https://w3id.org/np/RAkb9lmkKVrKgmBNiYuK1GSmTL5xlHVRVpbsCiVVROuPo
.trig | .trig.txt | .jelly | .jelly.txt | .jsonld | .jsonld.txt | .nq | .nq.txt | .xml | .xml.txt
@prefix this: <https://w3id.org/np/RAkb9lmkKVrKgmBNiYuK1GSmTL5xlHVRVpbsCiVVROuPo> .
@prefix sub: <https://w3id.org/np/RAkb9lmkKVrKgmBNiYuK1GSmTL5xlHVRVpbsCiVVROuPo/> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix dct: <http://purl.org/dc/terms/> .
@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#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
sub:Head {
this: a np:Nanopublication;
np:hasAssertion sub:assertion;
np:hasProvenance sub:provenance;
np:hasPublicationInfo sub:pubinfo .
}
sub:assertion {
sub:get-biochementities-from-space-members a <https://w3id.org/kpxl/grlc/grlc-query>;
dct:description "Like 'Get the classes of an ontology from space members', but links classes to the ontology via dct:isPartOf (the predicate used by the biochementity template). Returns the biochementities (owl:Class) that declare dct:isPartOf the given resource, restricted to nanopubs published by an admin, maintainer, or member of the space that maintains the resource. The maintaining space and its validated member public-key hashes are resolved server-side from the spaces repo (/repo/spaces); observers are excluded. Each class URI appears once, kept from the latest (by nanopub timestamp) member-published definition. Superclass labels are taken from the superclass' own rdfs:label when it is a biochementity in the same ontology. The status column is a multi-value literal listing the curation states that \"approved\", apply to the winning definition: \"deprecated\" (owl:DeprecatedClass), \"withdrawn\" (gen:WithdrawnTerm) and \"example\" (npx:ExampleNanopub), in that order. It replaces the former types column. A version counts as approved when the newest non-invalidated approval/disapproval nanopublication targeting it is an npx:approvesOf (latest wins across all publishers: a later npx:disapprovesOf neutralises an earlier approval, and a later approval reinstates it), its publisher signed with a key that belongs to a current member+ of the maintaining space, and that publisher is not the signer of the nanopublication being approved (self-approval never counts). The approve_target, disapprove_target and approval_choice columns are action data rather than content: exactly one of the two targets is non-empty per row -- approve_target while the row is unapproved, disapprove_target once it is approved -- so a view can offer a per-row approve/disapprove action whose label follows the current state, and approval_choice carries the matching npx predicate to pre-fill in the approval template. A contribution signed by a software agent (an npx:SoftwareAgent that declares its own key, e.g. a curation bot) counts as approved by default, on the grounds that the space admitted it as a member: no separate npx:approvesOf is needed. The default is only a starting point -- an outstanding member disapproval overrides it, and disapproving then re-approving returns the nanopublication to the explicit state. Human contributions carry no default and start out unapproved. The winning verdict per target is now selected by a max() over member-signed verdicts rather than by a nested not-exists, so the disapproval that overturns an approval must itself come from a member -- matching get-term-version-history, and keeping every federated call at one SERVICE level. Approval is judged on the winning definition only, so publishing a new version starts it out unapproved. Because approval nanopublications do not carry the owl:Class nanopub type they are absent from the type-scoped endpoint this query runs on, so the set of currently approved class nanopublications is resolved once per request by a self-contained sub-select that federates to /repo/full for the approvals and to /repo/spaces for the approvers' member keys. Note that \"withdrawn\" can never appear here because withdrawn classes are excluded by the filter below; the branch is kept so the expression matches the one in get-term-version-history and still works if that filter is ever relaxed. Classes whose winning definition types them gen:WithdrawnTerm are withdrawn from the vocabulary and are excluded entirely; withdrawal is judged on the winning definition only, so publishing a new version without that type reinstates the class. The last_modified_by/last_modified columns give the signer and timestamp of that latest definition; the signer name is resolved from the trust repo (/repo/trust) or left blank.";
dct:license <http://www.apache.org/licenses/LICENSE-2.0>;
rdfs:label "Get the biochementities of an ontology from space members";
<https://w3id.org/kpxl/grlc/endpoint> <https://w3id.org/np/l/nanopub-query-1.1/repo/type/e8cc5bb29ec5597303f8f101c65c545dc124ee0df68ce733764b03adc3237184>;
<https://w3id.org/kpxl/grlc/sparql> """prefix owl: <http://www.w3.org/2002/07/owl#>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix dct: <http://purl.org/dc/terms/>
prefix np: <http://www.nanopub.org/nschema#>
prefix npa: <http://purl.org/nanopub/admin/>
prefix npx: <http://purl.org/nanopub/x/>
prefix skos: <http://www.w3.org/2004/02/skos/core#>
prefix gen: <https://w3id.org/kpxl/gen/terms/>
prefix foaf: <http://xmlns.com/foaf/0.1/>
select ?class ?class_label ?description ?superclasses_multi_iri ?superclasses_label_multi
?status_multi
?last_modified_by (sample(?lmbl) as ?last_modified_by_label) ?last_modified
(?np as ?override_target) ?approve_target ?disapprove_target ?approval_choice ?np ?np_label where {
{
select ?class ?class_label (?definition as ?description)
(group_concat(distinct str(?superclass); separator=\" \") as ?superclasses_multi_iri)
(group_concat(distinct replace(replace(coalesce(?superclass_lbl, str(?superclass)), \"\\\\\\\\\", \"\\\\\\\\\\\\\\\\\"), \"[\\r\\n]+\", \"\\\\\\\\n\"); separator=\"\\n\") as ?superclasses_label_multi)
?status_multi ?approve_target ?disapprove_target ?approval_choice
(sample(?user) as ?last_modified_by) (sample(?date) as ?last_modified)
?np (\"^\" as ?np_label) where {
values ?_ontology_multi_iri {}
service <https://w3id.org/np/l/nanopub-query-1.1/repo/spaces> {
select (group_concat(?mpk; separator=\" \") as ?memberPubkeys) where {
graph npa:graph { npa:thisRepo npa:hasCurrentSpaceState ?stateG . }
values ?_ontology_multi_iri {}
graph ?stateG {
?_ontology_multi_iri npa:isMaintainedBy? ?space .
?ri a gen:RoleInstantiation ; npa:forSpace ?space ; npa:forAgent ?agent ;
npa:hasRoleType ?rt .
filter(?rt in (gen:AdminRole, gen:MaintainerRole, gen:MemberRole))
?acct a npa:AccountState ; npa:agent ?agent ; npa:pubkey ?mpk .
}
}
}
graph npa:graph {
?np npx:hasNanopubType owl:Class .
?np npa:hasValidSignatureForPublicKeyHash ?pubkey .
filter not exists { ?npx npx:invalidates ?np ; npa:hasValidSignatureForPublicKeyHash ?pubkey . }
?np dct:created ?date .
?np npx:introduces ?class .
?np np:hasAssertion ?a .
optional { ?np npx:signedBy ?user . }
}
filter(contains(?memberPubkeys, ?pubkey))
{
select (group_concat(distinct ?apV; separator=\" \") as ?approvedNps)
(group_concat(distinct ?disV; separator=\" \") as ?disapprovedNps) where {
{
select ?vTarget (max(concat(str(?vDate), \">\", str(?vNp), \">\", ?vMark)) as ?vWin) where {
values ?_ontology_multi_iri {}
service <https://w3id.org/np/l/nanopub-query-1.1/repo/spaces> {
select (group_concat(?vpk; separator=\" \") as ?vMemberPubkeys) where {
graph npa:graph { npa:thisRepo npa:hasCurrentSpaceState ?vStateG . }
values ?_ontology_multi_iri {}
graph ?vStateG {
?_ontology_multi_iri npa:isMaintainedBy? ?vSpace .
?vRi a gen:RoleInstantiation ; npa:forSpace ?vSpace ; npa:forAgent ?vMember ;
npa:hasRoleType ?vRt .
filter(?vRt in (gen:AdminRole, gen:MaintainerRole, gen:MemberRole))
?vAcct a npa:AccountState ; npa:agent ?vMember ; npa:pubkey ?vpk .
}
}
}
service <https://w3id.org/np/l/nanopub-query-1.1/repo/full> {
select distinct ?vTarget ?vNp ?vDate ?vPubkey ?vMark where {
graph npa:graph {
?vTarget npx:hasNanopubType owl:Class ; npx:signedBy ?targetAgent .
?vNp npx:signedBy ?vAgent ;
npa:hasValidSignatureForPublicKeyHash ?vPubkey ;
dct:created ?vDate ;
np:hasAssertion ?vA .
filter not exists { ?vInv npx:invalidates ?vNp ; npa:hasValidSignatureForPublicKeyHash ?vPubkey . }
}
graph ?vA { ?vAgent ?vPred ?vTarget . }
values ?vPred { npx:approvesOf npx:disapprovesOf }
filter(?vAgent != ?targetAgent)
bind(if(?vPred = npx:approvesOf, \"a\", \"d\") as ?vMark)
}
}
filter(contains(?vMemberPubkeys, ?vPubkey))
} group by ?vTarget
}
bind(if(strends(?vWin, \"a\"), str(?vTarget), \"\") as ?apV)
bind(if(strends(?vWin, \"d\"), str(?vTarget), \"\") as ?disV)
}
}
{
select (group_concat(distinct str(?saAgent); separator=\" \") as ?trustedBots) where {
service <https://w3id.org/np/l/nanopub-query-1.1/repo/type/77757cabf6184c51c20b8b0fe5dc5e1365b7f628448335184ad54319a0affdfc> {
graph ?saA { ?saAgent a npx:SoftwareAgent . ?saKd npx:declaredBy ?saAgent . }
}
}
}
graph ?a {
?class dct:isPartOf ?_ontology_multi_iri .
optional { ?class rdfs:label ?class_label . filter(lang(?class_label) = \"\") }
optional { ?class skos:definition ?definition . }
optional { ?class rdfs:subClassOf ?superclass . filter(isIRI(?superclass)) }
}
filter not exists { graph ?a { ?class a gen:WithdrawnTerm } }
bind(coalesce(?user, <http://purl.org/nanopub/temp/none>) as ?userSafe)
bind(contains(concat(\" \", ?approvedNps, \" \"), concat(\" \", str(?np), \" \")) as ?explicitApproved)
bind(contains(concat(\" \", ?disapprovedNps, \" \"), concat(\" \", str(?np), \" \")) as ?explicitDisapproved)
bind(contains(concat(\" \", ?trustedBots, \" \"), concat(\" \", str(?userSafe), \" \")) as ?isTrustedBot)
bind(?explicitApproved || (?isTrustedBot && !?explicitDisapproved) as ?isApproved)
bind(if(?isApproved, \"\", str(?np)) as ?approve_target)
bind(if(?isApproved, str(?np), \"\") as ?disapprove_target)
bind(if(?isApproved, str(npx:disapprovesOf), str(npx:approvesOf)) as ?approval_choice)
bind(replace(concat(
if(?isApproved, \"approved\\n\", \"\"),
if(exists { graph ?a { ?class a owl:DeprecatedClass } }, \"deprecated\\n\", \"\"),
if(exists { graph ?a { ?class a gen:WithdrawnTerm } }, \"withdrawn\\n\", \"\"),
if(exists { graph npa:graph { ?np npx:hasNanopubType npx:ExampleNanopub } }, \"example\\n\", \"\")
), \"\\n$\", \"\") as ?status_multi)
filter not exists {
graph npa:graph {
?np2 npx:hasNanopubType owl:Class .
?np2 npa:hasValidSignatureForPublicKeyHash ?pubkey2 .
filter not exists { ?np2x npx:invalidates ?np2 ; npa:hasValidSignatureForPublicKeyHash ?pubkey2 . }
?np2 dct:created ?date2 .
?np2 npx:introduces ?class .
?np2 np:hasAssertion ?a2 .
}
filter(contains(?memberPubkeys, ?pubkey2))
graph ?a2 { ?class dct:isPartOf ?_ontology_multi_iri . }
filter(?date2 > ?date || (?date2 = ?date && str(?np2) > str(?np)))
}
optional {
select ?superclass (sample(?sclbl) as ?superclass_lbl) where {
values ?_ontology_multi_iri {}
graph npa:graph { ?scnp npx:hasNanopubType owl:Class ; npx:introduces ?superclass ; np:hasAssertion ?sca . }
graph ?sca { ?superclass dct:isPartOf ?_ontology_multi_iri ; rdfs:label ?sclbl . }
} group by ?superclass
}
} group by ?class ?class_label ?definition ?status_multi ?approve_target ?disapprove_target ?approval_choice ?np
}
optional {
service <https://w3id.org/np/l/nanopub-query-1.1/repo/trust> {
select ?last_modified_by ?lmbl where {
graph npa:graph { npa:thisRepo npa:hasCurrentTrustState ?tg . }
graph ?tg { ?last_modified_by foaf:name ?lmbl . }
}
}
}
}
group by ?class ?class_label ?description ?superclasses_multi_iri ?superclasses_label_multi ?status_multi ?last_modified_by ?last_modified ?approve_target ?disapprove_target ?approval_choice ?np ?np_label
order by ?class_label""" .
}
sub:provenance {
sub:assertion prov:wasAttributedTo orcid:0000-0002-1267-0234 .
}
sub:pubinfo {
orcid:0000-0002-1267-0234 foaf:name "Tobias Kuhn" .
this: dct:created "2026-08-12T08:51:20Z"^^xsd:dateTime;
dct:creator orcid:0000-0002-1267-0234;
dct:license <https://creativecommons.org/publicdomain/zero/1.0/>;
npx:embeds sub:get-biochementities-from-space-members;
npx:supersedes <https://w3id.org/np/RAyPwuo3lQ0wzSQaYHf30hkeI5BzKljRxp9hHJqsl9p9c>;
rdfs:label "Get the biochementities of an ontology from space members";
nt:wasCreatedFromProvenanceTemplate <https://w3id.org/np/RA7lSq6MuK_TIC6JMSHvLtee3lpLoZDOqLJCLXevnrPoU>;
nt:wasCreatedFromPubinfoTemplate <https://w3id.org/np/RACJ58Gvyn91LqCKIO9zu1eijDQIeEff28iyDrJgjSJF8>,
<https://w3id.org/np/RAoTD7udB2KtUuOuAe74tJi1t3VzK0DyWS7rYVAq1GRvw>, <https://w3id.org/np/RAukAcWHRDlkqxk7H2XNSegc1WnHI569INvNr-xdptDGI>;
nt:wasCreatedFromTemplate <https://w3id.org/np/RAEFAt-QcFK0ZhqfvlsmS10BnzGJA0xwOICZXkO-ai87k> .
sub:sig npx:hasAlgorithm "RSA";
npx:hasPublicKey "MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQCwUtewGCpT5vIfXYE1bmf/Uqu1ojqnWdYxv+ySO80ul8Gu7m8KoyPAwuvaPj0lvPtHrg000qMmkxzKhYknEjq8v7EerxZNYp5B3/3+5ZpuWOYAs78UnQVjbHSmDdmryr4D4VvvNIiUmd0yxci47dTFUj4DvfHnGd6hVe5+goqdcwIDAQAB";
npx:hasSignature "M+5etTlKdGWYWUJt4sFtb75FcyrNOo6Som2vkR+ZS7L1Z62wOTp2cI4o0wKSfCxaQtgPFr+fnTmTRHBg8nmQ5WlkFK2YXPlBVSDkWkGCs1lGAK9sZB+Nad3TRSWyf4C09S4ultyqB0YY2NTbH54UH8K047hhO6L0yp8EPfM6FeY=";
npx:hasSignatureTarget this:;
npx:signedBy orcid:0000-0002-1267-0234 .
}