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obophenotype / bio-attribute-ontology

source files for OBA (Ontology of Biological Attributes)
https://obophenotype.github.io/bio-attribute-ontology
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Add Swisslipid import to OBA #252

Closed matentzn closed 1 year ago

matentzn commented 1 year ago

Fixes #243

@udp @rays22 @dosumis

This is my suggestion for a fast swisslipid module based on the swisslipid SPARQL endpoint.

  1. given the seed,
  2. All metadata for all terms in the seeds are queried
  3. All parents are queried
  4. All CHEBI alignments are queried, as superclasses of Swisslipid rather than equivalent
  5. all part of and has part relations between terms in the seed are queried

Its very fast, I think we can roll with this for now.

image
jamesamcl commented 1 year ago

Great idea to use the SPARQL endpoint to extract a subset.

Is there any reason you changed all the mirrors to use TMPDIR instead?

matentzn commented 1 year ago

@rays22 thanks for the review - I will leave it to you to finish it, if that's ok!

rays22 commented 1 year ago

@rays22 thanks for the review - I will leave it to you to finish it, if that's ok!

@matentzn , I am confused. What exactly do I need to finish here? I have looked at the linked ticket, and the tickets linked to that ticket, but I am still confused.

  1. Is there a list of lipid terms with standard identifiers that I need to add? If yes, where is that list.
  2. Or, is my task only to fix the QC errors in this PR by updating the imports (or doing something similar to achieve the same) for the two new example OBA terms?
matentzn commented 1 year ago

@rays22 this PR is mostly about adding the imports, so you can do it in two steps: fix QC for this PR here, merge it, and then make a new PR adding the missing LIPID terms (which I don't know where they are, but @zoependlington or @ar-ibrahim can point you to the issue on the GWAS side.

rays22 commented 1 year ago

Hi @matentzn , I am out of ideas of how to fix this PR.

  1. The Lipid Maps imports appear to work fine.
  2. The Swisslipids imports do not not work properly. Other than SLM:000064388 Phosphatidylcholine (20:4_0:0), the Swisslipids imports did not work.
  3. There are several CL-related errors that may be unrelated to the lipid imports.
rays22 commented 1 year ago

Hi @matentzn , I am out of ideas of how to fix this PR.

  1. The Lipid Maps imports appear to work fine.
  2. The Swisslipids imports do not not work properly. Other than SLM:000064388 Phosphatidylcholine (20:4_0:0), the Swisslipids imports did not work.

The Swisslipids imports are working now. Thanks for the fix @matentzn .

  1. There are several CL-related errors that may be unrelated to the lipid imports.

I still need to debug and fix the remaining QC errors that I suspect are unrelated to the lipid imports, but may be related to the CL import:

  Level Rule Name Subject Label Property Value
1 ERROR biological-attribute-child-violation OBA:0004713 cell of skeletal muscle amount rdfs:subClassOf Not a subclass of biological attribute
2 ERROR biological-attribute-child-violation OBA:0005633 hepatoblast morphology rdfs:subClassOf Not a subclass of biological attribute
3 ERROR biological-attribute-child-violation OBA:0004714 cell of skeletal muscle spatial pattern rdfs:subClassOf Not a subclass of biological attribute
4 ERROR biological-attribute-child-violation OBA:VT1000743 skeletal muscle fiber quantity rdfs:subClassOf Not a subclass of biological attribute
5 ERROR biological-attribute-child-violation OBA:0005509 vomeronasal sensory neuron functionality rdfs:subClassOf Not a subclass of biological attribute
6 ERROR biological-attribute-child-violation OBA:0004716 cell of skeletal muscle degeneration rdfs:subClassOf Not a subclass of biological attribute
7 ERROR biological-attribute-child-violation OBA:VT0010132 DN2 thymocyte quantity rdfs:subClassOf Not a subclass of biological attribute
8 ERROR biological-attribute-child-violation OBA:0005905 mature natural killer cell morphology rdfs:subClassOf Not a subclass of biological attribute
9 ERROR biological-attribute-child-violation OBA:0003992 organ of Corti supporting cell degeneration rdfs:subClassOf Not a subclass of biological attribute
10 ERROR biological-attribute-child-violation OBA:VT0010134 DN3 thymocyte quantity rdfs:subClassOf Not a subclass of biological attribute
11 ERROR biological-attribute-child-violation OBA:1000559 natural killer cell quality rdfs:subClassOf Not a subclass of biological attribute
12 ERROR biological-attribute-child-violation OBA:0005240 central memory CD8-positive, alpha-beta T cell amount rdfs:subClassOf Not a subclass of biological attribute
13 ERROR biological-attribute-child-violation OBA:VT0008043 NK cell quantity rdfs:subClassOf Not a subclass of biological attribute
14 ERROR biological-attribute-child-violation OBA:0005241 effector memory CD8-positive, alpha-beta T cell morphology rdfs:subClassOf Not a subclass of biological attribute
15 ERROR biological-attribute-child-violation OBA:0005219 type II pneumocyte amount rdfs:subClassOf Not a subclass of biological attribute
16 ERROR biological-attribute-child-violation OBA:VT0003879 hair cell physiology trait rdfs:subClassOf Not a subclass of biological attribute
17 ERROR biological-attribute-child-violation OBA:VT1000612 type IIb muscle fiber quantity rdfs:subClassOf Not a subclass of biological attribute
18 ERROR biological-attribute-child-violation OBA:VT0001365 Deiters cell quantity rdfs:subClassOf Not a subclass of biological attribute
19 ERROR biological-attribute-child-violation OBA:0004609 decidual natural killer cell, human functionality rdfs:subClassOf Not a subclass of biological attribute
20 ERROR biological-attribute-child-violation OBA:VT0015046 hippocampus neuron morphology trait rdfs:subClassOf Not a subclass of biological attribute
21 ERROR biological-attribute-child-violation OBA:VT0001366 pillar cell quantity rdfs:subClassOf Not a subclass of biological attribute
22 ERROR biological-attribute-child-violation OBA:VT0004300 organ of Corti supporting cell morphology trait rdfs:subClassOf Not a subclass of biological attribute
23 ERROR biological-attribute-child-violation OBA:VT0002407 double-negative T cell morphology trait rdfs:subClassOf Not a subclass of biological attribute
24 ERROR biological-attribute-child-violation OBA:0003458 bone marrow cell amount rdfs:subClassOf Not a subclass of biological attribute
25 ERROR biological-attribute-child-violation OBA:VT0004302 Deiters cell morphology trait rdfs:subClassOf Not a subclass of biological attribute
26 ERROR biological-attribute-child-violation OBA:0005212 intestinal enteroendocrine cell morphology rdfs:subClassOf Not a subclass of biological attribute
27 ERROR biological-attribute-child-violation OBA:VT0004303 Hensen cell morphology trait rdfs:subClassOf Not a subclass of biological attribute
28 ERROR biological-attribute-child-violation OBA:0005213 stomach enteroendocrine cell morphology rdfs:subClassOf Not a subclass of biological attribute
29 ERROR biological-attribute-child-violation OBA:0005239 central memory CD8-positive, alpha-beta T cell morphology rdfs:subClassOf Not a subclass of biological attribute
30 ERROR biological-attribute-child-violation OBA:0005436 fetal cardiomyocyte functionality rdfs:subClassOf Not a subclass of biological attribute
31 ERROR biological-attribute-child-violation OBA:VT0005068 NK cell morphology trait rdfs:subClassOf Not a subclass of biological attribute
32 ERROR biological-attribute-child-violation OBA:0003589 chemoreceptor cell morphology rdfs:subClassOf Not a subclass of biological attribute
33 ERROR biological-attribute-child-violation OBA:VT0005069 NK cell physiology trait rdfs:subClassOf Not a subclass of biological attribute
34 ERROR biological-attribute-child-violation OBA:VT0001005 retinal rod cell morphology trait rdfs:subClassOf Not a subclass of biological attribute
35 ERROR biological-attribute-child-violation OBA:0004415 retinal cone cell degeneration rdfs:subClassOf Not a subclass of biological attribute
36 ERROR biological-attribute-child-violation OBA:VT0001006 retinal cone cell morphology trait rdfs:subClassOf Not a subclass of biological attribute
37 ERROR biological-attribute-child-violation OBA:0004379 adrenocorticotropic hormone secreting cell amount rdfs:subClassOf Not a subclass of biological attribute
38 ERROR biological-attribute-child-violation OBA:0004030 Deiter's cell degeneration rdfs:subClassOf Not a subclass of biological attribute
39 ERROR biological-attribute-child-violation OBA:0004416 retinal cone cell amount rdfs:subClassOf Not a subclass of biological attribute
40 ERROR biological-attribute-child-violation OBA:VT0003084 skeletal muscle fiber morphology trait rdfs:subClassOf Not a subclass of biological attribute
41 ERROR biological-attribute-child-violation OBA:0005510 vomeronasal sensory neuron morphology rdfs:subClassOf Not a subclass of biological attribute
42 ERROR biological-attribute-child-violation OBA:VT0007010 cardiomyocyte quantity rdfs:subClassOf Not a subclass of biological attribute
43 ERROR biological-attribute-child-violation OBA:0003953 vestibular hair cell degeneration rdfs:subClassOf Not a subclass of biological attribute
44 ERROR biological-attribute-child-violation OBA:VT0001038 cholinergic neuron morphology trait rdfs:subClassOf Not a subclass of biological attribute
45 ERROR biological-attribute-child-violation OBA:0004283 decidual natural killer cell, human amount rdfs:subClassOf Not a subclass of biological attribute
46 ERROR biological-attribute-child-violation OBA:0003954 vestibular hair cell amount rdfs:subClassOf Not a subclass of biological attribute
47 ERROR biological-attribute-child-violation OBA:0004418 retinal rod cell degeneration rdfs:subClassOf Not a subclass of biological attribute
48 ERROR biological-attribute-child-violation OBA:0004286 decidual natural killer cell, human morphology rdfs:subClassOf Not a subclass of biological attribute
49 ERROR biological-attribute-child-violation OBA:0004419 retinal rod cell amount rdfs:subClassOf Not a subclass of biological attribute
50 ERROR biological-attribute-child-violation OBA:0005233 CD8-positive, alpha-beta memory T cell morphology rdfs:subClassOf Not a subclass of biological attribute
51 ERROR biological-attribute-child-violation OBA:0005242 effector memory CD8-positive, alpha-beta T cell amount rdfs:subClassOf Not a subclass of biological attribute
52 ERROR biological-attribute-child-violation OBA:0005234 CD8-positive, alpha-beta memory T cell amount rdfs:subClassOf Not a subclass of biological attribute
53 ERROR biological-attribute-child-violation OBA:0003581 hair-tylotrich neuron morphology rdfs:subClassOf Not a subclass of biological attribute
54 ERROR biological-attribute-child-violation OBA:0003582 hair-down neuron morphology rdfs:subClassOf Not a subclass of biological attribute
55 ERROR biological-attribute-child-violation OBA:0003583 hair-down neuron amount rdfs:subClassOf Not a subclass of biological attribute
56 ERROR biological-attribute-child-violation OBA:0002442 cell of skeletal muscle variability of size rdfs:subClassOf Not a subclass of biological attribute
57 ERROR biological-attribute-child-violation OBA:0004371 melanocyte stimulating hormone secreting cell morphology rdfs:subClassOf Not a subclass of biological attribute
58 ERROR biological-attribute-child-violation OBA:0004370 prolactin secreting cell morphology rdfs:subClassOf Not a subclass of biological attribute
59 ERROR biological-attribute-child-violation OBA:0004916 hippocampal granule cell morphology rdfs:subClassOf Not a subclass of biological attribute
60 ERROR biological-attribute-child-violation OBA:VT0005089 double-negative T cell quantity rdfs:subClassOf Not a subclass of biological attribute
61 ERROR biological-attribute-child-violation OBA:0004374 adrenocorticotropic hormone secreting cell morphology rdfs:subClassOf Not a subclass of biological attribute
62 ERROR biological-attribute-child-violation OBA:VT0004432 cochlear hair cell physiology trait rdfs:subClassOf Not a subclass of biological attribute
63 ERROR biological-attribute-child-violation OBA:0003973 auditory hair cell amount rdfs:subClassOf Not a subclass of biological attribute
64 ERROR biological-attribute-child-violation OBA:1000764 bone marrow cell quality rdfs:subClassOf Not a subclass of biological attribute
65 ERROR biological-attribute-child-violation OBA:0004375 somatotropin secreting cell amount rdfs:subClassOf Not a subclass of biological attribute
66 ERROR biological-attribute-child-violation OBA:VT0004433 cochlear inner hair cell physiology trait rdfs:subClassOf Not a subclass of biological attribute
67 ERROR biological-attribute-child-violation OBA:0005532 Boettcher cell morphology rdfs:subClassOf Not a subclass of biological attribute
68 ERROR biological-attribute-child-violation OBA:0004376 prolactin secreting cell amount rdfs:subClassOf Not a subclass of biological attribute
69 ERROR biological-attribute-child-violation OBA:VT0002400 multipotent stem cell morphology trait rdfs:subClassOf Not a subclass of biological attribute
70 ERROR biological-attribute-child-violation OBA:VT0004438 vestibular hair cell physiology trait rdfs:subClassOf Not a subclass of biological attribute
71 ERROR biological-attribute-child-violation OBA:0004020 pillar cell degeneration rdfs:subClassOf Not a subclass of biological attribute
72 ERROR biological-attribute-child-violation OBA:VT0002398 bone marrow cell morphology trait rdfs:subClassOf Not a subclass of biological attribute
73 ERROR biological-attribute-child-violation OBA:0004369 somatotropin secreting cell morphology rdfs:subClassOf Not a subclass of biological attribute
74 ERROR biological-attribute-child-violation OBA:0003580 cutaneous/subcutaneous mechanoreceptor cell morphology rdfs:subClassOf Not a subclass of biological attribute
75 ERROR biological-attribute-child-violation OBA:0004180 retinal progenitor cell morphology rdfs:subClassOf Not a subclass of biological attribute
76 ERROR biological-attribute-child-violation OBA:VT0003240 hippocampus neuron quantity rdfs:subClassOf Not a subclass of biological attribute
77 ERROR biological-attribute-child-violation OBA:VT0004100 spinal cord interneuron morphology trait rdfs:subClassOf Not a subclass of biological attribute
78 ERROR biological-attribute-child-violation OBA:0005528 cerebral cortex neuron displaced rdfs:subClassOf Not a subclass of biological attribute
79 ERROR biological-attribute-child-violation OBA:0004246 spermatogonium morphology rdfs:subClassOf Not a subclass of biological attribute
80 ERROR biological-attribute-child-violation OBA:0003947 organ of Corti supporting cell amount rdfs:subClassOf Not a subclass of biological attribute
81 ERROR biological-attribute-child-violation OBA:0003970 cochlear inner hair cell degeneration rdfs:subClassOf Not a subclass of biological attribute
82 ERROR biological-attribute-child-violation OBA:VT0004430 Claudius cell morphology trait rdfs:subClassOf Not a subclass of biological attribute
83 ERROR biological-attribute-child-violation OBA:0004679 bone marrow cell functionality rdfs:subClassOf Not a subclass of biological attribute
84 ERROR biological-attribute-child-violation OBA:VT0004326 vestibular hair cell quantity rdfs:subClassOf Not a subclass of biological attribute
85 ERROR biological-attribute-child-violation OBA:0004362 organ of Corti supporting cell functionality rdfs:subClassOf Not a subclass of biological attribute
86 ERROR biological-attribute-child-violation OBA:0003961 auditory hair cell degeneration rdfs:subClassOf Not a subclass of biological attribute
87 ERROR biological-attribute-child-violation OBA:VT0000045 hair cell morphology trait rdfs:subClassOf Not a subclass of biological attribute
88 ERROR biological-attribute-child-violation OBA:VT0010136 DN4 thymocyte quantity rdfs:subClassOf Not a subclass of biological attribute
89 ERROR biological-attribute-child-violation OBA:VT0004393 cochlear inner hair cell morphology trait rdfs:subClassOf Not a subclass of biological attribute
90 ERROR biological-attribute-child-violation OBA:VT0004394 cochlear inner hair cell quantity rdfs:subClassOf Not a subclass of biological attribute
91 ERROR biological-attribute-child-violation OBA:0005900 immature natural killer cell amount rdfs:subClassOf Not a subclass of biological attribute
92 ERROR biological-attribute-child-violation OBA:0005901 mature natural killer cell amount rdfs:subClassOf Not a subclass of biological attribute
93 ERROR biological-attribute-child-violation OBA:0004493 fetal cardiomyocyte morphology rdfs:subClassOf Not a subclass of biological attribute
94 ERROR biological-attribute-child-violation OBA:VT0003825 pillar cell morphology trait rdfs:subClassOf Not a subclass of biological attribute
95 ERROR biological-attribute-child-violation OBA:1000886 DN2 thymocyte quality rdfs:subClassOf Not a subclass of biological attribute
96 ERROR biological-attribute-child-violation OBA:0003969 cochlear inner hair cell amount rdfs:subClassOf Not a subclass of biological attribute
97 ERROR biological-attribute-child-violation OBA:0005904 immature natural killer cell morphology rdfs:subClassOf Not a subclass of biological attribute
98 ERROR biological-attribute-child-violation OBA:VT0004406 cochlear hair cell quantity rdfs:subClassOf Not a subclass of biological attribute
99 ERROR biological-attribute-child-violation OBA:0005634 hepatoblast amount rdfs:subClassOf Not a subclass of biological attribute
100 ERROR biological-attribute-child-violation OBA:VT0002274 type I pneumocyte morphology trait rdfs:subClassOf Not a subclass of biological attribute
101 ERROR biological-attribute-child-violation OBA:0003353 natural killer cell amount rdfs:subClassOf Not a subclass of biological attribute
102 ERROR biological-attribute-child-violation OBA:VT0002275 type II pneumocyte morphology trait rdfs:subClassOf Not a subclass of biological attribute
103 ERROR biological-attribute-child-violation OBA:0004013 cardiac muscle cell size rdfs:subClassOf Not a subclass of biological attribute
104 ERROR biological-attribute-child-violation OBA:0004014 cardiac muscle cell degeneration rdfs:subClassOf Not a subclass of biological attribute
105 ERROR biological-attribute-child-violation OBA:VT1000747 type I muscle fiber quantity rdfs:subClassOf Not a subclass of biological attribute
106 ERROR biological-attribute-child-violation OBA:0004015 cardiac muscle cell amount rdfs:subClassOf Not a subclass of biological attribute
107 ERROR biological-attribute-child-violation OBA:0004401 somatotropin secreting cell size rdfs:subClassOf Not a subclass of biological attribute
108 ERROR biological-attribute-child-violation OBA:VT1000748 type IIa muscle fiber quantity rdfs:subClassOf Not a subclass of biological attribute
109 ERROR biological-attribute-child-violation OBA:0003552 hippocampal neuron degeneration rdfs:subClassOf Not a subclass of biological attribute
110 ERROR biological-attribute-child-violation OBA:0003579 thermoreceptor cell morphology rdfs:subClassOf Not a subclass of biological attribute
111 ERROR biological-attribute-child-violation OBA:VT0003399 skeletal muscle fiber size trait rdfs:subClassOf Not a subclass of biological attribute
112 ERROR biological-attribute-child-violation OBA:0003932 cardiac muscle cell functionality rdfs:subClassOf Not a subclass of biological attribute
113 ERROR biological-attribute-child-violation OBA:VT0002622 cochlear hair cell morphology trait rdfs:subClassOf Not a subclass of biological attribute
114 ERROR biological-attribute-child-violation OBA:0004638 pancreatic epsilon cell morphology rdfs:subClassOf Not a subclass of biological attribute
115 ERROR biological-attribute-child-violation OBA:0004405 prolactin secreting cell size rdfs:subClassOf Not a subclass of biological attribute
116 ERROR biological-attribute-child-violation OBA:VT0002623 vestibular hair cell morphology trait rdfs:subClassOf Not a subclass of biological attribute
117 ERROR biological-attribute-child-violation OBA:0004639 pancreatic epsilon cell altered number of rdfs:subClassOf Not a subclass of biological attribute
118 ERROR biological-attribute-child-violation OBA:0004407 adrenocorticotropic hormone secreting cell size rdfs:subClassOf Not a subclass of biological attribute
119 ERROR biological-attribute-child-violation OBA:0005221 type I pneumocyte amount rdfs:subClassOf Not a subclass of biological attribute
120 ERROR biological-attribute-child-violation OBA:0003286 skeletal muscle fiber size rdfs:subClassOf Not a subclass of biological attribute
121 ERROR biological-attribute-child-violation OBA:0004640 pancreatic epsilon cell amount rdfs:subClassOf Not a subclass of biological attribute
122 ERROR biological-attribute-child-violation OBA:0004712 cell of skeletal muscle length rdfs:subClassOf Not a subclass of biological attribute
123 ERROR biological-attribute-child-violation OBA:0004641 pancreatic epsilon cell functionality rdfs:subClassOf Not a subclass of biological attribute
124 ERROR biological-attribute-child-violation OBA:VT0000061 cardiomyocyte morphology trait rdfs:subClassOf Not a subclass of biological attribute
rays22 commented 1 year ago

biological-attribute-child-violation errors

Every OBA class that produces this error contains a CL component. The hierarchy of CL classes in oba-edit.obo appears to be wrong and differs from the original class hierarchy in CL. For example, CL:0000188 cell of skeletal muscle is not a subclass of CL:0000000 cell in oba-edit.obo (in the current git branch) . eukaryotic cell is not a subclass of cell in OBA (in the current git branch), but it is in the current cl-edit.owl.CL owl:versionInfo "2023-06-22". The unique CL component classes are as follows:

CLASS LABEL
CL:0000020 spermatogonium
CL:0000048 multi fate stem cell
CL:0000108 cholinergic neuron
CL:0000188 cell of skeletal muscle
CL:0000202 auditory hair cell
CL:0000205 thermoreceptor cell
CL:0000206 chemoreceptor cell
CL:0000295 somatotropin secreting cell
CL:0000439 prolactin secreting cell
CL:0000440 melanocyte stimulating hormone secreting cell
CL:0000467 adrenocorticotropic hormone secreting cell
CL:0000573 retinal cone cell
CL:0000589 cochlear inner hair cell
CL:0000604 retinal rod cell
CL:0000609 vestibular hair cell
CL:0000623 natural killer cell
CL:0000633 Hensen cell
CL:0000634 Claudius cell
CL:0000635 Deiter's cell
CL:0000746 cardiac muscle cell
CL:0000806 DN2 thymocyte
CL:0000807 DN3 thymocyte
CL:0000808 DN4 thymocyte
CL:0000823 immature natural killer cell
CL:0000824 mature natural killer cell
CL:0000855 sensory hair cell
CL:0000907 central memory CD8-positive, alpha-beta T cell
CL:0000909 CD8-positive, alpha-beta memory T cell
CL:0000913 effector memory CD8-positive, alpha-beta T cell
CL:0001033 hippocampal granule cell
CL:0002062 type I pneumocyte
CL:0002063 type II pneumocyte
CL:0002084 Boettcher cell
CL:0002092 bone marrow cell
CL:0002211 type I muscle cell
CL:0002214 type IIa muscle cell
CL:0002215 type IIb muscle cell
CL:0002343 decidual natural killer cell, human
CL:0002487 cutaneous/subcutaneous mechanoreceptor cell
CL:0002489 double negative thymocyte
CL:0002490 organ of Corti supporting cell
CL:0002495 fetal cardiomyocyte
CL:0002608 hippocampal neuron
CL:0002672 retinal progenitor cell
CL:0005000 spinal cord interneuron
CL:0005019 pancreatic epsilon cell
CL:0005026 hepatoblast
CL:0008002 skeletal muscle fiber
CL:0010012 cerebral cortex neuron
CL:1000191 pillar cell
CL:1001436 hair-tylotrich neuron
CL:1001437 hair-down neuron
CL:1001516 intestinal enteroendocrine cell
CL:1001517 stomach enteroendocrine cell
CL:1001561 vomeronasal sensory neuron
matentzn commented 1 year ago

Isn't there a general "cell trait" grouping under which all of these should automatically classify? If not, create one, and manually put it under "biological attribute"

rays22 commented 1 year ago

Isn't there a general "cell trait" grouping under which all of these should automatically classify? If not, create one, and manually put it under "biological attribute"

Yes, there is a cell trait grouping class and all these classes that cause the QC error should be a subclass of that. The problem is that in the current branch eukaryotic cell is NOT a subclass of native cell
and therefore not a subclass of cell.

I suspect the reason is that the logical definition of eukaryotic cell is somehow lost in the current OBA branch which in turn results of eukaryotic cell being a direct subclass of owl:Thing:

current_branch current_branch-EQ

It should look like this

In the latest OBA release these look correct (and agree with the current CL, so there is no recent change in CL either): previously

previously-EQ

@matentzn , do you have any idea why the he logical definition of eukaryotic cell is lost in the current OBA branch? Fixing that would fix the QC errors.

rays22 commented 1 year ago 
8256   │     <!-- http://purl.obolibrary.org/obo/CL_0000255 -->
8257   │ 
8258   │     <owl:Class rdf:about="http://purl.obolibrary.org/obo/CL_0000255">
8259   │         <owl:equivalentClass>
8260   │             <owl:Class>
8261   │                 <owl:intersectionOf rdf:parseType="Collection">
8262   │                     <rdf:Description rdf:about="http://purl.obolibrary.org/obo/CL_0000003"/>
8263   │                     <owl:Restriction>
8264   │                         <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002160"/>
8265   │                         <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_2759"/>
8266   │                     </owl:Restriction>
8267   │                 </owl:intersectionOf>
8268   │             </owl:Class>
8269   │         </owl:equivalentClass>
8270   │         <owl:disjointWith rdf:resource="http://purl.obolibrary.org/obo/CL_0000520"/>
8271   │         <oboInOwl:hasDbXref>MESH:D005057</oboInOwl:hasDbXref>
8272   │         <rdfs:label>eukaryotic cell</rdfs:label>
8273   │     </owl:Class>
8274   │     
46291:# Class: <http://purl.obolibrary.org/obo/CL_0000255> (eukaryotic cell)
46292-
46293:AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/CL_0000255> "eukaryotic cell")
46294-
rays22 commented 1 year ago

I have updated oba-okd.yaml so that the OBA imports use cl base-plus, and

  1. updated 
    sh run.sh make update_repo
  2. refreshed merged_import 
    sh run.sh make imports/merged_import.owl

    This has fixed the CL-hierarchy bug in OBA caused by missing CL logical axioms in OBA merged_import.