</span>
882874
</span>

0 commit comments

Comments
 (0)