Update DOSDP template and SPARQL qc documentation (#8088)

Co-authored-by: twhetzel <[email protected]>

docs/editors-guide/patterns/OMIM_disease_series_by_gene.md

@@ -12,17 +12,17 @@ This pattern is meant to be used for (1) OMIM Mendelian diseases (ie unitary gen
 * [https://orcid.org/0000-0002-4142-7153](https://orcid.org/0000-0002-4142-7153) 
 ## Name 
 
-{[disease](http://purl.obolibrary.org/obo/MONDO_0000001)} caused by variation in {[gene](http://purl.obolibrary.org/obo/SO_0000704)}
+{[disease](http://purl.obolibrary.org/obo/MONDO_0700096)} caused by variation in {[gene](http://purl.obolibrary.org/obo/SO_0000704)}
 
 ## Annotations 
 
-* [exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym): {[gene](http://purl.obolibrary.org/obo/SO_0000704)} {[disease](http://purl.obolibrary.org/obo/MONDO_0000001)}
+* [exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym): {[gene](http://purl.obolibrary.org/obo/SO_0000704)} {[disease](http://purl.obolibrary.org/obo/MONDO_0700096)}
 
 ## Definition 
 
-Any {[disease](http://purl.obolibrary.org/obo/MONDO_0000001)} in which the cause of the disease is a variation in the {[gene](http://purl.obolibrary.org/obo/SO_0000704)} gene.
+Any {[disease](http://purl.obolibrary.org/obo/MONDO_0700096)} in which the cause of the disease is a variation in the {[gene](http://purl.obolibrary.org/obo/SO_0000704)} gene.
 
 ## Equivalent to 
 
-{[disease](http://purl.obolibrary.org/obo/MONDO_0000001)} and [has material basis in germline mutation in](http://purl.obolibrary.org/obo/RO_0004003) some {[gene](http://purl.obolibrary.org/obo/SO_0000704)}
+{[disease](http://purl.obolibrary.org/obo/MONDO_0700096)} and [has material basis in germline mutation in](http://purl.obolibrary.org/obo/RO_0004003) some {[gene](http://purl.obolibrary.org/obo/SO_0000704)}
 

docs/editors-guide/patterns/OMIM_phenotypic_series.md

@@ -11,5 +11,5 @@ Examples: [holoprosencephaly](http://purl.obolibrary.org/obo/MONDO_0016296) [OMI
 * [https://orcid.org/0000-0001-5208-3432](https://orcid.org/0000-0001-5208-3432) 
 ## Name 
 
-{[disease](http://purl.obolibrary.org/obo/MONDO_0000001)}
+{[disease](http://purl.obolibrary.org/obo/MONDO_0700096)}
 

docs/editors-guide/patterns/disease_series_by_gene.md

@@ -9,21 +9,21 @@ This pattern is for diseases that are caused by a single variation or mutation i
 * [https://orcid.org/0000-0001-5208-3432](https://orcid.org/0000-0001-5208-3432) 
 ## Name 
 
-{[disease](http://purl.obolibrary.org/obo/MONDO_0000001)} caused by variation in {[gene](http://purl.obolibrary.org/obo/SO_0001217)}
+{[disease](http://purl.obolibrary.org/obo/MONDO_0700096)} caused by variation in {[gene](http://purl.obolibrary.org/obo/SO_0000704)}
 
 ## Annotations 
 
-* [exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym): {[gene](http://purl.obolibrary.org/obo/SO_0001217)} {[disease](http://purl.obolibrary.org/obo/MONDO_0000001)}
+* [exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym): {[gene](http://purl.obolibrary.org/obo/SO_0000704)} {[disease](http://purl.obolibrary.org/obo/MONDO_0700096)}
 
-* [exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym): {[gene](http://purl.obolibrary.org/obo/SO_0001217)} related {[disease](http://purl.obolibrary.org/obo/MONDO_0000001)}
+* [exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym): {[gene](http://purl.obolibrary.org/obo/SO_0000704)} related {[disease](http://purl.obolibrary.org/obo/MONDO_0700096)}
 
-* [exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym): {[disease](http://purl.obolibrary.org/obo/MONDO_0000001)} caused by mutation in {[gene](http://purl.obolibrary.org/obo/SO_0001217)}
+* [exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym): {[disease](http://purl.obolibrary.org/obo/MONDO_0700096)} caused by mutation in {[gene](http://purl.obolibrary.org/obo/SO_0000704)}
 
 ## Definition 
 
-Any {[disease](http://purl.obolibrary.org/obo/MONDO_0000001)} in which the cause of the disease is a variation in the {[gene](http://purl.obolibrary.org/obo/SO_0001217)} gene.
+Any {[disease](http://purl.obolibrary.org/obo/MONDO_0700096)} in which the cause of the disease is a variation in the {[gene](http://purl.obolibrary.org/obo/SO_0000704)} gene.
 
 ## Equivalent to 
 
-{[disease](http://purl.obolibrary.org/obo/MONDO_0000001)} and [has material basis in germline mutation in](http://purl.obolibrary.org/obo/RO_0004003) some {[gene](http://purl.obolibrary.org/obo/SO_0001217)}
+{[disease](http://purl.obolibrary.org/obo/MONDO_0700096)} and [has material basis in germline mutation in](http://purl.obolibrary.org/obo/RO_0004003) some {[gene](http://purl.obolibrary.org/obo/SO_0000704)}
 

docs/editors-guide/patterns/disease_series_by_gene_and_inheritance.md

@@ -12,21 +12,21 @@ Examples: [Growth hormone insensitivity syndrome with immune dysregulation](http
 * [https://orcid.org/0000-0002-7356-1779](https://orcid.org/0000-0002-7356-1779) 
 ## Name 
 
-{[disease](http://purl.obolibrary.org/obo/MONDO_0000001)} caused by mutation in {[gene](http://purl.obolibrary.org/obo/SO_0000704)}, {[mode_of_inheritance](http://purl.obolibrary.org/obo/HP_0000005)}
+{[disease](http://purl.obolibrary.org/obo/MONDO_0700096)} caused by mutation in {[gene](http://purl.obolibrary.org/obo/SO_0000704)}, {[mode_of_inheritance](http://purl.obolibrary.org/obo/HP_0000005)}
 
 ## Annotations 
 
-* [exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym): {[gene](http://purl.obolibrary.org/obo/SO_0000704)} {[disease](http://purl.obolibrary.org/obo/MONDO_0000001)}, {[mode_of_inheritance](http://purl.obolibrary.org/obo/HP_0000005)}
+* [exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym): {[gene](http://purl.obolibrary.org/obo/SO_0000704)} {[disease](http://purl.obolibrary.org/obo/MONDO_0700096)}, {[mode_of_inheritance](http://purl.obolibrary.org/obo/HP_0000005)}
 
-* [exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym): {[gene](http://purl.obolibrary.org/obo/SO_0000704)} related {[disease](http://purl.obolibrary.org/obo/MONDO_0000001)}, {[mode_of_inheritance](http://purl.obolibrary.org/obo/HP_0000005)}
+* [exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym): {[gene](http://purl.obolibrary.org/obo/SO_0000704)} related {[disease](http://purl.obolibrary.org/obo/MONDO_0700096)}, {[mode_of_inheritance](http://purl.obolibrary.org/obo/HP_0000005)}
 
 ## Definition 
 
-Any {[disease](http://purl.obolibrary.org/obo/MONDO_0000001)} in which the cause of the disease is a mutation in the {[gene](http://purl.obolibrary.org/obo/SO_0000704)} gene, and has {[mode_of_inheritance](http://purl.obolibrary.org/obo/HP_0000005)}.
+Any {[disease](http://purl.obolibrary.org/obo/MONDO_0700096)} in which the cause of the disease is a mutation in the {[gene](http://purl.obolibrary.org/obo/SO_0000704)} gene, and has {[mode_of_inheritance](http://purl.obolibrary.org/obo/HP_0000005)}.
 
 ## Equivalent to 
 
-{[disease](http://purl.obolibrary.org/obo/MONDO_0000001)} and [has material basis in germline mutation in](http://purl.obolibrary.org/obo/RO_0004003) some {[gene](http://purl.obolibrary.org/obo/SO_0000704)} and [has characteristic](http://purl.obolibrary.org/obo/RO_0000053) some {[mode_of_inheritance](http://purl.obolibrary.org/obo/HP_0000005)}
+{[disease](http://purl.obolibrary.org/obo/MONDO_0700096)} and [has material basis in germline mutation in](http://purl.obolibrary.org/obo/RO_0004003) some {[gene](http://purl.obolibrary.org/obo/SO_0000704)} and [has characteristic](http://purl.obolibrary.org/obo/RO_0000053) some {[mode_of_inheritance](http://purl.obolibrary.org/obo/HP_0000005)}
 
 ## Data preview 
 | defined_class                                | defined_class_label                                                       | disease                                      | disease_label                 | gene                              | gene_label   | mode_of_inheritance                       | mode_of_inheritance_label       |

docs/editors-guide/patterns/index.md

@@ -70,6 +70,7 @@
 | [neoplasm](neoplasm/) | <br/>Neoplasms are benign or malignant tissue growths resulting from uncontrolled cell proliferation cell types.<br/>This is a design pattern for classes representing neoplasms based on their location. This may be the site of origin, but it can also represent a secondary site for malignant neoplasms that have metastasized.<br/>We use the generic 'disease has location' relation, which generalized over primary and secondary sites.<br/>Note that tumor is typically a synonym for neoplasm, although this can be context dependent. For NETs, NCIT uses the nomenclature 'tumor' to indicate 'well differentiated, low or intermediate grade tumor'. This can also be called carcinoid, see https://www.cancer.org/cancer/gastrointestinal-carcinoid-tumor/about/what-is-gastrointestinal-carcinoid.html We attempt to spell this out in our labels. | 
 | [neoplasm](neoplasm_by_origin/) | TBD. | 
 | [nonhuman_disease](nonhuman_disease/) | This pattern should be used for diseases affecting non-human animal which have a corresponding/an analog disease in human, AND the taxon affected is NOT known. Examples: [leukemia, non-human animal](http://purl.obolibrary.org/obo/MONDO_0700100), [hepatitis, viral, animal](http://purl.obolibrary.org/obo/MONDO_0025085) | 
+| [nonhuman_disease_series_by_gene](nonhuman_disease_series_by_gene/) | This pattern is for non-human diseases that are defined based on a variation in one gene, such as many genetic diseases from the Online Mendelian Inheritance in Animals (OMIA).  Examples: TBD  | 
 | [nonhuman_disease_taxon](nonhuman_disease_taxon/) | This pattern should be used for diseases affecting non-human animal which have a corresponding/an analog disease in human AND the taxon affected is known. Examples: [leukemia, feline](http://purl.obolibrary.org/obo/MONDO_0025488) | 
 | [nuclear_subtype](nuclear_subtype/) | A disease that is classified as a nuclear subtype, due to a defect in a nuclear gene, such as MONDO:0009640 'mitochondrial complex I deficiency, nuclear type'. | 
 | [OMIM_disease_series_by_gene](OMIM_disease_series_by_gene/) | <br/>This pattern is meant to be used for (1) OMIM Mendelian diseases (ie unitary genetic diseases, as described in [PMID:33417889](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7820621/)), including children of OMIM phenotypic series (OMIMPS), which are represented as grouping classes in Mondo, and (2) OMIA Mendelian diseases (https://omia.org/) which are defined by a variation in a gene. Notes about the OMIMPS (see also OMIM_phenotypic_series.yaml):  - every instance of the OMIMPS metaclass should be equivalent to (via annotated xref) to something in OMIMPS namespace - the OMIMPS will never have an asserted causative gene as logical axiom (and no single causative gene in text def) - the OMIMPS must never be equivalent to an OMIM:nnnnnn (often redundant with the above rule) - the OMIMPS must have an acronym synonym, e.g. HPE - the OMIMPS must have two or more subclasses (direct or indirect) that are equivalent to OMIMs and conform to this pattern - the subclasses should (not must) have a logical def that uses the PS as a genus  - the OMIM subclasses must have acronym synonyms that are the parent syn + number, e.g. HPE1, HPE2 - the primary label for the children should also be parent + {"type"} + number - the first member will usually have the same number local ID as the PS Examples: [holoprosencephaly 1](http://purl.obolibrary.org/obo/MONDO_0009349), [3M syndrome 1](http://purl.obolibrary.org/obo/MONDO_0010117) | 

docs/editors-guide/patterns/nonhuman_disease_series_by_gene.md

@@ -0,0 +1,29 @@
+# nonhuman_disease_series_by_gene 
+
+[http://purl.obolibrary.org/obo/mondo/patterns/nonhuman_disease_series_by_gene.yaml](http://purl.obolibrary.org/obo/mondo/patterns/nonhuman_disease_series_by_gene.yaml)
+## Description 
+
+This pattern is for non-human diseases that are defined based on a variation in one gene, such as many genetic diseases from the Online Mendelian Inheritance in Animals (OMIA).  Examples: TBD 
+## Contributors 
+* [https://orcid.org/0000-0002-4142-7153](https://orcid.org/0000-0002-4142-7153) 
+* [https://orcid.org/0000-0002-5002-8648](https://orcid.org/0000-0002-5002-8648) 
+## Name 
+
+{[disease](http://purl.obolibrary.org/obo/MONDO_0005583)} caused by variation in {[gene](http://purl.obolibrary.org/obo/SO_0000704)}, {[taxon](http://purl.obolibrary.org/obo/NCBITaxon_1)}
+
+## Annotations 
+
+* [exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym): {[gene](http://purl.obolibrary.org/obo/SO_0000704)} {[disease](http://purl.obolibrary.org/obo/MONDO_0005583)}, {[taxon](http://purl.obolibrary.org/obo/NCBITaxon_1)}
+
+* [exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym): {[gene](http://purl.obolibrary.org/obo/SO_0000704)} related {[disease](http://purl.obolibrary.org/obo/MONDO_0005583)}, {[taxon](http://purl.obolibrary.org/obo/NCBITaxon_1)}
+
+* [exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym): {[disease](http://purl.obolibrary.org/obo/MONDO_0005583)} caused by mutation in {[gene](http://purl.obolibrary.org/obo/SO_0000704)}, {[taxon](http://purl.obolibrary.org/obo/NCBITaxon_1)}
+
+## Definition 
+
+Any {[disease](http://purl.obolibrary.org/obo/MONDO_0005583)}, occuring in {[taxon](http://purl.obolibrary.org/obo/NCBITaxon_1)}, in which the cause of the disease is a variation in the {[gene](http://purl.obolibrary.org/obo/SO_0000704)} gene.
+
+## Equivalent to 
+
+{[disease](http://purl.obolibrary.org/obo/MONDO_0005583)} and ([has material basis in germline mutation in](http://purl.obolibrary.org/obo/RO_0004003) some {[gene](http://purl.obolibrary.org/obo/SO_0000704)}) and ([in taxon](http://purl.obolibrary.org/obo/RO_0002162) some {[taxon](http://purl.obolibrary.org/obo/NCBITaxon_1)})
+

docs/editors-guide/quality-control-tests.md

@@ -574,6 +574,36 @@ ORDER BY ?entity
 
 ```
 
+###  qc-obsoletionprotected.sparql
+
+```
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX replaced_by: <http://purl.obolibrary.org/obo/IAO_0100001>
+PREFIX MONDO: <http://purl.obolibrary.org/obo/MONDO_>
+prefix oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
+
+#this query reports when an obsoletion-candidate tag is added to a protected term
+
+SELECT ?entity ?property ?value
+WHERE 
+  { 
+
+VALUES ?property { <http://purl.obolibrary.org/obo/mondo#obsoletion_candidate> }
+?entity <http://www.geneontology.org/formats/oboInOwl#inSubset> ?property.
+
+?entity a owl:Class; 
+  		rdfs:label ?value .
+
+?entity <http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/mondo#obsoletion_protected>.
+
+  FILTER( !isBlank(?entity) && regex(str(?entity), "^http://purl.obolibrary.org/obo/MONDO_"))
+}
+
+```
+
 ###  qc-omim-subsumption.sparql
 
 ```
@@ -822,7 +852,7 @@ SELECT DISTINCT ?entity ?property ?value WHERE {
   	FILTER ((str(?source2)="MONDO:equivalentTo") || (str(?source2)="MONDO:obsoleteEquivalent") || (str(?source2)="MONDO:equivalentObsolete") || (str(?source2)="MONDO:obsoleteEquivalentObsolete"))
     FILTER (isIRI(?entity) && STRSTARTS(str(?entity), "http://purl.obolibrary.org/obo/MONDO_"))
     FILTER (isIRI(?entity2) && STRSTARTS(str(?entity2), "http://purl.obolibrary.org/obo/MONDO_"))
-    BIND(?xref as ?property)
+    BIND(IRI(CONCAT("http://mondo.source/", ?xref)) AS ?property)
     BIND(str(?entity2) as ?value)
 }
 ORDER BY ?entity
@@ -1002,7 +1032,7 @@ SELECT ?entity ?property ?value
 
 WHERE
 {
-  VALUES ?property { RO:0004003 RO:0004029 }
+#  VALUES ?property { RO:0004003 RO:0004029 }
   ?entity rdfs:subClassOf [
         owl:onProperty ?property ;
         owl:someValuesFrom ?entity