http://purl.org/np/RABf4z3vjQrAOkGQRHvW82MrZTqtAsGWU7C9W1niaMOPw
.trig | .trig.txt | .jelly | .jelly.txt
@prefix ns1: <http://purl.org/np/> .
@prefix this: <http://purl.org/np/RABf4z3vjQrAOkGQRHvW82MrZTqtAsGWU7C9W1niaMOPw> .
@prefix sub: <http://purl.org/np/RABf4z3vjQrAOkGQRHvW82MrZTqtAsGWU7C9W1niaMOPw#> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix nt: <https://w3id.org/np/o/ntemplate/> .
@prefix npx: <http://purl.org/nanopub/x/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix orcid: <https://orcid.org/> .
@prefix prov: <http://www.w3.org/ns/prov#> .
sub:Head {
this: a np:Nanopublication;
np:hasAssertion sub:assertion;
np:hasProvenance sub:provenance;
np:hasPublicationInfo sub:pubinfo .
}
sub:assertion {
sub:assertion a nt:AssertionTemplate;
dct:description """<p>This nanopublication makes a statement that in the context of a thing of a certain type (e.g. a mouse), another thing of a certain type (e.g. a gene) tends to have a relation (such as causing) to another thing of a certain type (e.g. a disease) in the same context.</p>
<p>Note that the context is <strong>not</strong> a reference to a general topic or field. It denotes the class for the context in which the relations happen. If each relation is happening in a human, for example, such as a certain condition leading to a certain symptom, then the context class should be 'human'.</p>
<p>The technical background of the super-pattern can be found in <a href=\"https://doi.org/10.1145/3460210.3493561\">this publication</a>.</p>
<p>This is the \"hypothesis\" version of the super-pattern template, where the qualifier is optional.</p>""";
rdfs:label "Expressing a general hypothesis with a super-pattern";
nt:hasStatement sub:st0, sub:st1, sub:st2, sub:st3, sub:st4, sub:st5, sub:st6;
nt:hasTag "Claims" .
sub:contextClass a nt:GuidedChoicePlaceholder;
rdfs:label "URI of the context class";
nt:possibleValue <https://w3id.org/linkflows/superpattern/terms/UniversalContext>;
nt:possibleValuesFromApi "http://purl.org/nanopub/api/find_signed_things?type=http%3A%2F%2Fwww.w3.org%2F2002%2F07%2Fowl%23Class&searchterm=",
"https://www.wikidata.org/w/api.php?action=wbsearchentities&language=en&format=json&limit=5&search=" .
sub:label a nt:LiteralPlaceholder;
rdfs:label "informal label or text for the whole superpattern instance" .
sub:objectClass a nt:GuidedChoicePlaceholder;
rdfs:label "URI of the object class";
nt:possibleValuesFromApi "http://purl.org/nanopub/api/find_signed_things?type=http%3A%2F%2Fwww.w3.org%2F2002%2F07%2Fowl%23Class&searchterm=",
"https://www.wikidata.org/w/api.php?action=wbsearchentities&language=en&format=json&limit=5&search=" .
sub:qualifier a nt:RestrictedChoicePlaceholder;
rdfs:label "URI of the qualifier";
nt:possibleValue <https://w3id.org/linkflows/superpattern/terms/alwaysQualifier>,
<https://w3id.org/linkflows/superpattern/terms/canAlwaysQualifier>, <https://w3id.org/linkflows/superpattern/terms/canFrequentlyNotQualifier>,
<https://w3id.org/linkflows/superpattern/terms/canFrequentlyQualifier>, <https://w3id.org/linkflows/superpattern/terms/canGenerallyNotQualifier>,
<https://w3id.org/linkflows/superpattern/terms/canGenerallyQualifier>, <https://w3id.org/linkflows/superpattern/terms/canMostlyNotQualifier>,
<https://w3id.org/linkflows/superpattern/terms/canMostlyQualifier>, <https://w3id.org/linkflows/superpattern/terms/canNeverQualifier>,
<https://w3id.org/linkflows/superpattern/terms/canSometimesNotQualifier>, <https://w3id.org/linkflows/superpattern/terms/canSometimesQualifier>,
<https://w3id.org/linkflows/superpattern/terms/frequentlyNotQualifier>, <https://w3id.org/linkflows/superpattern/terms/frequentlyQualifier>,
<https://w3id.org/linkflows/superpattern/terms/generallyNotQualifier>, <https://w3id.org/linkflows/superpattern/terms/generallyQualifier>,
<https://w3id.org/linkflows/superpattern/terms/mostlyNotQualifier>, <https://w3id.org/linkflows/superpattern/terms/mostlyQualifier>,
<https://w3id.org/linkflows/superpattern/terms/neverQualifier>, <https://w3id.org/linkflows/superpattern/terms/sometimesNotQualifier>,
<https://w3id.org/linkflows/superpattern/terms/sometimesQualifier> .
sub:relation a nt:GuidedChoicePlaceholder;
rdfs:label "URI of the relation type";
nt:possibleValue <https://w3id.org/linkflows/superpattern/terms/affects>, <https://w3id.org/linkflows/superpattern/terms/causes>,
<https://w3id.org/linkflows/superpattern/terms/contributesTo>, <https://w3id.org/linkflows/superpattern/terms/cooccursWith>,
<https://w3id.org/linkflows/superpattern/terms/decreases>, <https://w3id.org/linkflows/superpattern/terms/enables>,
<https://w3id.org/linkflows/superpattern/terms/follows>, <https://w3id.org/linkflows/superpattern/terms/hasDifferentValueFrom>,
<https://w3id.org/linkflows/superpattern/terms/hasLargerValueThan>, <https://w3id.org/linkflows/superpattern/terms/hasSameValueAs>,
<https://w3id.org/linkflows/superpattern/terms/hasSimilarValueAs>, <https://w3id.org/linkflows/superpattern/terms/hasSmallerValueThan>,
<https://w3id.org/linkflows/superpattern/terms/includes>, <https://w3id.org/linkflows/superpattern/terms/increases>,
<https://w3id.org/linkflows/superpattern/terms/inhibits>, <https://w3id.org/linkflows/superpattern/terms/isCausedBy>,
<https://w3id.org/linkflows/superpattern/terms/isFollowedBy>, <https://w3id.org/linkflows/superpattern/terms/isIncludedIn>,
<https://w3id.org/linkflows/superpattern/terms/isNecessaryAndSufficientFor>, <https://w3id.org/linkflows/superpattern/terms/isSameAs>,
<https://w3id.org/linkflows/superpattern/terms/prevents>, <https://w3id.org/linkflows/superpattern/terms/requires> .
sub:spi a nt:IntroducedResource, nt:LocalResource;
rdfs:label "SPI: - this super-pattern instance" .
sub:st0 rdf:object <https://w3id.org/linkflows/superpattern/terms/SuperPatternInstance>;
rdf:predicate rdf:type;
rdf:subject sub:spi .
sub:st1 rdf:object sub:label;
rdf:predicate rdfs:label;
rdf:subject sub:spi .
sub:st2 rdf:object sub:contextClass;
rdf:predicate <https://w3id.org/linkflows/superpattern/terms/hasContextClass>;
rdf:subject sub:spi .
sub:st3 rdf:object sub:subjectClass;
rdf:predicate <https://w3id.org/linkflows/superpattern/terms/hasSubjectClass>;
rdf:subject sub:spi .
sub:st4 a nt:OptionalStatement;
rdf:object sub:qualifier;
rdf:predicate <https://w3id.org/linkflows/superpattern/terms/hasQualifier>;
rdf:subject sub:spi .
sub:st5 rdf:object sub:relation;
rdf:predicate <https://w3id.org/linkflows/superpattern/terms/hasRelation>;
rdf:subject sub:spi .
sub:st6 rdf:object sub:objectClass;
rdf:predicate <https://w3id.org/linkflows/superpattern/terms/hasObjectClass>;
rdf:subject sub:spi .
sub:subjectClass a nt:GuidedChoicePlaceholder;
rdfs:label "URI of the subject class";
nt:possibleValuesFromApi "http://purl.org/nanopub/api/find_signed_things?type=http%3A%2F%2Fwww.w3.org%2F2002%2F07%2Fowl%23Class&searchterm=",
"https://www.wikidata.org/w/api.php?action=wbsearchentities&language=en&format=json&limit=5&search=" .
rdf:type rdfs:label "This is a - links a thing (left) to a class it belongs (right)" .
rdfs:label rdfs:label "Informally, it can be shown as - links a formal identifier (left) to a human-readable name (right)" .
<https://w3id.org/linkflows/superpattern/terms/SuperPatternInstance> rdfs:label "super-pattern instance - a statement that conforms to the super-pattern" .
<https://w3id.org/linkflows/superpattern/terms/UniversalContext> rdfs:label "universal context (i.e. no context restriction) - The universal context is used in a super-pattern when the subject and object instances of a super-pattern statement happen outside of any obvious context entities (such as the context of \"organism\" in the case of genes affecting diseases)" .
<https://w3id.org/linkflows/superpattern/terms/affects> rdfs:label "affects - the subject instance positively or negatively affects the intensity or frequency of the activity instance of the object" .
<https://w3id.org/linkflows/superpattern/terms/alwaysQualifier> rdfs:label "always - true in 100% of cases" .
<https://w3id.org/linkflows/superpattern/terms/canAlwaysQualifier> rdfs:label "can always - can be made true in 100% cases" .
<https://w3id.org/linkflows/superpattern/terms/canFrequentlyNotQualifier> rdfs:label
"can frequently not - can be made true in at most 90% of cases" .
<https://w3id.org/linkflows/superpattern/terms/canFrequentlyQualifier> rdfs:label
"can frequently - can be made true in at least 10% of cases" .
<https://w3id.org/linkflows/superpattern/terms/canGenerallyNotQualifier> rdfs:label
"can generally not - can be made true in at most 10% of cases" .
<https://w3id.org/linkflows/superpattern/terms/canGenerallyQualifier> rdfs:label "can generally - can be made true in at least 90% of cases" .
<https://w3id.org/linkflows/superpattern/terms/canMostlyNotQualifier> rdfs:label "can mostly not - can be made true in at most 50% of cases" .
<https://w3id.org/linkflows/superpattern/terms/canMostlyQualifier> rdfs:label "can mostly - can be made true in at least 50% of cases" .
<https://w3id.org/linkflows/superpattern/terms/canNeverQualifier> rdfs:label "can never - can be made true in 0% of cases" .
<https://w3id.org/linkflows/superpattern/terms/canSometimesNotQualifier> rdfs:label
"can sometimes not - can be made true in at most 99.9% of cases" .
<https://w3id.org/linkflows/superpattern/terms/canSometimesQualifier> rdfs:label "can sometimes - can be made true in at least 0.1% of cases" .
<https://w3id.org/linkflows/superpattern/terms/causes> rdfs:label "causes - the subject instance causes the existence of the object instance" .
<https://w3id.org/linkflows/superpattern/terms/contributesTo> rdfs:label "contributes to - the subject instance positively affects the intensity or frequency of the activity instance of the object" .
<https://w3id.org/linkflows/superpattern/terms/cooccursWith> rdfs:label "co-occurs with - the subject instance is close to the object instance in terms of space and time" .
<https://w3id.org/linkflows/superpattern/terms/decreases> rdfs:label "decreases - the subject instance causes the value of the object instance to decrease" .
<https://w3id.org/linkflows/superpattern/terms/enables> rdfs:label "enables - the subject instance causes the activity instance of the object to happen" .
<https://w3id.org/linkflows/superpattern/terms/follows> rdfs:label "follows - the object instance came into existence before the subject instance" .
<https://w3id.org/linkflows/superpattern/terms/frequentlyNotQualifier> rdfs:label
"frequently not - true in at most 90% of cases" .
<https://w3id.org/linkflows/superpattern/terms/frequentlyQualifier> rdfs:label "frequently - true in at least 10% of cases" .
<https://w3id.org/linkflows/superpattern/terms/generallyNotQualifier> rdfs:label "generally not - true in at most 10% of cases" .
<https://w3id.org/linkflows/superpattern/terms/generallyQualifier> rdfs:label "generally - true in at least 90% of the cases" .
<https://w3id.org/linkflows/superpattern/terms/hasContextClass> rdfs:label "In the context of all things of type - specifies the context class (right) for the given super-pattern instance (left)" .
<https://w3id.org/linkflows/superpattern/terms/hasDifferentValueFrom> rdfs:label "has different value from - the quantifiable subject instance has a value that is different from the quantifiable object instance" .
<https://w3id.org/linkflows/superpattern/terms/hasLargerValueThan> rdfs:label "has larger value than - the quantifiable subject instance has a larger value than the quantifiable object instance" .
<https://w3id.org/linkflows/superpattern/terms/hasObjectClass> rdfs:label "... to things of type - specifies the object class (right) for the given super-pattern instance (left)" .
<https://w3id.org/linkflows/superpattern/terms/hasQualifier> rdfs:label "... (qualifier) - specifies the qualifier (right) for the given super-pattern statement (left)" .
<https://w3id.org/linkflows/superpattern/terms/hasRelation> rdfs:label "... have a relation of type - specifies the relation type (right) for the given super-pattern statement (left)" .
<https://w3id.org/linkflows/superpattern/terms/hasSameValueAs> rdfs:label "has same value as - the quantifiable subject instance has the same value as the quantifiable object instance" .
<https://w3id.org/linkflows/superpattern/terms/hasSimilarValueAs> rdfs:label "has similar value as - the quantifiable subject instance has a similar value as the quantifiable object instance" .
<https://w3id.org/linkflows/superpattern/terms/hasSmallerValueThan> rdfs:label "has smaller value than - the quantifiable subject instance has a smaller value than the quantifiable object instance" .
<https://w3id.org/linkflows/superpattern/terms/hasSubjectClass> rdfs:label "... things of type - specifies the subject class (right) for the given super-pattern instance (left)" .
<https://w3id.org/linkflows/superpattern/terms/includes> rdfs:label "includes - the subject instance spatiotemporally includes the object instance" .
<https://w3id.org/linkflows/superpattern/terms/increases> rdfs:label "increases - the subject instance causes the value of the object instance to increase" .
<https://w3id.org/linkflows/superpattern/terms/inhibits> rdfs:label "inhibits - the subject instance negatively affects the intensity or frequency of the activity instance of the object" .
<https://w3id.org/linkflows/superpattern/terms/isCausedBy> rdfs:label "is caused by - the existence of the subject instance is caused by the object instance" .
<https://w3id.org/linkflows/superpattern/terms/isFollowedBy> rdfs:label "is followed by - the subject instance comes into existence before the object instance" .
<https://w3id.org/linkflows/superpattern/terms/isIncludedIn> rdfs:label "is included in - the object instance spatiotemporally includes the subject instance" .
<https://w3id.org/linkflows/superpattern/terms/isNecessaryAndSufficientFor> rdfs:label
"is necessary and sufficient for - the subject instance causes the existence of the object instance, which would not come to exist if the subject did not exist" .
<https://w3id.org/linkflows/superpattern/terms/isSameAs> rdfs:label "is same as - the subject instance and the object instance are the same individual" .
<https://w3id.org/linkflows/superpattern/terms/mostlyNotQualifier> rdfs:label "mostly not - true in at most 50% of cases" .
<https://w3id.org/linkflows/superpattern/terms/mostlyQualifier> rdfs:label "mostly - true in at least 50% of cases" .
<https://w3id.org/linkflows/superpattern/terms/neverQualifier> rdfs:label "never - true in 0% of cases" .
<https://w3id.org/linkflows/superpattern/terms/prevents> rdfs:label "prevents - the subject instance causes the activity instance of the object not to happen" .
<https://w3id.org/linkflows/superpattern/terms/requires> rdfs:label "requires - the subject instance would not come to exist if the object instance did not exist" .
<https://w3id.org/linkflows/superpattern/terms/sometimesNotQualifier> rdfs:label "sometimes not - true in at most 99.9% of cases" .
<https://w3id.org/linkflows/superpattern/terms/sometimesQualifier> rdfs:label "sometimes - true in at least 0.1% of cases" .
}
sub:provenance {
sub:assertion prov:wasAttributedTo orcid:0000-0002-1267-0234 .
}
sub:pubinfo {
sub:sig npx:hasAlgorithm "RSA";
npx:hasPublicKey "MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQCjDGQCS1S+SRnERDuYDXOugdYUP0efEquHJEEHAbU/uLzBVlga89zqrNPCS7fBE6lArBUWEmT8eLKdMapyqvAzI1J3jUWTMhDJF+XFBkUiuiFfNSc4vJJcmi0yujtnuzXsRIG202jyaP4f5ULoskFwaZOSBZJfiE0dsB3D7DTIAQIDAQAB";
npx:hasSignature "JuxS39+z6yhDGj/dCHsWZBe7iLBkwP+XHfoRb5TEvPdurHeKR+6dX4f+iR90hRRCTWKLexkC3Ymz4ZR4P90PhQwZXYVQoXZ0x1WOQdzh1xWy4dlJUZHGkGU8t+ns1SwWlR+6XPwVB5o+a+fc5TfyLkM6X4hRc5BdYW5WprLdwks=";
npx:hasSignatureTarget this: .
this: dct:created "2023-07-26T15:27:42.150Z"^^xsd:dateTime;
dct:creator orcid:0000-0002-1267-0234;
dct:license <https://creativecommons.org/licenses/by/4.0/>;
npx:supersedes ns1:RAuMEJ02d8nri9gs9dPOP5L2orn49VrSHT1K5Pjumit1w;
nt:wasCreatedFromProvenanceTemplate ns1:RANwQa4ICWS5SOjw7gp99nBpXBasapwtZF1fIM3H2gYTM;
nt:wasCreatedFromPubinfoTemplate ns1:RAA2MfqdBCzmz9yVWjKLXNbyfBNcwsMmOqcNUxkk1maIM,
ns1:RAh1gm83JiG5M6kDxXhaYT1l49nCzyrckMvTzcPn-iv90, ns1:RAjpBMlw3owYhJUBo3DtsuDlXsNAJ8cnGeWAutDVjuAuI;
nt:wasCreatedFromTemplate ns1:RAcePQpCDGpHwy7tKiEkZ-r1dqWahglraKXhSAwXp_nEs .
}