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Update DOSDP and SPARQL docs (#7759)
* Update DOSDP template and SPARQL qc documentation * fix typos --------- Co-authored-by: sabrinatoro <[email protected]> Co-authored-by: Trish Whetzel <[email protected]>
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‎docs/editors-guide/patterns/OMIM_disease_series_by_gene.md

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This pattern is meant to be used for 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. 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)
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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)
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## Contributors
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* [https://orcid.org/0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165)
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* [https://orcid.org/0000-0001-5208-3432](https://orcid.org/0000-0001-5208-3432)
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* [https://orcid.org/0000-0002-4142-7153](https://orcid.org/0000-0002-4142-7153)
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## Name
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{[disease](http://purl.obolibrary.org/obo/MONDO_0000001)} caused by variation in {[gene](http://purl.obolibrary.org/obo/SO_0000704)}

‎docs/editors-guide/patterns/index.md

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

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"ICD10CM",
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"ICD10WHO",
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"ICD11",
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"icd11.foundation",
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"ICD9",
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"ICD9CM",
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"ICDO",
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"ICD10EXP",
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"ICD10WHO",
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"ICD11",
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"icd11.foundation",
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"ICD9",
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"ICD9CM",
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"ICDO",
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"MONDO",
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"MPATH",
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"MTH",
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"NANDO",
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"NCIT",
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"NDFRT",
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"NIFSTD",
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oboInOwl:hasSynonymType <http://purl.obolibrary.org/obo/mondo#ABBREVIATION> .
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}
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FILTER NOT EXISTS { ?entity owl:deprecated true }
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FILTER NOT EXISTS { ?entity1 owl:deprecated true }
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FILTER NOT EXISTS { ?entity2 owl:deprecated true }
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FILTER (?entity1 != ?entity2)
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FILTER (!isBlank(?entity1))
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```
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### qc-excluded-subclass.sparql
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```
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PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
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prefix IAO: <http://purl.obolibrary.org/obo/IAO_>
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prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
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prefix oio: <http://www.geneontology.org/formats/oboInOwl#>
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prefix def: <http://purl.obolibrary.org/obo/IAO_0000115>
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prefix owl: <http://www.w3.org/2002/07/owl#>
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PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
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prefix oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
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# Tests if an animal disease made it into the rare disease subset
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SELECT DISTINCT ?entity ?property ?value
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WHERE
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{
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VALUES ?property { <http://purl.obolibrary.org/obo/mondo#excluded_subClassOf> }
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?entity ?property ?value .
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FILTER(!isIRI(?value) || !STRSTARTS(STR(?value),"http://purl.obolibrary.org/obo/MONDO_"))
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FILTER( !isBlank(?entity) && STRSTARTS(str(?entity), "http://purl.obolibrary.org/obo/MONDO_"))
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}
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```
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### qc-illegal-axiom-annotation.sparql
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```
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dc:conformsTo,
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dc:creator,
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dce:date,
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mondo:confidence,
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mondo:excluded_from_qc_check,
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mondo:excluded_subClassOf,
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mondo:excluded_synonym,
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```
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### qc-provenance-missing.sparql
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```
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PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
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prefix IAO: <http://purl.obolibrary.org/obo/IAO_>
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prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
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prefix oio: <http://www.geneontology.org/formats/oboInOwl#>
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prefix def: <http://purl.obolibrary.org/obo/IAO_0000115>
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prefix owl: <http://www.w3.org/2002/07/owl#>
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PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
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prefix oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
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# Tests for excluded_subClassOf relationships that do not also have a source annotation with an ORCID.
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SELECT DISTINCT ?entity ?property ?value
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WHERE
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{
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VALUES ?property { <http://purl.obolibrary.org/obo/mondo#excluded_subClassOf> }
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?entity ?property ?value .
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FILTER NOT EXISTS {
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[] owl:annotatedSource ?entity ;
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owl:annotatedProperty ?property ;
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owl:annotatedTarget ?value ;
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oboInOwl:source ?orcid .
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FILTER(STRSTARTS(STR(?orcid),"https://orcid.org/"))
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}
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FILTER( !isBlank(?entity) && STRSTARTS(str(?entity), "http://purl.obolibrary.org/obo/MONDO_"))
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}
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```
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### qc-proxy-merge-missing-preferred.sparql
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```
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### qc-xref-syntax.sparql
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```
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# home: hp
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prefix hasDbXref: <http://www.geneontology.org/formats/oboInOwl#hasDbXref>
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prefix oio: <http://www.geneontology.org/formats/oboInOwl#>
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prefix owl: <http://www.w3.org/2002/07/owl#>
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prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
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# # Invalid Xref
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#
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# **Problem:** A database_cross_reference is not in CURIE format.
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#
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# **Solution:** Replace the reference with a [CURIE](https://www.w3.org/TR/2010/NOTE-curie-20101216/).
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SELECT DISTINCT ?entity ?property ?value WHERE
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{
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?entity hasDbXref: ?x .
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PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
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PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
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FILTER( regex(STR(?x), " ") || regex(STR(?x), ";") || STR(?x) = "" )
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BIND(hasDbXref: AS ?property)
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SELECT DISTINCT ?entity ?property ?value
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WHERE {
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VALUES ?property {oboInOwl:hasDbXref}
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?entity ?property ?value .
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FILTER (!regex(?value, "^[A-Za-z_][A-Za-z0-9_.-]*[A-Za-z0-9_]:[^\\s]+$"))
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FILTER (!isBlank(?entity))
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}
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ORDER BY ?entity
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‎src/patterns/dosdp-patterns/README.md

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## Patterns in dosdp-patterns
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### Omim disease series by gene
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*This pattern is meant to be used for 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. 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)*
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*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)*
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| Attribute | Info |
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|----------|----------|
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| IRI | http://purl.obolibrary.org/obo/mondo/patterns/disease_series_by_gene.yaml |
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| Name | OMIM_disease_series_by_gene |
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| Classes | MONDO:0000001, SO:0000704, |
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| Variables | disease (MONDO:0000001), gene (SO:0000704), |
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| Contributors | [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165), [0000-0001-5208-3432](https://orcid.org/0000-0001-5208-3432), |
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| Contributors | [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165), [0000-0001-5208-3432](https://orcid.org/0000-0001-5208-3432), [0000-0002-4142-7153](https://orcid.org/0000-0002-4142-7153), |
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| Examples | |
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### Omim phenotypic series

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