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LOVD.ttl
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LOVD.ttl
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PREFIX lovd: <https://databases.lovd.nl/shared/>
PREFIX ncit: <http://purl.obolibrary.org/obo/NCIT_>
PREFIX omim: <https://www.omim.org/entry/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX sio: <https://sio.semanticscience.org/resource/SIO_>
## Example TTL file, based on https://databases.lovd.nl/shared/individuals/00000125.
# EJP-RD CDE standard element.
# This Identifier is an Identifier;
lovd:individuals\/00000125\#identifier a sio:000115;
# has label "Identifier";
rdfs:label "Identifier";
# denotes a Role;
sio:000020 lovd:individuals\/00000125\#role;
# has value "00000125".
sio:000300 "00000125" .
# Individual; an EJP-RD CDE standard element.
# This Individual is a Person;
lovd:individuals\/00000125 a sio:000498;
# has label "Person";
rdfs:label "Person";
# has an identifier;
sio:000671 lovd:individuals\/00000125\#identifier;
# has a Role;
sio:000228 lovd:individuals\/00000125\#role;
# has attributes Examination and Genotype.
sio:000008 lovd:individuals\/00000125\#examination,
lovd:screenings\/0000000117\#genotype .
# Role; an EJP-RD CDE standard element.
# This Role is a Role and a Patient role;
lovd:individuals\/00000125\#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 lovd:individuals\/00000125\#examination,
lovd:screenings\/0000000117 .
# Examination; an EJP-RD CDE standard element. This is the "Diagnosis measurement process".
# This Examination is a Process and a Diagnosis;
# FIXME: I don't agree with the latter; wouldn't it better be described as a "Diagnostic procedure" (ncit:C18020)?
lovd:individuals\/00000125\#examination a sio:000006,
ncit:C15220;
# has label "Diagnosis measurement process";
rdfs:label "Diagnosis measurement process";
# has output Findings.
sio:000229 lovd:individuals\/00000125\#findings .
# Findings; an EJP-RD CDE standard element. This is the "Diagnosis output".
# These Findings are an Observation result and an Information content entity;
# FIXME: There are actually no values here. There are units and frequency, but it's not clear what we can store here.
lovd:individuals\/00000125\#findings a ncit:C70856,
sio:000015;
# has label "Diagnosis measurement output";
rdfs:label "Diagnosis measurement output";
# refers to Diagnosis.
sio:000628 lovd:individuals\/00000125\#diagnosis .
# Diagnosis; an EJP-RD CDE standard element. This is the "Diagnosis attribute".
# Diagnosis is a Attribute and Isovaleric acidemia;
lovd:individuals\/00000125\#diagnosis a sio:000614,
omim:243500;
# has label "Diagnosis attribute";
rdfs:label "Diagnosis attribute";
# is about Disease or disorder.
sio:000332 ncit:C2991 .
# Screening; an EJP-RD CDE standard element, with custom additions. This is the "Genotype measurement process".
# This Screening is a Process and a Genetic Testing;
lovd:screenings\/0000000117 a sio:000006,
ncit:C15709;
# has label "Genetic measurement process";
rdfs:label "Genetic measurement process";
# has participant IVD gene;
# NOTE: This was added for LOVD; genes are screened, so they are participants, not output.
sio:000132 <https://identifiers.org/hgnc:6186>;
# has input DNA and RNA;
sio:000230 sio:010010,
sio:010450;
# has output Variants.
sio:000229 lovd:variants\/0000001344,
lovd:variants\/0000001345 .
# Genotype; an EJP-RD CDE standard element. This is the "Genotype attribute".
# This Genotype is an Attribute and a Genetic finding;
# FIXME: There are actually no values here. It's not clear what we can store here.
lovd:screenings\/0000000117\#genotype a sio:000614,
ncit:C103223;
# has label "Genetic attribute".
rdfs:label "Genetic attribute".
# Genetic code; an EJP-RD CDE standard element, with custom additions.
# 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;
lovd:variants\/0000001344 a sio:000015,
ncit:C45766;
# has label "Genetic measurement output";
rdfs:label "Genetic measurement output";
# refers to Genotype;
sio:000628 lovd:screenings\/0000000117\#genotype;
# has part VOG + VOTs.
# NOTE: This was added for LOVD; a variant contains one VOG and any number of VOTs.
sio:000028 lovd:variants\/0000001344\#vog,
lovd:variants\/0000001344\#00000064 .
# VOG; a custom element added for LOVD.
# This VOG is an Information content entity and HGVS Genomic Variation Annotation;
lovd: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; a custom element added for LOVD.
# This VOT is an Information content entity and HGVS Transcript Variation Annotation;
lovd:variants\/0000001344\#00000064 a sio:000015,
ncit:C172244;
# Gene identifier;
ncit:C48664 <https://identifiers.org/hgnc:6186>;
# Gene symbol;
ncit:C43568 "IVD";
# NCBI transcript identifier;
ncit:C171335 "NM_002225.3";
# has value "c.465+1G>A";
sio:000300 "c.465+1G>A";
# is transcribed into "r.296_465del";
sio:010080 "r.296_465del";
# is translated into "p.Val99Alafs*5";
sio:010082 "p.Val99Alafs*5";
# has ACMG classification "pathogenic".
ncit:C168798 "pathogenic" .
# Genetic code; an EJP-RD CDE standard element, with custom additions.
# 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;
lovd:variants\/0000001345 a sio:000015,
ncit:C45766;
# has label "Genetic measurement output";
rdfs:label "Genetic measurement output";
# refers to Genotype;
sio:000628 lovd:screenings\/0000000117\#genotype;
# has part VOG + VOTs.
# NOTE: This was added for LOVD; a variant contains one VOG and any number of VOTs.
sio:000028 lovd:variants\/0000001345\#vog,
lovd:variants\/0000001345\#00000064 .
# VOG; a custom element added for LOVD.
# This VOG is an Information content entity and HGVS Genomic Variation Annotation;
lovd: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; a custom element added for LOVD.
# This VOT is an Information content entity and HGVS Transcript Variation Annotation;
lovd:variants\/0000001345\#00000064 a sio:000015,
ncit:C172244;
# Gene identifier;
ncit:C48664 <https://identifiers.org/hgnc:6186>;
# Gene symbol;
ncit:C43568 "IVD";
# NCBI transcript identifier;
ncit:C171335 "NM_002225.3";
# has value "c.214G>A";
sio:000300 "c.214G>A";
# is transcribed into "r.[214g>a; 154_243del]";
sio:010080 "r.[214g>a,154_243del]";
# is translated into "p.[Asp72Asn,Leu52_Arg81del]";
sio:010082 "p.[Asp72Asn,Leu52_Arg81del]";
# has ACMG classification "pathogenic".
ncit:C168798 "pathogenic" .