Get the biochementities of an ontology from space members
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listing the curation states that "approved", apply to the winning definition: "deprecated" (owl:DeprecatedClass), "withdrawn" (gen:WithdrawnTerm) and "example" (npx:ExampleNanopub), in that order.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.
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