the manifest can be used in:
- ShEx.JS shex-simple interface
using the rawlink address
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October 4, 2023 10:00
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| - schemaLabel: some example schema | |
| schemaURL: example.shex | |
| dataLabel: and example data | |
| dataURL: example.ttl | |
| queryMap: |- | |
| <https://databases.lovd.nl/shared/variants/0000001345#00000064>@<#VariantOnTranscription>, | |
| <https://databases.lovd.nl/shared/variants/0000001344#00000064>@<#VariantOnTranscription>, | |
| <https://databases.lovd.nl/shared/variants/0000001345#vog>@<#VariantOnGenome>, | |
| <https://databases.lovd.nl/shared/variants/0000001344#vog>@<#VariantOnGenome>, | |
| <https://databases.lovd.nl/shared/variants/0000001345>@<#GeneticMeasurementOutput>, | |
| <https://databases.lovd.nl/shared/variants/0000001344>@<#GeneticMeasurementOutput>, | |
| <https://databases.lovd.nl/shared/screenings/0000000117#genotype>@<#GenotypeAttribute>, | |
| <https://databases.lovd.nl/shared/screenings/0000000117>@<#GeneticMeasurementProcess>, | |
| indiv:diagnosis@<#DiagnosisAttribute>, | |
| indiv:findings@<#DiagnosisMeasurementOutput>, | |
| indiv:examination@<#DiagnosisMeasurementProcess>, | |
| indiv:role@<#PatientRoleShape>, | |
| <https://databases.lovd.nl/shared/individuals/00000125>@<#PersonShape>, | |
| indiv:identifier@<#PatientIdentifierShape>, | |
| status: conformant |
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| PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | |
| PREFIX indiv: <https://databases.lovd.nl/shared/individuals/00000125#> | |
| PREFIX sio: <https://sio.semanticscience.org/resource/SIO_> | |
| PREFIX ncit: <http://purl.obolibrary.org/obo/NCIT_> | |
| <#PatientIdentifierShape> CLOSED { | |
| a [sio:000115]; # identifier | |
| rdfs:label ["Identifier"]?; | |
| /*denotes */ sio:000020 @<#PatientRoleShape>; | |
| /*has value */ sio:000300 /[0-9]+/ | |
| } | |
| <#PersonShape> CLOSED { | |
| a [sio:000498]; # person | |
| rdfs:label ["Person"]?; | |
| /*has identifier */ sio:000671 @<#PatientIdentifierShape>; | |
| /*has role */ sio:000228 @<#PatientRoleShape>; | |
| /*has attribute */ sio:000008 @<#DiagnosisMeasurementProcess>; | |
| sio:000008 @<#GenotypeAttribute>+ | |
| } | |
| <#PatientRoleShape> CLOSED { | |
| a [sio:000016]; # role | |
| a [<http://purl.obolibrary.org/obo/OBI_0000093>]; | |
| rdfs:label ["Patient role"]; | |
| /*is realized in */ sio:000356 @<#DiagnosisMeasurementProcess>; | |
| sio:000356 @<#GeneticMeasurementProcess> | |
| } | |
| <#DiagnosisMeasurementProcess> CLOSED { | |
| a [sio:000006]; # process | |
| a [ncit:C15220]; # Diagnosis | |
| rdfs:label ["Diagnosis measurement process"]; | |
| /*has output */ sio:000229 @<#DiagnosisMeasurementOutput> | |
| } | |
| <#DiagnosisMeasurementOutput> CLOSED { | |
| a [ncit:C70856]; # Observation Result | |
| a [sio:000015]; # information content entity | |
| rdfs:label ["Diagnosis measurement output"]; | |
| /*refers to */ sio:000628 @<#DiagnosisAttribute> | |
| } | |
| <#DiagnosisAttribute> CLOSED { | |
| a [sio:000614]; # attribute | |
| a [<https://www.omim.org/entry/243500>]; | |
| rdfs:label ["Diagnosis attribute"]; | |
| /*is about */ sio:000332 [ncit:C2991] # Disease or Disorder | |
| } | |
| <#GeneticMeasurementProcess> CLOSED { | |
| a [sio:000006]; # process | |
| a [ncit:C15709]; # Genetic Testing | |
| rdfs:label ["Genetic measurement process"]; | |
| /*has participant */ sio:000132 IRI; # should a regex enforce this as a HUGO URL? | |
| /*has input */ sio:000230 [sio:010010]; # deoxyribonucleic acid | |
| sio:000230 [sio:010450]; # RNA transcript | |
| /*has output */ sio:000229 @<#GeneticMeasurementOutput>+ | |
| } | |
| <#GenotypeAttribute> CLOSED { | |
| a [sio:000614]; | |
| a [ncit:C103223]; # Genetic Finding | |
| rdfs:label ["Genetic attribute"] | |
| } | |
| <#GeneticMeasurementOutput> CLOSED { | |
| a [sio:000015]; # information content entity | |
| a [ncit:C45766]; # Genomic Identifier | |
| rdfs:label ["Genetic measurement output"]; | |
| /*refers to */ sio:000628 @<#GenotypeAttribute>; | |
| /*has part */ sio:000028 @<#VariantOnGenome>; | |
| sio:000028 @<#VariantOnTranscription> | |
| } | |
| <#VariantOnGenome> CLOSED { | |
| a [sio:000015]; # information content entity | |
| a [ncit:C172243]; # HGVS Genomic Variation Annotation | |
| /*has value */ sio:000300 /NC_[0-9]+\.[0-9]:g\.[0-9]+G>A/ | |
| } | |
| <#VariantOnTranscription> CLOSED { | |
| a [sio:000015]; # information content entity | |
| a [ncit:C172244]; # HGVS Transcript Variation Annotation | |
| /*Gene identifier */ ncit:C48664 IRI; # HUGO URL? | |
| /*Gene symbol */ ncit:C43568 ["IVD"]; | |
| /*NCBI transcript ID*/ ncit:C171335 /NM_[0-9]+\.[0-9]/; | |
| /*has value */ sio:000300 /NM_[0-9]+\.[0-9]:[c]\.[0-9]{3}(\+1G>A)?/ | |
| } | |
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| PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | |
| PREFIX indiv: <https://databases.lovd.nl/shared/individuals/00000125#> | |
| PREFIX sio: <https://sio.semanticscience.org/resource/SIO_> | |
| PREFIX ncit: <http://purl.obolibrary.org/obo/NCIT_> | |
| # Example TTL file, based on https://databases.lovd.nl/shared/individuals/00000125. | |
| # This Identifier is an Identifier; | |
| indiv:identifier a sio:000115; | |
| # has label "Identifier"; | |
| rdfs:label "Identifier"; | |
| # denotes a Role; | |
| sio:000020 indiv:role; | |
| # has value "00000125". | |
| sio:000300 "00000125" . | |
| # This Individual is a Person; | |
| <https://databases.lovd.nl/shared/individuals/00000125> a sio:000498; | |
| # has label "Person"; | |
| rdfs:label "Person"; | |
| # has an identifier; | |
| sio:000671 indiv:identifier; | |
| # has a Role; | |
| sio:000228 indiv:role; | |
| # has attributes Examination and Genotype. | |
| sio:000008 indiv:examination, | |
| <https://databases.lovd.nl/shared/screenings/0000000117#genotype> . | |
| # This Role is a Role and a Patient role; | |
| indiv:role a sio:000016, | |
| <http://purl.obolibrary.org/obo/OBI_0000093>; | |
| # has label "Patient role"; | |
| rdfs:label "Patient role"; | |
| # is realized in Examination and Screening. | |
| sio:000356 indiv:examination, | |
| <https://databases.lovd.nl/shared/screenings/0000000117> . | |
| # Examination. This is the "Diagnosis measurement process". | |
| # This Examination is a Process and a Diagnosis; (I don't agree with the latter; it would better be described as a "Diagnostic procedure" (http://purl.obolibrary.org/obo/NCIT_C18020).) | |
| indiv:examination a sio:000006, | |
| ncit:C15220; | |
| # has label "Diagnosis measurement process"; | |
| rdfs:label "Diagnosis measurement process"; | |
| # has output Findings. | |
| sio:000229 indiv:findings . | |
| # Findings. This is the "Diagnosis output". | |
| # There are actually no values here. There are units and frequency, but it's not clear what we can store here. | |
| # These Findings are an Observation result and an Information content entity; | |
| indiv:findings a ncit:C70856, | |
| sio:000015; | |
| # has label "Diagnosis measurement output"; | |
| rdfs:label "Diagnosis measurement output"; | |
| # refers to Diagnosis. | |
| sio:000628 indiv:diagnosis . | |
| # Diagnosis. This is the "Diagnosis attribute". | |
| # Diagnosis is a Attribute and Isovaleric acidemia; | |
| indiv:diagnosis a sio:000614, | |
| <https://www.omim.org/entry/243500>; | |
| # has label "Diagnosis attribute"; | |
| rdfs:label "Diagnosis attribute"; | |
| # is about Disease or disorder. | |
| sio:000332 ncit:C2991 . | |
| # Screening. This is the "Genotype measurement process". | |
| # This Screening is a Process and a Genetic Testing; | |
| <https://databases.lovd.nl/shared/screenings/0000000117> a sio:000006, | |
| ncit:C15709; | |
| # has label "Genetic measurement process"; | |
| rdfs:label "Genetic measurement process"; | |
| # has participant IVD gene; (this was added by me; I am trying to explain genes are screened and couldn't find a better relationship than participant; the example data uses SIO_000229, has_output, which makes no sense at all.) | |
| sio:000132 <https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:6186>; | |
| # has input DNA and RNA; | |
| sio:000230 sio:010010, | |
| sio:010450; | |
| # has output Variants. | |
| sio:000229 <https://databases.lovd.nl/shared/variants/0000001344>, | |
| <https://databases.lovd.nl/shared/variants/0000001345> . | |
| # Genotype. This is the "Genotype attribute". There is actually no data here, so what is the sense? | |
| # This Genotype is an Attribute and a Genetic finding. | |
| <https://databases.lovd.nl/shared/screenings/0000000117#genotype> a sio:000614, | |
| ncit:C103223; | |
| # has label "Genetic attribute". | |
| rdfs:label "Genetic attribute". | |
| # Genetic code. This doesn't seem to have a name in the graph, it's merely described as "HGVS/OMIM/HGNC genetic code". | |
| # This Genetic code is an Information content entity and a Genomic identifier; | |
| <https://databases.lovd.nl/shared/variants/0000001344> a sio:000015, | |
| ncit:C45766; | |
| # has label "Genetic measurement output"; | |
| rdfs:label "Genetic measurement output"; | |
| # refers to Genotype; (I don't know why, because Genotype doesn't contain any data.) | |
| sio:000628 <https://databases.lovd.nl/shared/screenings/0000000117#genotype>; | |
| # has part VOG + VOTs. I added this myself, as I don't want to add loose values. | |
| sio:000028 <https://databases.lovd.nl/shared/variants/0000001344#vog>, | |
| <https://databases.lovd.nl/shared/variants/0000001344#00000064> . | |
| # VOG (added by me). | |
| # This VOG is an Information content entity and HGVS Genomic Variation Annotation; | |
| <https://databases.lovd.nl/shared/variants/0000001344#vog> a sio:000015, | |
| ncit:C172243; | |
| # has value "NC_000015.9:g.40702997G>A". | |
| sio:000300 "NC_000015.9:g.40702997G>A" . | |
| # VOT (added by me). | |
| # This VOT is an Information content entity and HGVS Transcript Variation Annotation; | |
| <https://databases.lovd.nl/shared/variants/0000001344#00000064> a sio:000015, | |
| ncit:C172244; | |
| # Gene identifier; | |
| ncit:C48664 <https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:6186>; | |
| # Gene symbol; | |
| ncit:C43568 "IVD"; | |
| # NCBI transcript identifier; | |
| ncit:C171335 "NM_002225.3"; | |
| # has value "NM_002225.3:c.465+1G>A". | |
| sio:000300 "NM_002225.3:c.465+1G>A" . | |
| # Genetic code. This doesn't seem to have a name in the graph, it's merely described as "HGVS/OMIM/HGNC genetic code". | |
| # This Genetic code is an Information content entity and a Genomic identifier; | |
| <https://databases.lovd.nl/shared/variants/0000001345> a sio:000015, | |
| ncit:C45766; | |
| # has label "Genetic measurement output"; | |
| rdfs:label "Genetic measurement output"; | |
| # refers to Genotype; (I don't know why, because Genotype doesn't contain any data.) | |
| sio:000628 <https://databases.lovd.nl/shared/screenings/0000000117#genotype>; | |
| # has part VOG + VOTs. I added this myself, as I don't want to add loose values. | |
| sio:000028 <https://databases.lovd.nl/shared/variants/0000001345#vog>, | |
| <https://databases.lovd.nl/shared/variants/0000001345#00000064> . | |
| # VOG (added by me). | |
| # This VOG is an Information content entity and HGVS Genomic Variation Annotation; | |
| <https://databases.lovd.nl/shared/variants/0000001345#vog> a sio:000015, | |
| ncit:C172243; | |
| # has value "NC_000015.9:g.40699897G>A". | |
| sio:000300 "NC_000015.9:g.40699897G>A" . | |
| # VOT (added by me). | |
| # This VOT is an Information content entity and HGVS Transcript Variation Annotation; | |
| <https://databases.lovd.nl/shared/variants/0000001345#00000064> a sio:000015, | |
| ncit:C172244; | |
| # Gene identifier; | |
| ncit:C48664 <https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:6186>; | |
| # Gene symbol; | |
| ncit:C43568 "IVD"; | |
| # NCBI transcript identifier; | |
| ncit:C171335 "NM_002225.3"; | |
| # has value "NM_002225.3:c.214G>A". | |
| sio:000300 "NM_002225.3:c.214G>A" . | |
| # FIXME: Classification? Effect? | |
| # affects: http://semanticscience.org/resource/SIO_001158 | |
| # function: http://semanticscience.org/resource/SIO_000017 |
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