MAC FDT v2 status update for KP office hours 2026-06-03 (explore)

MAC FDT v2 status update for KP office hours 2026-06-03

https://w3id.org/np/RAeNRMdW7E7NbJ8kYqvzcoetiGxLZTLELHH6gjHovPPI4

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MAC FDT v2 status update for KP office hours 2026-06-03 Statement comment... approve/disapprove... edit as derived nanopublication...

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAeNRMdW7E.../mac-fdt-v2-cleanup-status

mac-fdt-v2-cleanup-status

http://purl.org/dc/terms/creator

creator

https://orcid.org/0000-0001-8888-635X

Erik Schultes

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAeNRMdW7E.../mac-fdt-v2-cleanup-status

mac-fdt-v2-cleanup-status

http://purl.org/dc/terms/date

date

(this is a literal)

"2026-06-03"

(xsd:date) .

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mac-fdt-v2-cleanup-status

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description

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"**MAC FDT v2 catalogue cleanup pass — CLOSED.** 48 nanopub operations on the live Nanopublication Server Network across 5 commits on branch cleanup-upstream-v2: - 3 upstream /-form v2 re-mints (StayAhead Project FDO + ESM Dataset FDO + AlphaFold Dataset FDO) supersede v1 directly. - 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 §6 Appendix C.10 documents the pitfall; the three retraction nanopubs are on-network for verification. - 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 × 3 variants × 2 methods), 12 final observations (real-world occurrence × 3 + AgMata × 3 + DMS × 3 + WHO × 3). Authoritative v1→v2 mapping at docs/v2-cleanup/supersession_registry.md. - 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. SPARQL verification on query.knowledgepixels.com/repo/full: 38 distinct npx:supersedes Stage 3 v2→v1 pairs; 4 distinct npx:supersedes Stage 4 v2→v1 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× because /repo/full indexes triples across multiple graph views — note for the Tobias addendum). Three 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. Honest commit history preserved on PR #5: the false-start #-form upstream commit 7f7389e remains visible as audit trail rather than rebased away — the false start is the empirical evidence for the nanopub-py defect. FDT paper v1.0 consolidated on sibling branch paper-v06-consolidation (HEAD 061eefb): §5 Trusty URI tables fully populated with v2 referents (38 substitutions, all HTTP GET-verified at consolidation time); §6.4 expanded with substrate-landscape calibration and variant-PID novelty recalibration; §6.6 regulatory-salience paragraph (EU AI Act, model collapse); §6.7 three-paper companion sequence; §6.8 (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 — only catalogue addressing and §6 narrative. Tobias second-PR addendum draft (docs/tobias_skill_addendum.md) ready for submission to the nanopub-skill repo: four operational findings — 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. Workstreams 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. PR #5 remains open (awaiting paper §4 + 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)."

(en) .

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAeNRMdW7E.../mac-fdt-v2-cleanup-status

mac-fdt-v2-cleanup-status

http://purl.org/dc/terms/references

references

https://github.com/easchultes/mac-fdt-staging/pull/5

pull/5

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAeNRMdW7E.../mac-fdt-v2-cleanup-status

mac-fdt-v2-cleanup-status

http://purl.org/dc/terms/references

references

https://w3id.org/np/RAPZD8J9da.../alpha-knowlet

alpha-knowlet

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAeNRMdW7E.../mac-fdt-v2-cleanup-status

mac-fdt-v2-cleanup-status

http://purl.org/dc/terms/references

references

https://w3id.org/np/RAXPu-iuez.../StayAhead-Project

StayAhead-Project

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAeNRMdW7E.../mac-fdt-v2-cleanup-status

mac-fdt-v2-cleanup-status

http://purl.org/dc/terms/references

references

https://w3id.org/np/RAbvDm28nN.../STAYAHEAD-Dataset2

STAYAHEAD-Dataset2

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAeNRMdW7E.../mac-fdt-v2-cleanup-status

mac-fdt-v2-cleanup-status

http://purl.org/dc/terms/references

references

https://w3id.org/np/RAngbyT2iZ.../Alpha-RBD-Variant

Alpha-RBD-Variant

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAeNRMdW7E.../mac-fdt-v2-cleanup-status

mac-fdt-v2-cleanup-status

http://purl.org/dc/terms/references

references

https://w3id.org/np/RAuqwhkDJg.../STAYAHEAD-Dataset1

STAYAHEAD-Dataset1

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAeNRMdW7E.../mac-fdt-v2-cleanup-status

mac-fdt-v2-cleanup-status

http://purl.org/dc/terms/title

title

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"MAC FDT v2 Catalogue Cleanup — Status Update for KP Office Hours 2026-06-03"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAeNRMdW7E.../mac-fdt-v2-cleanup-status

mac-fdt-v2-cleanup-status

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type

http://purl.org/spar/fabio/Statement

Statement

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mac-fdt-v2-cleanup-status

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"MAC FDT v2 status update (2026-06-03)"

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https://w3id.org/spaces/knowledgepixels/incubator/officehours/20260603

Knowledge Pixels Incubator Office Hour 3 June 2026

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wasAttributedTo

https://orcid.org/0000-0001-8888-635X

Erik Schultes

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mac-fdt-v2-cleanup-status

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Erik Schultes

This is the identifier for this whole nanopublication. https://w3id.org/np/RAeNRMdW7E...

this nanopublication

http://purl.org/dc/terms/creator

creator

https://orcid.org/0000-0001-8888-635X

Erik Schultes

This is the identifier for this whole nanopublication. https://w3id.org/np/RAeNRMdW7E...

this nanopublication

http://purl.org/dc/terms/license

license

https://creativecommons.org/licenses/by/4.0/

4.0

Erik Schultes, 3 Jun 2026, 09:00:00 UTC

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