2397 ns forest markers #2439
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| Original file line number | Diff line number | Diff line change |
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| 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 |
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| Original file line number | Diff line number | Diff line change |
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| defined_class Marker_set_of Minimal_markers Minimal_markers_label Organ Species_abbv Organ_region Parent FBeta_confidence_score | ||
| 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 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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" | ||
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| classes: | ||
| "thing": "owl:Thing" | ||
| "Metazoa": "NCBITaxon:33208" | ||
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| relations: | ||
| has part: "BFO:0000051" | ||
| has characterizing marker set: "RO:0015004" | ||
| present in taxon: "RO:0002175" | ||
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| vars: | ||
| species: "'Metazoa'" | ||
| has_characterization_set: "'thing'" | ||
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| 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" | ||
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| data_list_vars: | ||
| Marker_set: "xsd:string" | ||
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| logical_axioms: | ||
| - axiom_type: subClassOf | ||
| text: "('present in taxon' some %s) and ('has characterizing marker set' some %s)" | ||
| vars: | ||
| - species | ||
| - has_characterization_set | ||
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| 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 | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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." | ||
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| classes: | ||
| "thing": "owl:Thing" | ||
| "sequence_feature": "SO:0000110" | ||
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| relations: | ||
| has_part: "BFO:0000051" | ||
| # has_anatomical_context: "PCL:0010063" | ||
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| vars: | ||
| Organ_region: "'regional part of brain'" | ||
| Parent: "'thing'" | ||
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| list_vars: | ||
| Minimal_markers: "'sequence_feature'" | ||
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| data_vars: | ||
| Marker_set_of: "xsd:string" | ||
| Organ: "xsd:string" | ||
| Species_abbv: "xsd:string" | ||
| FBeta_confidence_score: "xsd:double" | ||
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| annotationProperties: | ||
| fbetaConfidenceScore: "PCL:0010062" | ||
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There was a problem hiding this comment. Recently STATO added a new term for F Beta Score ISA-tools/stato#86 (comment). Should we use STATO:0000663(F-beta score) instead of |
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| name: | ||
| text: "NS forest marker set of %s (%s %s)." | ||
| vars: | ||
| - Marker_set_of | ||
| - Species_abbv | ||
| - Organ | ||
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| logical_axioms: | ||
| - axiom_type: subClassOf | ||
| multi_clause: | ||
| sep: " and " | ||
| clauses: | ||
| - text: "'has_part' some %s" | ||
| vars: | ||
| - Minimal_markers | ||
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There was a problem hiding this comment. Now the marker urls are generated like To do this we need to override the make file rules that run There was a problem hiding this comment. We will also need an import file for these to get labels. (I think we had ensembl & NCBI for BDSO). I'm wondering whether, longer term, a more sustainable approach would be to have a separate repo for generating marker objects and make imports from that to the KG and CL. |
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| - axiom_type: subClassOf | ||
| text: "%s" | ||
| vars: | ||
| - Parent | ||
| # - axiom_type: subClassOf | ||
| # text: "'has_anatomical_context' some %s" | ||
| # vars: | ||
| # - Brain_region | ||
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| annotations: | ||
| - annotationProperty: fbetaConfidenceScore | ||
| text: "%s" | ||
| vars: | ||
| - FBeta_confidence_score | ||
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I don't think this pattern is running at all. I couldn't see any terms generated by this template in the
definitions.owl. I couldn't see any terms in my local build as well.Errors are: