From e0d0fd06d5211bfe59626f6ea86c6255caf825d3 Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Tue, 18 Jun 2024 13:36:33 +0100 Subject: [PATCH 1/7] Add NSForest marker sets Marker sets cannot be visualized yet, probably because they don't have a valid parent term. --- src/patterns/data/default/NSForestMarkers.tsv | 8 +++ src/patterns/definitions.owl | 61 ++++++++++++++++++- .../dosdp-patterns/NSForestMarkers.yaml | 57 +++++++++++++++++ src/patterns/pattern.owl | 12 ++++ 4 files changed, 136 insertions(+), 2 deletions(-) create mode 100644 src/patterns/data/default/NSForestMarkers.tsv create mode 100644 src/patterns/dosdp-patterns/NSForestMarkers.yaml diff --git a/src/patterns/data/default/NSForestMarkers.tsv b/src/patterns/data/default/NSForestMarkers.tsv new file mode 100644 index 000000000..084210d17 --- /dev/null +++ b/src/patterns/data/default/NSForestMarkers.tsv @@ -0,0 +1,8 @@ +defined_class Marker_set_of Minimal_markers Minimal_markers_label Organ Species_abbv Organ_region Parent FBeta_confidence_score +http://purl.obolibrary.org/obo/CL_4037001 Adventitial fibroblasts entrez:286133|entrez:57124 "['SCARA5', 'CD248']" Lung Human UBERON:0002048 SO:0001260 0.85 +http://purl.obolibrary.org/obo/CL_4037002 Alveolar fibroblasts entrez:8639|entrez:4060 "['AOC3', 'LUM']" Lung Human UBERON:0002048 SO:0001260 0.70 +http://purl.obolibrary.org/obo/CL_4037003 Alveolar macrophages "['MSR1', 'FABP4']" Lung Human UBERON:0002048 SO:0001260 0.80 +http://purl.obolibrary.org/obo/CL_4037004 Alveolar Mph CCL3+ "['TNIP3', 'CXCL5']" Lung Human UBERON:0002048 SO:0001260 0.67 +http://purl.obolibrary.org/obo/CL_4037005 Alveolar Mph MT-positive "['HMOX1', 'HPGD']" Lung Human UBERON:0002048 SO:0001260 0.41 +http://purl.obolibrary.org/obo/CL_4037006 Alveolar Mph proliferating "['PCLAF', 'RRM2', 'UBE2C', 'NUSAP1']" Lung Human UBERON:0002048 SO:0001260 0.26 + \ No newline at end of file diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl index 046777e53..f866be4f7 100644 --- a/src/patterns/definitions.owl +++ b/src/patterns/definitions.owl @@ -7,9 +7,66 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-02-13") + +Annotation(owl:versionInfo "2024-06-18") +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(ObjectProperty()) +Declaration(AnnotationProperty()) + + + +############################ +# Classes +############################ + +# Class: (NS forest marker set of Adventitial fibroblasts (Human Lung).) + +AnnotationAssertion( "0.85") +AnnotationAssertion(rdfs:label "NS forest marker set of Adventitial fibroblasts (Human Lung).") +SubClassOf( ) +SubClassOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + +# Class: (NS forest marker set of Alveolar fibroblasts (Human Lung).) + +AnnotationAssertion( "0.70") +AnnotationAssertion(rdfs:label "NS forest marker set of Alveolar fibroblasts (Human Lung).") +SubClassOf( ) +SubClassOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + +# Class: (NS forest marker set of Alveolar macrophages (Human Lung).) + +AnnotationAssertion( "0.80") +AnnotationAssertion(rdfs:label "NS forest marker set of Alveolar macrophages (Human Lung).") +SubClassOf( ) + +# Class: (NS forest marker set of Alveolar Mph CCL3+ (Human Lung).) + +AnnotationAssertion( "0.67") +AnnotationAssertion(rdfs:label "NS forest marker set of Alveolar Mph CCL3+ (Human Lung).") +SubClassOf( ) + +# Class: (NS forest marker set of Alveolar Mph MT-positive (Human Lung).) + +AnnotationAssertion( "0.41") +AnnotationAssertion(rdfs:label "NS forest marker set of Alveolar Mph MT-positive (Human Lung).") +SubClassOf( ) + +# Class: (NS forest marker set of Alveolar Mph proliferating (Human Lung).) + +AnnotationAssertion( "0.26") +AnnotationAssertion(rdfs:label "NS forest marker set of Alveolar Mph proliferating (Human Lung).") +SubClassOf( ) ) \ No newline at end of file diff --git a/src/patterns/dosdp-patterns/NSForestMarkers.yaml b/src/patterns/dosdp-patterns/NSForestMarkers.yaml new file mode 100644 index 000000000..e4a3c9459 --- /dev/null +++ b/src/patterns/dosdp-patterns/NSForestMarkers.yaml @@ -0,0 +1,57 @@ +pattern_name: NSForestMarkers +pattern_iri: http://purl.obolibrary.org/obo/cl/NSForestMarkers.yaml +description: "Characterizing marker sets template for cell terms." + +classes: + "thing": "owl:Thing" + "sequence_feature": "SO:0000110" + +relations: + has_part: "BFO:0000051" +# has_anatomical_context: "PCL:0010063" + +vars: + Organ_region: "'regional part of brain'" + Parent: "'thing'" + +list_vars: + Minimal_markers: "'sequence_feature'" + +data_vars: + Marker_set_of: "xsd:string" + Organ: "xsd:string" + Species_abbv: "xsd:string" + FBeta_confidence_score: "xsd:double" + +annotationProperties: + fbetaConfidenceScore: "PCL:0010062" + +name: + text: "NS forest marker set of %s (%s %s)." + vars: + - Marker_set_of + - Species_abbv + - Organ + +logical_axioms: + - axiom_type: subClassOf + multi_clause: + sep: " and " + clauses: + - text: "'has_part' some %s" + vars: + - Minimal_markers + - axiom_type: subClassOf + text: "%s" + vars: + - Parent +# - axiom_type: subClassOf +# text: "'has_anatomical_context' some %s" +# vars: +# - Brain_region + +annotations: + - annotationProperty: fbetaConfidenceScore + text: "%s" + vars: + - FBeta_confidence_score \ No newline at end of file diff --git a/src/patterns/pattern.owl b/src/patterns/pattern.owl index 917125176..4aa3837b0 100644 --- a/src/patterns/pattern.owl +++ b/src/patterns/pattern.owl @@ -14,18 +14,22 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -36,6 +40,14 @@ Declaration(AnnotationProperty( (NS forest marker set of xsd:string (xsd:string xsd:string).) + +AnnotationAssertion( "xsd:double"^^xsd:string) +AnnotationAssertion( "NSForestMarkers"^^xsd:string) +AnnotationAssertion(rdfs:label "NS forest marker set of xsd:string (xsd:string xsd:string)."^^xsd:string) +SubClassOf( owl:Thing) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: ('quality' 'cell') AnnotationAssertion( "Any 'cell' that is 'quality'"^^xsd:string) From d14f6c707a88a5860bb307111ed576beb4f05bc4 Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Tue, 18 Jun 2024 14:55:27 +0100 Subject: [PATCH 2/7] Add missing genes --- src/patterns/data/default/NSForestMarkers.tsv | 8 ++++---- src/patterns/definitions.owl | 14 ++++++++++++++ 2 files changed, 18 insertions(+), 4 deletions(-) diff --git a/src/patterns/data/default/NSForestMarkers.tsv b/src/patterns/data/default/NSForestMarkers.tsv index 084210d17..559de0682 100644 --- a/src/patterns/data/default/NSForestMarkers.tsv +++ b/src/patterns/data/default/NSForestMarkers.tsv @@ -1,8 +1,8 @@ defined_class Marker_set_of Minimal_markers Minimal_markers_label Organ Species_abbv Organ_region Parent FBeta_confidence_score http://purl.obolibrary.org/obo/CL_4037001 Adventitial fibroblasts entrez:286133|entrez:57124 "['SCARA5', 'CD248']" Lung Human UBERON:0002048 SO:0001260 0.85 http://purl.obolibrary.org/obo/CL_4037002 Alveolar fibroblasts entrez:8639|entrez:4060 "['AOC3', 'LUM']" Lung Human UBERON:0002048 SO:0001260 0.70 -http://purl.obolibrary.org/obo/CL_4037003 Alveolar macrophages "['MSR1', 'FABP4']" Lung Human UBERON:0002048 SO:0001260 0.80 -http://purl.obolibrary.org/obo/CL_4037004 Alveolar Mph CCL3+ "['TNIP3', 'CXCL5']" Lung Human UBERON:0002048 SO:0001260 0.67 -http://purl.obolibrary.org/obo/CL_4037005 Alveolar Mph MT-positive "['HMOX1', 'HPGD']" Lung Human UBERON:0002048 SO:0001260 0.41 -http://purl.obolibrary.org/obo/CL_4037006 Alveolar Mph proliferating "['PCLAF', 'RRM2', 'UBE2C', 'NUSAP1']" Lung Human UBERON:0002048 SO:0001260 0.26 +http://purl.obolibrary.org/obo/CL_4037003 Alveolar macrophages entrez:4481|entrez:2168 "['MSR1', 'FABP4']" Lung Human UBERON:0002048 SO:0001260 0.80 +http://purl.obolibrary.org/obo/CL_4037004 Alveolar Mph CCL3+ entrez:79931|entrez:6374 "['TNIP3', 'CXCL5']" Lung Human UBERON:0002048 SO:0001260 0.67 +http://purl.obolibrary.org/obo/CL_4037005 Alveolar Mph MT-positive entrez:3162|entrez:3248 "['HMOX1', 'HPGD']" Lung Human UBERON:0002048 SO:0001260 0.41 +http://purl.obolibrary.org/obo/CL_4037006 Alveolar Mph proliferating entrez:9768|entrez:6241|entrez:11065|entrez:51203 "['PCLAF', 'RRM2', 'UBE2C', 'NUSAP1']" Lung Human UBERON:0002048 SO:0001260 0.26 \ No newline at end of file diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl index f866be4f7..fea63ba4f 100644 --- a/src/patterns/definitions.owl +++ b/src/patterns/definitions.owl @@ -17,10 +17,20 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(ObjectProperty()) Declaration(AnnotationProperty()) @@ -49,24 +59,28 @@ SubClassOf( ObjectIntersectionOf(Obje AnnotationAssertion( "0.80") AnnotationAssertion(rdfs:label "NS forest marker set of Alveolar macrophages (Human Lung).") SubClassOf( ) +SubClassOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (NS forest marker set of Alveolar Mph CCL3+ (Human Lung).) AnnotationAssertion( "0.67") AnnotationAssertion(rdfs:label "NS forest marker set of Alveolar Mph CCL3+ (Human Lung).") SubClassOf( ) +SubClassOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (NS forest marker set of Alveolar Mph MT-positive (Human Lung).) AnnotationAssertion( "0.41") AnnotationAssertion(rdfs:label "NS forest marker set of Alveolar Mph MT-positive (Human Lung).") SubClassOf( ) +SubClassOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (NS forest marker set of Alveolar Mph proliferating (Human Lung).) AnnotationAssertion( "0.26") AnnotationAssertion(rdfs:label "NS forest marker set of Alveolar Mph proliferating (Human Lung).") SubClassOf( ) +SubClassOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) ) \ No newline at end of file From e1ae63d853f6be12980687a35ad7b627b77a7ab0 Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Tue, 18 Jun 2024 15:39:28 +0100 Subject: [PATCH 3/7] Change purl to ID in tsv file --- src/patterns/data/default/NSForestMarkers.tsv | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/src/patterns/data/default/NSForestMarkers.tsv b/src/patterns/data/default/NSForestMarkers.tsv index 559de0682..8015dfbae 100644 --- a/src/patterns/data/default/NSForestMarkers.tsv +++ b/src/patterns/data/default/NSForestMarkers.tsv @@ -1,8 +1,7 @@ defined_class Marker_set_of Minimal_markers Minimal_markers_label Organ Species_abbv Organ_region Parent FBeta_confidence_score -http://purl.obolibrary.org/obo/CL_4037001 Adventitial fibroblasts entrez:286133|entrez:57124 "['SCARA5', 'CD248']" Lung Human UBERON:0002048 SO:0001260 0.85 -http://purl.obolibrary.org/obo/CL_4037002 Alveolar fibroblasts entrez:8639|entrez:4060 "['AOC3', 'LUM']" Lung Human UBERON:0002048 SO:0001260 0.70 -http://purl.obolibrary.org/obo/CL_4037003 Alveolar macrophages entrez:4481|entrez:2168 "['MSR1', 'FABP4']" Lung Human UBERON:0002048 SO:0001260 0.80 -http://purl.obolibrary.org/obo/CL_4037004 Alveolar Mph CCL3+ entrez:79931|entrez:6374 "['TNIP3', 'CXCL5']" Lung Human UBERON:0002048 SO:0001260 0.67 -http://purl.obolibrary.org/obo/CL_4037005 Alveolar Mph MT-positive entrez:3162|entrez:3248 "['HMOX1', 'HPGD']" Lung Human UBERON:0002048 SO:0001260 0.41 -http://purl.obolibrary.org/obo/CL_4037006 Alveolar Mph proliferating entrez:9768|entrez:6241|entrez:11065|entrez:51203 "['PCLAF', 'RRM2', 'UBE2C', 'NUSAP1']" Lung Human UBERON:0002048 SO:0001260 0.26 - \ No newline at end of file +CL:4037001 Adventitial fibroblasts entrez:286133|entrez:57124 "['SCARA5', 'CD248']" Lung Human UBERON:0002048 SO:0001260 0.85 +CL:4037002 Alveolar fibroblasts entrez:8639|entrez:4060 "['AOC3', 'LUM']" Lung Human UBERON:0002048 SO:0001260 0.7 +CL:4037003 Alveolar macrophages entrez:4481|entrez:2168 "['MSR1', 'FABP4']" Lung Human UBERON:0002048 SO:0001260 0.8 +CL:4037004 Alveolar Mph CCL3+ entrez:79931|entrez:6374 "['TNIP3', 'CXCL5']" Lung Human UBERON:0002048 SO:0001260 0.67 +CL:4037005 Alveolar Mph MT-positive entrez:3162|entrez:3248 "['HMOX1', 'HPGD']" Lung Human UBERON:0002048 SO:0001260 0.41 +CL:4037006 Alveolar Mph proliferating entrez:9768|entrez:6241|entrez:11065|entrez:51203 "['PCLAF', 'RRM2', 'UBE2C', 'NUSAP1']" Lung Human UBERON:0002048 SO:0001260 0.26 \ No newline at end of file From 1ca1785ba6dd2cec68cf3ba3f4261bf6a3cfe62b Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Wed, 19 Jun 2024 11:10:14 +0100 Subject: [PATCH 4/7] Update catalog and import definitions to cl-edit.owl --- src/ontology/catalog-v001.xml | 3 ++- src/ontology/cl-edit.owl | 1 + 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml index 67df007a1..233d85e83 100644 --- a/src/ontology/catalog-v001.xml +++ b/src/ontology/catalog-v001.xml @@ -13,7 +13,8 @@ - + + diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index f5a4d592c..8615fa595 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -30,6 +30,7 @@ Import() Import() Import() Import() +Import() Annotation(obo:IAO_0000700 obo:CL_0000000) Annotation(dc:description "An ontology of cell types.") Annotation(dc:title "Cell Ontology") From 293f5fc0e140054c4b43409306673b048442598c Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Mon, 15 Jul 2024 14:43:37 +0100 Subject: [PATCH 5/7] Markers to cells DOSDP --- src/patterns/data/default/MarkersToCells.tsv | 6 +++ .../dosdp-patterns/MarkersToCells.yaml | 44 +++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 src/patterns/data/default/MarkersToCells.tsv create mode 100644 src/patterns/dosdp-patterns/MarkersToCells.yaml diff --git a/src/patterns/data/default/MarkersToCells.tsv b/src/patterns/data/default/MarkersToCells.tsv new file mode 100644 index 000000000..ed56037ab --- /dev/null +++ b/src/patterns/data/default/MarkersToCells.tsv @@ -0,0 +1,6 @@ +defined_class Cell_type Minimal_markers_label Organ Species_abbv species FBeta_confidence_score +CL:4028006 alveolar type 2 fibroblast cell "SCARA5, CD248" Lung Human NCBITaxon:9606 0.85 +CL:4028004 alveolar type 1 fibroblast cell "AOC3, LUM" Lung Human NCBITaxon:9606 0.7 +CL:0000583 alveolar macrophage "MSR1, FABP4" Lung Human NCBITaxon:9606 0.8 +CL:4033041 CCL3-positive alveolar macrophage "TNIP3, CXCL5" Lung Human NCBITaxon:9606 0.67 +CL:4033042 metallothionein-positive alveolar macrophage "HMOX1, HPGD" Lung Human NCBITaxon:9606 0.41 \ No newline at end of file diff --git a/src/patterns/dosdp-patterns/MarkersToCells.yaml b/src/patterns/dosdp-patterns/MarkersToCells.yaml new file mode 100644 index 000000000..75f8cc6ed --- /dev/null +++ b/src/patterns/dosdp-patterns/MarkersToCells.yaml @@ -0,0 +1,44 @@ +pattern_name: NSForestMarkers +pattern_iri: http://purl.obolibrary.org/obo/cl/MarkersToCells.yaml +description: "Adds marker sets to cell types logically and documentation" + +classes: + "thing": "owl:Thing" + "Metazoa": "NCBITaxon:33208" + +relations: + has part: "BFO:0000051" + has characterizing marker set: "RO:0015004" + present in taxon: "RO:0002175" + +vars: + species: "'Metazoa'" + has_characterization_set: "'thing'" + +data_vars: + Marker_set_xref: "xsd:string" + Organ: "xsd:string" + Species_abbv: "xsd:string" + FBeta_confidence_score: "xsd:string" + Cell_type: "xsd:string" + Marker_set: "xsd:string" + +data_list_vars + Marker_set: "xsd:string" + +logical axioms: + - axiom_type: subClassOf + text: "('present in taxon' some %s) and ('has characterizing marker set' some %s)" + vars: + - species + - has_characterization_set + +comment: + text: "A %s in the %s %s has the gene markers %s with a NS-Forest FBeta value of %s." + vars: + - Cell_type + - Species_abbv + - Organ + - Marker_set + - FBeta_confidence_score + xrefs: Marker_set_xref \ No newline at end of file From 8c28f4a41efe3e4226b31443a0694bf0aacffc88 Mon Sep 17 00:00:00 2001 From: David Osumi-Sutherland Date: Tue, 23 Jul 2024 13:38:14 +0100 Subject: [PATCH 6/7] Update MarkersToCells.yaml Fixed YAML syntax error --- src/patterns/dosdp-patterns/MarkersToCells.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/patterns/dosdp-patterns/MarkersToCells.yaml b/src/patterns/dosdp-patterns/MarkersToCells.yaml index 75f8cc6ed..38fe84c4b 100644 --- a/src/patterns/dosdp-patterns/MarkersToCells.yaml +++ b/src/patterns/dosdp-patterns/MarkersToCells.yaml @@ -23,7 +23,7 @@ data_vars: Cell_type: "xsd:string" Marker_set: "xsd:string" -data_list_vars +data_list_vars: Marker_set: "xsd:string" logical axioms: @@ -41,4 +41,4 @@ comment: - Organ - Marker_set - FBeta_confidence_score - xrefs: Marker_set_xref \ No newline at end of file + xrefs: Marker_set_xref From ec300d151112c4af32d02b71371b037b5a167c9e Mon Sep 17 00:00:00 2001 From: David Osumi-Sutherland Date: Tue, 23 Jul 2024 13:52:01 +0100 Subject: [PATCH 7/7] Update MarkersToCells.yaml Fixing dosdp schema fail --- src/patterns/dosdp-patterns/MarkersToCells.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/patterns/dosdp-patterns/MarkersToCells.yaml b/src/patterns/dosdp-patterns/MarkersToCells.yaml index 38fe84c4b..3a03f7571 100644 --- a/src/patterns/dosdp-patterns/MarkersToCells.yaml +++ b/src/patterns/dosdp-patterns/MarkersToCells.yaml @@ -26,7 +26,7 @@ data_vars: data_list_vars: Marker_set: "xsd:string" -logical axioms: +logical_axioms: - axiom_type: subClassOf text: "('present in taxon' some %s) and ('has characterizing marker set' some %s)" vars: