rows { options { physical_type: PHYSICAL_STREAM_TYPE_QUADS max_name_table_size: 128 max_prefix_table_size: 16 max_datatype_table_size: 16 logical_type: LOGICAL_STREAM_TYPE_DATASETS version: 2 } } rows { prefix { value: "https://w3id.org/np/" } } rows { name { value: "RAeNRMdW7E7NbJ8kYqvzcoetiGxLZTLELHH6gjHovPPI4" } } rows { namespace { name: "this" value { prefix_id: 1 } } } rows { prefix { value: "https://w3id.org/np/RAeNRMdW7E7NbJ8kYqvzcoetiGxLZTLELHH6gjHovPPI4/" } } rows { name { } } rows { namespace { name: "sub" value { prefix_id: 2 } } } rows { prefix { value: "http://www.nanopub.org/nschema#" } } rows { namespace { name: "np" value { prefix_id: 3 name_id: 2 } } } rows { prefix { value: "http://purl.org/dc/terms/" } } rows { namespace { name: "dct" value { prefix_id: 4 name_id: 2 } } } rows { prefix { value: "http://purl.org/nanopub/x/" } } rows { namespace { name: "npx" value { prefix_id: 5 name_id: 2 } } } rows { prefix { value: "http://www.w3.org/2001/XMLSchema#" } } rows { namespace { name: "xsd" value { prefix_id: 6 name_id: 2 } } } rows { prefix { value: "http://www.w3.org/2000/01/rdf-schema#" } } rows { namespace { name: "rdfs" value { prefix_id: 7 name_id: 2 } } } rows { prefix { value: "https://orcid.org/" } } rows { namespace { name: "orcid" value { prefix_id: 8 name_id: 2 } } } rows { prefix { value: "http://www.w3.org/ns/prov#" } } rows { namespace { name: "prov" value { prefix_id: 9 name_id: 2 } } } rows { name { value: "hasAssertion" } } rows { name { value: "assertion" } } rows { name { value: "Head" } } rows { quad { s_iri { prefix_id: 1 name_id: 1 } p_iri { prefix_id: 3 name_id: 3 } o_iri { prefix_id: 2 } g_iri { } } } rows { name { value: "hasProvenance" } } rows { name { value: "provenance" } } rows { quad { p_iri { prefix_id: 3 } o_iri { prefix_id: 2 } } } rows { name { value: "hasPublicationInfo" } } rows { name { value: "pubinfo" } } rows { quad { p_iri { prefix_id: 3 } o_iri { prefix_id: 2 } } } rows { prefix { value: "http://www.w3.org/1999/02/22-rdf-syntax-ns#" } } rows { name { value: "type" } } rows { name { value: "Nanopublication" } } rows { quad { p_iri { prefix_id: 10 } o_iri { prefix_id: 3 } } } rows { name { value: "mac-fdt-v2-cleanup-status" } } rows { name { value: "creator" } } rows { name { value: "0000-0001-8888-635X" } } rows { quad { s_iri { prefix_id: 2 } p_iri { prefix_id: 4 } o_iri { prefix_id: 8 } g_iri { prefix_id: 2 name_id: 4 } } } rows { name { value: "date" } } rows { datatype { value: "http://www.w3.org/2001/XMLSchema#date" } } rows { quad { p_iri { prefix_id: 4 name_id: 15 } o_literal { lex: "2026-06-03" datatype: 1 } } } rows { name { value: "description" } } rows { quad { p_iri { } o_literal { lex: "**MAC FDT v2 catalogue cleanup pass \342\200\224 CLOSED.**\n\n48 nanopub operations on the live Nanopublication Server Network across 5 commits on branch cleanup-upstream-v2:\n\n- 3 upstream /-form v2 re-mints (StayAhead Project FDO + ESM Dataset FDO + AlphaFold Dataset FDO) supersede v1 directly.\n- 3 retractions of intermediate #-form upstream defectives. The nanopub-py 2.0.1 signing pipeline hard-codes # as the FDO referent separator; the MAC catalogue convention is /. Defect surfaced and worked around by switching the signer to nanopub-java 1.88.0 (preserves /). Implementation Guide \302\2476 Appendix C.10 documents the pitfall; the three retraction nanopubs are on-network for verification.\n- 38 Stage 3 v2 instance mints: 3 Type 1 anchors (Alpha N169Y, Epsilon L120R, Eta E152K), 5 method FDOs (ESM2, AlphaFold 2, Bio2Byte AgMata, Bloom Lab DMS, GISAID), 18 computational predictions (RMSD/SASA/pLDDT \303\227 3 variants \303\227 2 methods), 12 final observations (real-world occurrence \303\227 3 + AgMata \303\227 3 + DMS \303\227 3 + WHO \303\227 3). Authoritative v1\342\206\222v2 mapping at docs/v2-cleanup/supersession_registry.md.\n- 4 Stage 4 v2 mints (Alpha knowlet view set: query + pin-action + wrapper + view-display), re-minted June 2 against the Alpha-RBD-Variant v2 referent.\n\nSPARQL verification on query.knowledgepixels.com/repo/full: 38 distinct npx:supersedes Stage 3 v2\342\206\222v1 pairs; 4 distinct npx:supersedes Stage 4 v2\342\206\222v1 pairs; 38 distinct dct:isPartOf to Project v2 referent; 21 distinct dct:source to Dataset v2 referents (12 ESM + 9 AlphaFold); 57 distinct mac:* intra-Stage-3 cross-references to Pass-1 v2 referents. All counts confirmed with SELECT DISTINCT (raw COUNT(*) over-reports 3\303\227 because /repo/full indexes triples across multiple graph views \342\200\224 note for the Tobias addendum).\n\nThree asymmetric Stage 4 URI-form conventions locked + documented: gen:hasViewQuery targets bare query Trusty URI (query as artifact); gen:isDisplayOfView targets gen:View referent URI (View FDO); pin-action nanopubs have no introduced referent (target Space directly). Material for the nanopub-skill second-PR addendum.\n\nHonest commit history preserved on PR #5: the false-start #-form upstream commit 7f7389e remains visible as audit trail rather than rebased away \342\200\224 the false start is the empirical evidence for the nanopub-py defect.\n\nFDT paper v1.0 consolidated on sibling branch paper-v06-consolidation (HEAD 061eefb): \302\2475 Trusty URI tables fully populated with v2 referents (38 substitutions, all HTTP GET-verified at consolidation time); \302\2476.4 expanded with substrate-landscape calibration and variant-PID novelty recalibration; \302\2476.6 regulatory-salience paragraph (EU AI Act, model collapse); \302\2476.7 three-paper companion sequence; \302\2476.8 (new) catalogue refinement and audit trail with Git-parallel architectural framing; 15 new references; target venue updated from Frontiers in Big Data to Digital Twin (Taylor & Francis). No predicate, class, scientific-claim, or SPARQL changes \342\200\224 only catalogue addressing and \302\2476 narrative.\n\nTobias second-PR addendum draft (docs/tobias_skill_addendum.md) ready for submission to the nanopub-skill repo: four operational findings \342\200\224 npx:retracts subject convention, registry content negotiation, SPARQL DISTINCT on /repo/full, publish-to-GET propagation lag. Each section carries an Origin: PROMPT footer for traceability back to the cleanup-pass phase that produced the observation.\n\nWorkstreams unblocked: FDT paper v1.0 ready for review and submission to Digital Twin (Taylor & Francis); FDT pattern paper (3 domains: COVID variants, AMR, mass spectrometry); 45 Implementation Guide narrative refs (mechanical find-replace, deferred); external touchpoints (StayAhead final report, MAC_FAIR_v2 manuscript, slides/posters) catalogued in docs/v2-cleanup/downstream_doc_register.md for work when drafts stabilize.\n\nPR #5 remains open (awaiting paper \302\2474 + Tobias addendum citations before merge). Paper consolidation branch paper-v06-consolidation pushed to origin (PR not yet opened). Branch ahead of main by 6 commits (PR #5) + 2 commits (paper v1.0)." langtag: "en" } } } rows { name { value: "references" } } rows { prefix { value: "https://github.com/easchultes/mac-fdt-staging/pull/" } } rows { name { value: "5" } } rows { quad { p_iri { } o_iri { prefix_id: 11 } } } rows { prefix { value: "https://w3id.org/np/RAPZD8J9dac_FbBmOsjx_5vggqTFlprf_UpYUHgfJGHaM/" } } rows { name { value: "alpha-knowlet" } } rows { quad { o_iri { prefix_id: 12 } } } rows { prefix { value: "https://w3id.org/np/RAXPu-iuezz8swvd6RWIba3VzV0cp94Aq3pTzVst9_nPk/" } } rows { name { value: "StayAhead-Project" } } rows { quad { o_iri { prefix_id: 13 } } } rows { prefix { value: "https://w3id.org/np/RAbvDm28nNtScXcTXEKHbyYdx1yDXQ5zOViy_Dn7LOkkk/" } } rows { name { value: "STAYAHEAD-Dataset2" } } rows { quad { o_iri { prefix_id: 14 } } } rows { prefix { value: "https://w3id.org/np/RAngbyT2iZe4xYUcPnTnDFKDaiL5-tSmoUYzF9RK3LHdE/" } } rows { name { value: "Alpha-RBD-Variant" } } rows { quad { o_iri { prefix_id: 15 } } } rows { prefix { value: "https://w3id.org/np/RAuqwhkDJgVHU8_Fk2gsMw483Iml75Kc09XKR6h0ybO3Q/" } } rows { name { value: "STAYAHEAD-Dataset1" } } rows { quad { o_iri { prefix_id: 16 } } } rows { name { value: "title" } } rows { quad { p_iri { prefix_id: 4 } o_literal { lex: "MAC FDT v2 Catalogue Cleanup \342\200\224 Status Update for KP Office Hours 2026-06-03" } } } rows { prefix { id: 5 value: "http://purl.org/spar/fabio/" } } rows { name { value: "Statement" } } rows { quad { p_iri { prefix_id: 10 name_id: 10 } o_iri { prefix_id: 5 name_id: 25 } } } rows { name { value: "label" } } rows { quad { p_iri { prefix_id: 7 } o_literal { lex: "MAC FDT v2 status update (2026-06-03)" } } } rows { name { value: "wasGeneratedBy" } } rows { prefix { value: "https://w3id.org/spaces/knowledgepixels/incubator/officehours/" } } rows { name { value: "20260603" } } rows { quad { p_iri { prefix_id: 9 } o_iri { prefix_id: 6 } } } rows { name { value: "wasAttributedTo" } } rows { quad { s_iri { prefix_id: 2 name_id: 4 } p_iri { prefix_id: 9 name_id: 29 } o_iri { prefix_id: 8 name_id: 14 } g_iri { prefix_id: 2 name_id: 7 } } } rows { name { value: "created" } } rows { datatype { value: "http://www.w3.org/2001/XMLSchema#dateTime" } } rows { quad { s_iri { prefix_id: 1 name_id: 1 } p_iri { prefix_id: 4 name_id: 30 } o_literal { lex: "2026-06-03T09:00:00Z" datatype: 2 } g_iri { prefix_id: 2 name_id: 9 } } } rows { quad { p_iri { prefix_id: 4 name_id: 13 } o_iri { prefix_id: 8 } } } rows { name { value: "license" } } rows { prefix { id: 3 value: "https://creativecommons.org/licenses/by/4.0/" } } rows { quad { p_iri { prefix_id: 4 name_id: 31 } o_iri { prefix_id: 3 name_id: 2 } } } rows { prefix { id: 11 value: "http://purl.org/nanopub/x/" } } rows { name { value: "introduces" } } rows { quad { p_iri { prefix_id: 11 name_id: 32 } o_iri { prefix_id: 2 name_id: 12 } } } rows { quad { p_iri { prefix_id: 7 name_id: 26 } o_literal { lex: "MAC FDT v2 status update for KP office hours 2026-06-03" } } } rows { name { value: "sig" } } rows { name { value: "hasAlgorithm" } } rows { quad { s_iri { prefix_id: 2 name_id: 33 } p_iri { prefix_id: 11 } o_literal { lex: "RSA" } } } rows { name { value: "hasPublicKey" } } rows { quad { p_iri { } o_literal { lex: "MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQD3w/IUb755GIzp3ueODYkgELhyq4Clygb5Kspge50xo+n8uC/IvXwi+ukRjEpdfX/JZ09yKUCJ2AMMr/QchrsP1Xhg9Q3fEZ4E12XqFd5jX00Qs0K5XZwjBaV8NdDTJW9I4gpcyh0cry7hSBAWHkXEkqbK+lQvR4UFAKejFq6u/wIDAQAB" } } } rows { name { value: "hasSignature" } } rows { quad { p_iri { } o_literal { lex: "OJCrMMWi5+0TcstQvQSx0y5grcY/yajsO81/Z3Bn37hAPwOuYIG4WREgsM9fY6g9ib8mq13SsR+zo83VFQA734/0UcctW+t8IDTlZN23F5giEKYA1PQ3NitX5zmJYQ9Zl/cjmOckcTKCB4+DBoCEdRBkQmeMyLfNzKc3uORQjYk=" } } } rows { name { value: "hasSignatureTarget" } } rows { quad { p_iri { } o_iri { prefix_id: 1 name_id: 1 } } } rows { name { value: "signedBy" } } rows { quad { p_iri { prefix_id: 11 name_id: 38 } o_iri { prefix_id: 8 name_id: 14 } } }