https://w3id.org/np/RAkb6EioB4Ltw4vEeSvxtUNIQHyQiC94NEdrZmLjbob0k
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-30T08:00:00Z
creator: Tobias Kuhn
license: https://creativecommons.org/licenses/by/4.0/
embeds: 🏷 Assigned to
introduces: classes-view-kind

🏷 Assigned to
is version of: classes-view-kind
type: ListView
type: ResourceView
label: Assigned classes view
has structural position: 5.5.classes
has view query: Get the classes assigned to a thing (view)

Tobias Kuhn
P1344: sdsc-demo-20260528

sig
has algorithm: RSA
signed by: Tobias Kuhn

https://w3id.org/np/RAlKmJ7s87az7Holsof70-OZ5bm8eDdUmivrVw8mS0qM4
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-30T08:00:00Z
creator: Tobias Kuhn
license: https://creativecommons.org/licenses/by/4.0/
embeds: 🏷 Assigned to
introduces: classes-view-kind

🏷 Assigned to
is version of: classes-view-kind
type: ListView
type: ResourceView
label: Assigned classes view
has structural position: 5.5.classes
has view query: get-classes-for-thing-view

sig
has algorithm: RSA
signed by: Tobias Kuhn

https://w3id.org/np/RA-A6RMguvfzL0U4j1JRu7wPDtoDtODuK9PHk9A55sB_8
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-30T08:00:00Z
creator: Tobias Kuhn
license: https://creativecommons.org/licenses/by/4.0/
introduces: Get instances for class (view)

Get instances for class (view)
description: Returns the instances assigned to the given class, with view-friendly columns (instance / instance_label). Used by the /explore page as a resource view (the 'Has instances' list).
license: LICENSE-2.0
type: grlc-query
endpoint: full
sparql: prefix dct: <http://purl.org/dc/terms/> prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> prefix np: <http://www.nanopub.org/nschema#> prefix npa: <http://purl.org/nanopub/admin/> prefix npx: <http://purl.org/nanopub/x/> prefix nt: <https://w3id.org/np/o/ntemplate/> select distinct ?instance ?instance_label where { graph ?g { ?instance a ?_class_iri . } graph npa:graph { ?np npa:hasValidSignatureForPublicKey ?pubkey . filter not exists { ?npx npx:invalidates ?np ; npa:hasValidSignatureForPublicKey ?pubkey . } ?np npa:hasGraph ?g . ?np np:hasPublicationInfo ?i . } optional { graph ?g { ?instance rdfs:label ?instanceLabel1 . } } optional { graph ?g { ?instance dct:title ?instanceLabel2 . } } optional { graph ?i { ?instance rdfs:label ?instanceLabel3 . } } optional { graph ?i { ?instance nt:hasLabelFromApi ?instanceLabel4 . } } bind(coalesce(?instanceLabel1, ?instanceLabel2, ?instanceLabel3, ?instanceLabel4) as ?instance_label) } limit 1000

sig
has algorithm: RSA
signed by: Tobias Kuhn

https://w3id.org/np/RAheGTEIYh394SfNZx9MUKa0a4h7AIvoPnNS7Q-MP6cgk
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-30T08:00:00Z
creator: Tobias Kuhn
license: https://creativecommons.org/licenses/by/4.0/
introduces: Get parts of a thing (view)

Get parts of a thing (view)
description: Returns the things denoted as parts of the given thing, with view-friendly columns (part / part_label). Used by the /explore page as a resource view (the 'Has parts' list).
license: LICENSE-2.0
type: grlc-query
endpoint: full
sparql: prefix dct: <http://purl.org/dc/terms/> prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> prefix np: <http://www.nanopub.org/nschema#> prefix npa: <http://purl.org/nanopub/admin/> prefix npx: <http://purl.org/nanopub/x/> prefix nt: <https://w3id.org/np/o/ntemplate/> select ?part (sample(?partLabel) as ?part_label) where { { graph ?g { ?_thing_iri dct:hasPart ?part . } filter not exists { graph npa:graph { ?part npx:hasNanopubType npx:NanopubIndex . } } } union { graph ?g { ?part dct:partOf ?_thing_iri . } } union { graph ?gx { ?_thing_iri dct:hasPart ?index . } graph npa:graph { ?index npx:hasNanopubType npx:NanopubIndex . ?index np:hasAssertion ?a . } graph ?a { ?index npx:includesElement ?np . } graph npa:graph { ?np npx:introduces ?part . } } graph npa:graph { ?np npa:hasGraph ?g . ?np npa:hasValidSignatureForPublicKey ?pubkey . filter not exists { ?npx npx:invalidates ?np ; npa:hasValidSignatureForPublicKey ?pubkey . } ?np np:hasPublicationInfo ?i . } optional { graph ?g { ?part rdfs:label ?partLabel1 . } } optional { graph ?g { ?part dct:title ?partLabel2 . } } optional { graph ?i { ?part rdfs:label ?partLabel3 . } } optional { graph ?i { ?part nt:hasLabelFromApi ?partLabel4 . } } optional { graph ?x { ?part rdfs:label ?partLabel5 . } } bind(coalesce(?partLabel1, ?partLabel2, ?partLabel3, ?partLabel4, ?partLabel5) as ?partLabel) } group by ?part limit 1000

sig
has algorithm: RSA
signed by: Tobias Kuhn

https://w3id.org/np/RAvKwCvpsfTMs6xidHv14q4GVzK_zIwxqzX7uFlOid5HQ
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-30T08:00:00Z
creator: Tobias Kuhn
license: https://creativecommons.org/licenses/by/4.0/
introduces: Get the classes assigned to a thing (view)

Get the classes assigned to a thing (view)
description: Returns the classes assigned to the given thing, with view-friendly columns (class / class_label). Used by the /explore page as a resource view (the 'Assigned to' list).
license: LICENSE-2.0
type: grlc-query
endpoint: full
sparql: prefix dct: <http://purl.org/dc/terms/> prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> prefix np: <http://www.nanopub.org/nschema#> prefix npa: <http://purl.org/nanopub/admin/> prefix npx: <http://purl.org/nanopub/x/> prefix nt: <https://w3id.org/np/o/ntemplate/> select distinct ?class ?class_label where { graph ?g { ?_thing_iri a ?class . } graph npa:graph { ?np npa:hasValidSignatureForPublicKey ?pubkey . filter not exists { ?npx npx:invalidates ?np ; npa:hasValidSignatureForPublicKey ?pubkey . } ?np npa:hasGraph ?g . ?np np:hasPublicationInfo ?i . } optional { graph ?g { ?class rdfs:label ?classLabel1 . } } optional { graph ?g { ?class dct:title ?classLabel2 . } } optional { graph ?i { ?class rdfs:label ?classLabel3 . } } optional { graph ?i { ?class nt:hasLabelFromApi ?classLabel4 . } } bind(coalesce(?classLabel1, ?classLabel2, ?classLabel3, ?classLabel4) as ?class_label) } limit 1000

sig
has algorithm: RSA
signed by: Tobias Kuhn

https://w3id.org/np/RAQCo3WZZcqVzTGzidkkJc7kcTkWP77v64wQnmGKCeJlY
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-30T08:00:00Z
creator: Tobias Kuhn
license: https://creativecommons.org/licenses/by/4.0/
introduces: Get the templates using given URI (view)

Get the templates using given URI (view)
description: Returns the assertion templates that use the given URI in their statements, with view-friendly columns (template_iri / template_iri_label). Used by the /explore page as a resource view (the 'Related Templates' list).
license: LICENSE-2.0
type: grlc-query
sparql: prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> prefix dct: <http://purl.org/dc/terms/> prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> prefix np: <http://www.nanopub.org/nschema#> prefix npa: <http://purl.org/nanopub/admin/> prefix npx: <http://purl.org/nanopub/x/> prefix nt: <https://w3id.org/np/o/ntemplate/> select distinct ?template_iri ?template_iri_label where { graph ?assertion { ?statement ?relation ?_thing_iri . values ?relation { rdf:subject rdf:predicate rdf:object nt:possibleValue } } graph npa:graph { ?template_iri npa:hasValidSignatureForPublicKey ?pubkey . filter not exists { ?npx npx:invalidates ?template_iri ; npa:hasValidSignatureForPublicKey ?pubkey . } filter not exists { ?template_iri npx:hasNanopubType nt:UnlistedTemplate . } ?template_iri np:hasAssertion ?assertion . optional { ?template_iri rdfs:label ?template_iri_label } } } limit 1000

sig
has algorithm: RSA
signed by: Tobias Kuhn

https://w3id.org/np/RAUVsWFaipJFEAKB9Roq6LJCGt3pCD7i1x7rXJZxo-dDo
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-30T08:00:00Z
creator: Tobias Kuhn
license: https://creativecommons.org/licenses/by/4.0/
embeds: 🫧 Has instances
introduces: instances-view-kind

🫧 Has instances
is version of: instances-view-kind
type: ListView
type: ResourceView
label: Instances view
has structural position: 5.5.instances
has view query: Get instances for class (view)

sig
has algorithm: RSA
signed by: Tobias Kuhn

https://w3id.org/np/RAwfPE47Xk2NKsN2baNmJvEGZCiovRsp0apQm-p2s4Yeo
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-30T08:00:00Z
creator: Tobias Kuhn
license: https://creativecommons.org/licenses/by/4.0/
embeds: 🫧 Has instances
introduces: instances-view-kind

🫧 Has instances
is version of: instances-view-kind
type: ListView
type: ResourceView
label: Instances view
has structural position: 5.5.instances
has view query: get-instances-view

sig
has algorithm: RSA
signed by: Tobias Kuhn

https://w3id.org/np/RAgiIDYyV6VxK8p1pDIZ66S231rmOfVfPl7suRM1XxFg8
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-30T08:00:00Z
creator: Tobias Kuhn
license: https://creativecommons.org/licenses/by/4.0/
embeds: 🧩 Has parts
introduces: parts-view-kind

🧩 Has parts
is version of: parts-view-kind
type: ListView
type: ResourceView
label: Parts view
has structural position: 5.5.parts
has view query: get-parts-view

sig
has algorithm: RSA
signed by: Tobias Kuhn

https://w3id.org/np/RAjmTszsbe02nBxQtu7kDXmftdiPMhsfJ7B9iLQzSIxlk
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-30T08:00:00Z
creator: Tobias Kuhn
license: https://creativecommons.org/licenses/by/4.0/
embeds: 🧩 Has parts
introduces: parts-view-kind

🧩 Has parts
is version of: parts-view-kind
type: ListView
type: ResourceView
label: Parts view
has structural position: 5.5.parts
has view query: Get parts of a thing (view)

sig
has algorithm: RSA
signed by: Tobias Kuhn

https://w3id.org/np/RA_Xg6TL3r1doxa41IlsFzEPMJG5bWD6N_l_KoeFs6HOk
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-30T08:00:00Z
creator: Tobias Kuhn
license: https://creativecommons.org/licenses/by/4.0/
embeds: 📝 Related Templates
introduces: templates-view-kind

📝 Related Templates
is version of: templates-view-kind
type: ListView
type: ResourceView
label: Related templates view
has structural position: 5.5.templates
has view query: get-templates-with-uri-view

sig
has algorithm: RSA
signed by: Tobias Kuhn

https://w3id.org/np/RAfQw7aOfRJufYBFDBK4qrwpcqgjDGRuIcoUYOVRNPJRc
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-30T08:00:00Z
creator: Tobias Kuhn
license: https://creativecommons.org/licenses/by/4.0/
embeds: 📝 Related Templates
introduces: templates-view-kind

📝 Related Templates
is version of: templates-view-kind
type: ListView
type: ResourceView
label: Related templates view
has structural position: 5.5.templates
has view query: Get the templates using given URI (view)

sig
has algorithm: RSA
signed by: Tobias Kuhn

Citations for: RAsPjEImfZaXsIri0ny4j_s_k_6wyOlC6tkocl6w2y7f4
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T21:16:35.719Z
creator: Anne Fouilloux
license: https://creativecommons.org/licenses/by/4.0/
has nanopub type: cites
was created at: platform.sciencelive4all.org

Coverage-based rarefaction does not restore agreement between GBIF richness hotspots and the EU Article 12 expert-rangemap gold standard (Iberian birds, HEALPix-NESTED)
uses method in: https://doi.org/10.1890/11-1952.1
type: CreativeWork
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T21:11:28.079Z
creator: Anne Fouilloux
license: https://creativecommons.org/licenses/by/4.0/
introduces: Coverage-based rarefaction does not restore agreement between GBIF richness hotspots and the EU Article 12 expert-rangemap gold standard (Iberian birds, HEALPix-NESTED)
was created at: platform.sciencelive4all.org

sig
has algorithm: RSA
signed by: Anne Fouilloux

Coverage-based rarefaction does not restore agreement between GBIF richness hotspots and the EU Article 12 expert-rangemap gold standard (Iberian birds, HEALPix-NESTED)
end date: 2026-05-23
type: FORRT-Replication-Outcome
has conclusion description: Coverage-based rarefaction (Chao & Jost 2012) does NOT restore agreement between modern GBIF occurrence richness hotspots and the EU Article 12 expert-rangemap gold standard for Iberian birds. At the Hurlbert & Jetz reference scale (HEALPix-NESTED Nside 256, ≈ 25 km), standardising every cell to a common sample coverage leaves the top-5 % hotspot misidentification (symmetric set non-overlap vs the Article 12 expert polygons) at its best 87.4 % for the all-observations strategy and 96.6 % for the museum strategy, versus uncorrected baselines of 88.7 % and 94.2 % — a change of +1.3 and −2.4 percentage points respectively. Neither corrected value comes anywhere near the 47.8–68.6 % Hurlbert & Jetz reference range; the correction moves museum the wrong way. Standardising per-cell sample completeness does not remove the observer-effort distortion of which cells rank as biodiversity hotspots, because that distortion is a spatial sampling-location bias (where observers go versus where birds are biologically densest), not a per-cell completeness artefact that coverage standardisation can rescale away.
has confidence level: HighConfidence
has evidence description: Headline scale, HEALPix-NESTED Nside 256 (≈ 25 km), top-5 % hotspots, symmetric set non-overlap ("misidentification"). Against the EU Article 12 expert-rangemap gold standard (the pre-registered comparator, D9): - museum: uncorrected 94.2 % → best coverage-corrected 96.6 % (at target coverage C* = 0.80); change −2.4 percentage points (worse). All swept C* (0.80, 0.90, 0.95, 0.99) and Cmin give 96.6–98.0 %. - allbor: uncorrected 88.7 % → best coverage-corrected 87.4 % (at C* = 0.80); change +1.3 percentage points. Swept values 87.4–90.5 %. - Neither strategy reaches the Hurlbert & Jetz 47.8–68.6 % reference range at any sweep point. Against the historical EOO-hull rangemap (secondary comparator; reproduces the sibling baseline): - museum: uncorrected 89.9 % → corrected 90.6–94.4 % (worse across the sweep). - allbor: uncorrected 98.2 % → corrected best 92.0 % at C* = 0.80 (a 6.2-percentage-point improvement) but still far above the reference range. Baseline validation: the uncorrected EOO-hull numbers (museum 89.9 %, allbor 98.2 %) match the sibling chain's published Replication Outcome (89.9 % / 97.8 %), confirming the pipeline reproduces the prior result before the correction is applied. Coverage-based rarefaction was implemented from Chao & Jost (2012): per-cell sample coverage via the bias-corrected Good–Turing estimator; size-based rarefaction (Hurlbert/Good) inverted to the target coverage; coverage-based extrapolation (Chao1 f0) where the target exceeds a cell's observed coverage. Estimators validated standalone (rarefaction monotone, Ĉ(n) self-consistent with the full-sample estimator). Sweep: target coverage C* ∈ {0.80, 0.90, 0.95, 0.99} plus the minimum common coverage Cmin, both strategies, full Nside ladder 16–512. See notebooks/03_analysis.py and results/coverage_correction.parquet. Github repository: https://github.com/annefou/sdm-hotspot-effort-correction
has limitations description: 1. Coverage standardisation can only be applied to cells with enough records for a coverage estimate (here, ≥ 5). At Nside 256 this censors 698 of 1849 cells (38 %) for the museum strategy and 489 (26 %) for allbor. The censored cells are predominantly the effort-poor ones — exactly the under-sampled, potentially biologically-rich cells whose absence drives the hotspot mismatch. Coverage-based rarefaction therefore structurally cannot recover the hotspot status of cells it must exclude; this is an intrinsic limitation of the method for this problem, not a tuning choice, and is itself part of why the correction fails. 2. Extrapolating sparse cells up to a high fixed target coverage (e.g. C* = 0.99) relies on the Chao1-based extrapolation, which has wide uncertainty for very incomplete samples; this is why we swept a range of C* and also report the minimum-common-coverage standardisation, rather than committing to a single target. The conclusion (no restoration of agreement) holds across the whole sweep, so it does not depend on the extrapolation regime. 3. The comparison inherits the sibling chain's design choices: HEALPix-NESTED equal-area cells (vs Hurlbert & Jetz's lat-lon graticule), convex-hull EOO as the historical rangemap surrogate, and the top-5 % hotspot-threshold convention. The Article 12 gold-standard comparator removes the rangemap-substitute concern for that metric, and the negative result is consistent across both comparators. 4. The Article 12 comparison is restricted to the species intersection between each GBIF strategy and the Article 12 Iberian breeding set; species in one but not the other are excluded from that metric.
has outcome repository: zenodo.20451519
has validation status: Contradicted
is outcome of: Coverage-based effort correction of Iberian-bird richness hotspots (HEALPix-NESTED)

sig
has algorithm: RSA
signed by: Anne Fouilloux

Coverage-based effort correction of Iberian-bird richness hotspots (HEALPix-NESTED)
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T21:00:17.925Z
creator: Anne Fouilloux
license: https://creativecommons.org/licenses/by/4.0/
introduces: Coverage-based effort correction of Iberian-bird richness hotspots (HEALPix-NESTED)
was created at: platform.sciencelive4all.org

Coverage-based effort correction of Iberian-bird richness hotspots (HEALPix-NESTED)
type: FORRT-Replication-Study
type: Replication-Study
related: Q1531570
related: Q17146659
related: Q2725298
related: Q5629401
related: Q7294544
related: Q864294
has deviation description: Chao & Jost (2012) introduce coverage-based rarefaction for comparing whole-community samples by completeness. This study deviates by applying their estimator at a new unit of analysis — the individual HEALPix-NESTED grid cell as a "sample" — to correct a spatial biodiversity-hotspot comparison, an application the methods paper does not itself perform. Relative to the prior sibling chain (Hurlbert & Jetz 2007 scale-dependence replication), this study reuses that chain's GBIF download DOIs, Iberian study system, HEALPix-NESTED substrate, year-split, top-5% hotspot definition, and Article 12 comparator unchanged, and adds the coverage-correction layer plus the target-coverage sweep as the new method. The estimator can only be evaluated on cells with enough records, so effort-poor cells are necessarily censored; the consequence of that censoring for the comparison is reported in the linked Outcome's limitations.
has discipline: Q1886501
has methodology description: Iberian bird occurrences (Spain, Portugal, Andorra, Gibraltar) are taken from GBIF under two basis-of-record strategies with the prior chain's existing download DOIs (museum: PRESERVED_SPECIMEN + MACHINE_OBSERVATION, 10.15468/dl.r8pcat; all-observations: additionally HUMAN_OBSERVATION, 10.15468/dl.e9xv7p), and binned onto a HEALPix-NESTED ladder (Nside 16, 32, 64, 128, 256, 512) using the geographic, WGS84-aware healpix-geo library, NESTED ordering throughout. Records are year-split at 2000: post-2000 form the occurrence/atlas layer, pre-2000 the per-species convex-hull rangemap layer. For each cell, the per-species record-count vector is retained. Coverage-based rarefaction (Chao & Jost 2012) is applied per cell: sample coverage is estimated with the bias-corrected Good–Turing estimator; per-cell richness is then standardised to a common target sample coverage C* by size-based rarefaction (inverting the rarefied-sample coverage curve) where C* is at or below the cell's observed coverage, and by coverage-based extrapolation (Chao1 undetected-species term) where C* exceeds it. Cells with too few records for a stable coverage estimate are censored. The target coverage C* is swept over a grid (0.80, 0.90, 0.95, 0.99) plus the minimum common coverage Cmin, rather than fixed at one value. At each (strategy, Nside, C*), the top-5% richest cells of the coverage-standardised surface are recomputed and their symmetric set non-overlap ("misidentification") is measured against (a) the EU Birds Directive Article 12 expert distribution polygons (EEA 2013–2018, 10 km grid, reprojected to WGS84, matched to the species intersection) and (b) the pre-2000 occurrence-hull rangemap. The uncorrected raw-richness surface is computed identically as the baseline. The full pipeline is a Snakemake workflow (download → clean → analysis → figures) reproducible from a fresh checkout; the coverage estimators are validated standalone.
has scope description: Scope: whether standardising per-cell sample completeness removes observer-effort distortion of biodiversity-hotspot identity. The study tests whether coverage-standardising modern occurrence-derived per-cell bird richness makes the top-richest-cells ("hotspot") set agree with the hotspot set derived from an expert rangemap, in the same Iberian-bird, equal-area HEALPix system as the prior scale-dependence chain. In scope: the top-5% richest-cells hotspot definition; the symmetric set non-overlap between the occurrence-derived hotspot set and the expert-rangemap-derived hotspot set; how that non-overlap changes when occurrence richness is coverage-standardised rather than left raw; both basis-of-record strategies (museum-grade specimens/sensors vs all observations including citizen science); the EU Article 12 expert polygons as the gold-standard rangemap comparator, with the historical occurrence-hull rangemap as a secondary comparator. Out of scope: the scale-dependence-across-resolutions question itself (that is the prior chain's claim, which this study takes as given); non-bird taxa; regions outside the Iberian peninsula; and any correction of the rangemap layer (only the occurrence/atlas layer is corrected).
targets claim: Coverage-based rarefaction restores GBIF-vs-expert-rangemap hotspot agreement (Iberian birds, HEALPix-NESTED)

sig
has algorithm: RSA
signed by: Anne Fouilloux

Coverage-based rarefaction restores GBIF-vs-expert-rangemap hotspot agreement (Iberian birds, HEALPix-NESTED)
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T20:56:16.330Z
creator: Anne Fouilloux
license: https://creativecommons.org/licenses/by/4.0/
introduces: Coverage-based rarefaction restores GBIF-vs-expert-rangemap hotspot agreement (Iberian birds, HEALPix-NESTED)
was created at: platform.sciencelive4all.org

Coverage-based rarefaction restores GBIF-vs-expert-rangemap hotspot agreement (Iberian birds, HEALPix-NESTED)
source: https://doi.org/10.1890/11-1952.1
type: FORRT-Claim
type: descriptive pattern-FORRT-Claim
as aida statement: Standardising per-cell species richness to a common sample coverage by coverage-based rarefaction restores agreement between modern GBIF occurrence-derived bird-richness hotspots and expert-rangemap hotspots in the Iberian peninsula.

sig
has algorithm: RSA
signed by: Anne Fouilloux

https://w3id.org/sciencelive/np/RAuP2z6scqdWkG6A7RFK4kBSlbHjoDHEbXhoUS5BendEo
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T20:54:12.390Z
creator: Anne Fouilloux
license: https://creativecommons.org/licenses/by/4.0/
has nanopub type: hycl
introduces: Standardising per-cell species richness to a common sample coverage by coverage-based rarefaction restores agreement between modern GBIF occurrence-derived bird-richness hotspots and expert-rangemap hotspots in the Iberian peninsula.
was created at: platform.sciencelive4all.org
label: AIDA sentence: Standardising per-cell species richness to a common sample coverage by coverage-based rarefaction restores agreement between modern GBIF occurrence-derived bird-richness hotspots and expert-rangemap hotspots in the Iberian peninsula.

sig
has algorithm: RSA
signed by: Anne Fouilloux

https://w3id.org/sciencelive/np/RArxpQJ98cPc7V3uAWhjJQtriT7qjV40Ml-ciSREJSh3s
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T20:48:17.173Z
creator: Anne Fouilloux
license: https://creativecommons.org/licenses/by/4.0/
has nanopub type: cites
was created at: platform.sciencelive4all.org
label: Paper annotation: We propose an integrated sampling, rarefaction, and extrapolation methodology to compare species richness of a set of communities based on samples of equal completeness (as measured by sample coverage) instead of equal size.

https://doi.org/10.1890/11-1952.1
has quoted text: We propose an integrated sampling, rarefaction, and extrapolation methodology to compare species richness of a set of communities based on samples of equal completeness (as measured by sample coverage) instead of equal size.
comment: A sibling replication showed modern GBIF "biodiversity hotspots" for Iberian birds are inflated by survey effort: richest-ranked cells track where observers go, not where birds are densest, and even an EU Article 12 expert rangemap doesn't close the gap. Effort-rich cells reach higher completeness than effort-poor ones, so comparing raw per-cell richness is exactly the equal-size comparison this paper warns against. This study tests whether coverage-based rarefaction removes that effort bias.

sig
has algorithm: RSA
signed by: Anne Fouilloux

Read: OSPARK output - Managing Outreach on Open Research Material to Heterogeneous Groups
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T19:34:12.935Z
creator: Christian Meesters
license: https://creativecommons.org/licenses/by/4.0/
has nanopub type: ReadAction
introduces: readaction
was created at: nanodash.knowledgepixels.com

readaction
agent: Christian Meesters
end time: 2026-05-29
object: OSPARK output - Managing Outreach on Open Research Material to Heterogeneous Groups
type: ReadAction
comment: How to best manage Open Research / Science material to heterogeneous groups is an open challenge. Particularly, as there is a lot of resistance to overcome.

sig
has algorithm: RSA
signed by: Christian Meesters

https://w3id.org/np/RA_n91_kC4JB9gT1PmqkXZnJWfERB_TaNk8uNM1Y-HvRg
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T15:20:16.195+02:00
creator: Tobias Kuhn

sig
has algorithm: RSA
signed by: Tobias Kuhn

Cited papers view
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T13:14:57Z
creator: Tobias Kuhn
license: https://creativecommons.org/licenses/by/4.0/
embeds: 📚 Cited papers
introduces: cited-papers-view-kind

📚 Cited papers
is version of: cited-papers-view-kind
type: ResourceView
type: TabularView
label: Cited papers view
applies to instances of: MaintainedResource
has structural position: 5.2.cited-papers
has view query: Get cited papers for a resource
has view query target field: resource

sig
has algorithm: RSA
signed by: Tobias Kuhn

Claims view
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T13:14:57Z
creator: Tobias Kuhn
license: https://creativecommons.org/licenses/by/4.0/
embeds: 💬 Claims
introduces: claims-view-kind

💬 Claims
is version of: claims-view-kind
type: ResourceView
type: TabularView
label: Claims view
applies to instances of: MaintainedResource
has structural position: 5.3.claims
has view query: Get claims for a resource
has view query target field: resource

sig
has algorithm: RSA
signed by: Tobias Kuhn

From Waste to Worth cites Chakhmouradian & Wall (2012) as evidence
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T13:14:57Z
creator: Tobias Kuhn
license: https://creativecommons.org/licenses/by/4.0/

Explorative use case: from waste to worth
cites as evidence: Rare Earth Elements: Minerals, Mines, Magnets (and More)
cites as evidence: Recycling of the rare earth elements
cites as evidence: Scarcity of Rare Earth Elements
has label from api: Explorative use case: from waste to worth
description: Exploring how we can apply nanopubs for science-related blog posts.
type: MaintainedResource
is maintained by: Nanoreatch

sig
has algorithm: RSA
signed by: Tobias Kuhn

From Waste to Worth cites Jowitt et al. (2018) as evidence
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T13:14:57Z
creator: Tobias Kuhn
license: https://creativecommons.org/licenses/by/4.0/

sig
has algorithm: RSA
signed by: Tobias Kuhn

From Waste to Worth cites de Boer & Lammertsma (2013) as evidence
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T13:14:57Z
creator: Tobias Kuhn
license: https://creativecommons.org/licenses/by/4.0/

sig
has algorithm: RSA
signed by: Tobias Kuhn

Get cited papers for a resource
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T13:14:57Z
creator: Tobias Kuhn
license: https://creativecommons.org/licenses/by/4.0/
embeds: Get cited papers for a resource

Get cited papers for a resource
description: Given a resource, this query returns the papers it cites as evidence (via any CiTO relation), using the bibliographic metadata nanopublications that introduce those papers.
license: LICENSE-2.0
type: grlc-query
endpoint: full
sparql: 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/> select distinct ?title ?date ?np ("^" as ?np_label) where { graph npa:graph { ?citeNp np:hasAssertion ?ca . } graph ?ca { ?_resource_iri ?citoProp ?paper . } filter(strstarts(str(?citoProp), "http://purl.org/spar/cito/")) graph npa:graph { ?np npx:introduces ?paper . ?np np:hasAssertion ?pa . } graph ?pa { ?paper dct:title ?title . } optional { graph ?pa { ?paper dct:date ?date . } } graph npa:graph { ?np npa:hasValidSignatureForPublicKey ?pk . } filter not exists { graph npa:graph { ?inv npx:invalidates ?np ; npa:hasValidSignatureForPublicKey ?pk . } } } order by ?date ?title

sig
has algorithm: RSA
signed by: Tobias Kuhn

Get claims for a resource
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T13:14:57Z
creator: Tobias Kuhn
license: https://creativecommons.org/licenses/by/4.0/
embeds: Get claims for a resource

Get claims for a resource
description: Given a resource, this query returns the claims (AIDA sentences) it covers via gen:coversClaim.
license: LICENSE-2.0
type: grlc-query
endpoint: full
sparql: prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> prefix np: <http://www.nanopub.org/nschema#> prefix npa: <http://purl.org/nanopub/admin/> prefix npx: <http://purl.org/nanopub/x/> prefix gen: <https://w3id.org/kpxl/gen/terms/> select distinct ?statement ?np ("^" as ?np_label) where { graph npa:graph { ?np np:hasAssertion ?a . } graph ?a { ?_resource_iri gen:coversClaim ?claim . ?claim a <http://purl.org/petapico/o/hycl#AIDA-Sentence> . } optional { graph npa:graph { ?np rdfs:label ?statement . } } graph npa:graph { ?np npa:hasValidSignatureForPublicKey ?pk . } filter not exists { graph npa:graph { ?inv npx:invalidates ?np ; npa:hasValidSignatureForPublicKey ?pk . } } } order by ?statement

sig
has algorithm: RSA
signed by: Tobias Kuhn

Biodiversity Ontology displays view: simple message view
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T12:58:05.180Z
creator: Tobias Kuhn
license: https://creativecommons.org/publicdomain/zero/1.0/
embeds: display
was created at: nanodash.knowledgepixels.com

sig
has algorithm: RSA
signed by: Tobias Kuhn

ontology
has label from api: Biodiversity Ontology

Explorative use case: from waste to worth displays view: Claims view
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T12:32:15.187Z
creator: Tobias Kuhn
license: https://creativecommons.org/publicdomain/zero/1.0/
embeds: display
was created at: nanodash.knowledgepixels.com

claims-view
has label from api: Claims view

sig
has algorithm: RSA
signed by: Tobias Kuhn

Explorative use case: from waste to worth displays view: Cited papers view
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T12:31:47.478Z
creator: Tobias Kuhn
license: https://creativecommons.org/publicdomain/zero/1.0/
embeds: display
was created at: nanodash.knowledgepixels.com

sig
has algorithm: RSA
signed by: Tobias Kuhn

cited-papers-view
has label from api: Cited papers view

RAUUcQ4TA4Iv zMR9OC03S StdFeCEuycq8 fwbaXdWwI
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T14:27:50.310+02:00
creator: Tobias Kuhn

sig
has algorithm: RSA
has signature target: RAUUcQ4TA4Iv zMR9OC03S StdFeCEuycq8 fwbaXdWwI
signed by: Tobias Kuhn

https://w3id.org/np/RAdM-p7nV0rWA6KE8j2EsXQKHey1PvWkdau69Af6IWz_M
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T14:27:46.841+02:00
creator: Tobias Kuhn

sig
has algorithm: RSA
signed by: Tobias Kuhn

https://w3id.org/np/RAuOf1T2Dto4qh604lq9meHf7y-7jCKR_q7yXUuX-6-5c
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T11:54:11Z
creator: Tobias Kuhn
license: https://creativecommons.org/licenses/by/4.0/
embeds: 📄 Described in
introduces: described-in-view-kind

📄 Described in
is version of: described-in-view-kind
type: ListView
type: ResourceView
label: Described in view
has structural position: 5.5.described-in
has view query: Get term descriptions

sig
has algorithm: RSA
signed by: Tobias Kuhn

https://w3id.org/np/RANXZE_-eqI88cpm75fCtvxRttdnL_W66__HTGeFi0u_I
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T11:54:11Z
creator: Tobias Kuhn
license: https://creativecommons.org/licenses/by/4.0/
introduces: Get term descriptions

Get term descriptions
description: Returns the nanopublications that introduce, describe, or embed the given term, with view-friendly columns (np / np_label). Used by the /explore page as a resource view (the 'Described in' list).
license: LICENSE-2.0
type: grlc-query
endpoint: meta
sparql: 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/> select ?np ?np_label where { values ?__pubkey_multi {} graph npa:graph { ?np npa:hasValidSignatureForPublicKeyHash ?__pubkey_multi . filter not exists { ?npx npx:invalidates ?np ; npa:hasValidSignatureForPublicKeyHash ?__pubkey_multi . } ?np dct:created ?date . ?np npx:introduces|npx:describes|npx:embeds ?_term_iri . optional { ?np rdfs:label ?np_label . } } } order by desc(?date)

sig
has algorithm: RSA
signed by: Tobias Kuhn

https://w3id.org/np/RAIkMiJ2ujZHsJ6X-xxbkmTLUnRVCWA0nz_gGmY4PclsM
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T11:34:08.095Z
creator: Tobias Kuhn
license: https://creativecommons.org/publicdomain/zero/1.0/
introduces: Explorative use case: from waste to worth
was created at: nanodash.knowledgepixels.com

sig
has algorithm: RSA
signed by: Tobias Kuhn

Nanoreatch
has label from api: Nanoreatch
description: An informal group where Reatch and Knowledge Pixels discuss nanopublication applications.
type: Group
type: Space
has admin: Tobias Kuhn

https://w3id.org/np/RAUbky_SFQbedf5LvArtKWmKalD6CP0nSvhvgTLFpTlJA
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T11:32:06.516Z
creator: Tobias Kuhn
license: https://creativecommons.org/publicdomain/zero/1.0/
introduces: Nanoreatch
was created at: nanodash.knowledgepixels.com

sig
has algorithm: RSA
signed by: Tobias Kuhn

https://w3id.org/np/RAZ0EGsBlca8unLqQzGl5kVapGgllKvDbGFlTA_FFD7oM
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T11:24:54Z
creator: Tobias Kuhn
license: https://creativecommons.org/licenses/by/4.0/
embeds: 🔗 References (max. 100)
introduces: references-view-kind

🔗 References (max. 100)
is version of: references-view-kind
type: ResourceView
type: TabularView
label: References view
has structural position: 5.5.references
has view query: Get URI references

sig
has algorithm: RSA
signed by: Tobias Kuhn

Expressing a literature-derived statement as an AIDA sentence
has assertion: Expressing a literature-derived statement as an AIDA sentence
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T11:21:11Z
creator: Tobias Kuhn
license: https://creativecommons.org/licenses/by/4.0/

is about - connects a thing (left) to a subject matter that this thing is about (right)

is an - connects a thing (left) to a class it belongs to (right)

is derived from - connects the statement (left) to a source it is derived from (right)

Type your AIDA sentence here (needs to end with a full stop)
type: AutoEscapeUriPlaceholder
has prefix: http://purl.org/aida/
has prefix label: The sentence
has regex: [\S ]{5,500}\.

Expressing a literature-derived statement as an AIDA sentence
description: Such nanopublications use the concept of an AIDA sentence to express a (scientific) statement in an informal or semi-formal manner, and link it to the source it is derived from. AIDA sentences are: Atomic: a sentence describing one thought that cannot be further broken down in a practical way Independent: a sentence that can stand on its own, without external references like "this effect" or "we" Declarative: a complete sentence ending with a full stop that could in theory be either true or false Absolute: a sentence describing the core of a claim ignoring the (un)certainty about its truth and ignoring how it was discovered (no "probably" or "evaluation showed that"); typically in present tense In addition to the plain AIDA template, this variant records one or more sources (e.g. a paper DOI) the sentence is derived from, via prov:wasDerivedFrom in the assertion itself. You can find more information about AIDA sentences here.
type: AssertionTemplate
has nanopub label pattern: AIDA sentence: ${aida}
has statement: st0
has statement: st1
has statement: st2
has tag: Claims
has target nanopub type: AIDA sentence - an English sentence that is Atomic, Independent, Declarative, and Absolute
was attributed to: Tobias Kuhn

DOI (https://doi.org/10...) or URL of the source the sentence is derived from
type: ExternalUriPlaceholder

identifier of concept or topic the sentence is about
type: GuidedChoicePlaceholder
possible values from api: http://purl.org/nanopub/api/find_signed_things
possible values from api: https://www.wikidata.org/w/api.php

sig
has algorithm: RSA
signed by: Tobias Kuhn

https://w3id.org/np/RAHZTUImPCkBt_ZI21DLJR7JvAAHA8vSqb-g8Oo_FE3n8
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T11:14:15Z
creator: Tobias Kuhn
license: https://creativecommons.org/licenses/by/4.0/
introduces: Get URI references

Get URI references
description: Returns nanopublications referencing the given URI in subject, predicate, or object position, with view-friendly columns (part / subject / predicate / object / published_by / date / np). Used by the /references page as a resource view.
license: LICENSE-2.0
type: grlc-query
endpoint: full
sparql: prefix np: <http://www.nanopub.org/nschema#> prefix npa: <http://purl.org/nanopub/admin/> prefix npx: <http://purl.org/nanopub/x/> prefix xsd: <http://www.w3.org/2001/XMLSchema#> prefix dct: <http://purl.org/dc/terms/> select ?part ?subject ?predicate ?object ?published_by ?date ?np ("^" as ?np_label) where { graph ?g { { { bind(?_ref_iri as ?subject) } union { bind(?_ref_iri as ?predicate) } union { bind(?_ref_iri as ?object) } } ?subject ?predicate ?object . } graph npa:graph { ?np npa:hasValidSignatureForPublicKey ?__pubkey . filter not exists { ?npx npx:invalidates ?np ; npa:hasValidSignatureForPublicKey ?__pubkey . } ?np dct:created ?date . ?np ?__graphpred_iri ?g . values ?__graphpred_iri { np:hasAssertion np:hasProvenance np:hasPublicationInfo } } bind(strafter(str(?__graphpred_iri), "#has") as ?part) optional { graph npa:graph { ?np np:hasPublicationInfo ?__pig_iri . } graph ?__pig_iri { ?np dct:creator ?published_by . } } } limit 100

sig
has algorithm: RSA
signed by: Tobias Kuhn

Qualification of: RAPDqfuSrY
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T11:07:48.757Z
creator: Mauro Paschetta
license: https://creativecommons.org/licenses/by/4.0/
was created at: nanodash.petapico.org

sig
has algorithm: RSA
signed by: Mauro Paschetta

Article: Rare Earth Elements: Minerals, Mines, Magnets (and More)
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T11:07:22Z
creator: Tobias Kuhn
license: https://creativecommons.org/licenses/by/4.0/
introduces: Rare Earth Elements: Minerals, Mines, Magnets (and More)

Rare Earth Elements: Minerals, Mines, Magnets (and More)
date: 2012-10
is part of: Elements
author list: author-list
issue: 5
page end: 340
page start: 333
volume: 8
type: ReviewPaper

A. R. Chakhmouradian

F. Wall

sig
has algorithm: RSA
signed by: Tobias Kuhn

Article: Recycling of the rare earth elements
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T11:07:22Z
creator: Tobias Kuhn
license: https://creativecommons.org/licenses/by/4.0/
introduces: Recycling of the rare earth elements

Recycling of the rare earth elements
date: 2018-10
is part of: Current Opinion in Green and Sustainable Chemistry
author list: author-list
page end: 7
page start: 1
volume: 13
type: ReviewPaper

S. M. Jowitt

T. T. Werner

Z. Weng

G. M. Mudd

sig
has algorithm: RSA
signed by: Tobias Kuhn

Article: Scarcity of Rare Earth Elements
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T11:07:22Z
creator: Tobias Kuhn
license: https://creativecommons.org/licenses/by/4.0/
introduces: Scarcity of Rare Earth Elements

Scarcity of Rare Earth Elements
date: 2013
is part of: ChemSusChem
author list: author-list
issue: 11
page end: 2055
page start: 2045
volume: 6
type: ReviewPaper

M. A. de Boer

K. Lammertsma

sig
has algorithm: RSA
signed by: Tobias Kuhn

From Waste to Worth (Reatch overview article)
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T10:53:04Z
creator: Tobias Kuhn
license: https://creativecommons.org/licenses/by/4.0/
introduces: From waste to worth, let's reconcile the world through a new bio-recycling way!

From waste to worth, let's reconcile the world through a new bio-recycling way!
creator: Xulia Maillot Rodriguez
issued: 2025-10-24
language: en
publisher: Reatch
type: BlogPost

sig
has algorithm: RSA
signed by: Tobias Kuhn

Biodiversity has admin Ashley Caselli
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T10:24:57.707Z
creator: Tobias Kuhn
license: https://creativecommons.org/publicdomain/zero/1.0/
was created at: nanodash.knowledgepixels.com

biodiversity
has admin: https://orcid.org/0000-0001-8492-0354
has label from api: Biodiversity

sig
has algorithm: RSA
signed by: Tobias Kuhn

Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs displays view: fdt-alpha-knowlet-view
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T08:52:34Z
creator: Erik Schultes
license: https://creativecommons.org/licenses/by/4.0/
embeds: display

sig
has algorithm: RSA
signed by: Erik Schultes

Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs displays view: fdt-catalogue-summary-view
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T08:52:34Z
creator: Erik Schultes
license: https://creativecommons.org/licenses/by/4.0/
embeds: display

sig
has algorithm: RSA
signed by: Erik Schultes

Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs displays view: fdt-observations-per-method-view
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T08:52:34Z
creator: Erik Schultes
license: https://creativecommons.org/licenses/by/4.0/
embeds: display

sig
has algorithm: RSA
signed by: Erik Schultes

Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs displays view: fdt-variants-by-who-view
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T08:52:34Z
creator: Erik Schultes
license: https://creativecommons.org/licenses/by/4.0/
embeds: display

sig
has algorithm: RSA
signed by: Erik Schultes

MAC FDT — Alpha variant digital twin view
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T08:51:39Z
creator: Erik Schultes
license: https://creativecommons.org/licenses/by/4.0/
embeds: MAC FDT — Alpha variant digital twin
introduces: fdt-alpha-knowlet-view-kind

MAC FDT — Alpha variant digital twin
is version of: fdt-alpha-knowlet-view-kind
type: ResourceView
type: TabularView
label: MAC FDT — Alpha variant digital twin view
applies to instances of: Space
has structural position: 5.4.fdt-alpha-knowlet
has view query target field: resource

sig
has algorithm: RSA
signed by: Erik Schultes

MAC FDT — catalogue summary by type view
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T08:51:39Z
creator: Erik Schultes
license: https://creativecommons.org/licenses/by/4.0/
embeds: MAC FDT — catalogue summary by type
introduces: fdt-catalogue-summary-view-kind

MAC FDT — catalogue summary by type
is version of: fdt-catalogue-summary-view-kind
type: ResourceView
type: TabularView
label: MAC FDT — catalogue summary by type view
applies to instances of: Space
has structural position: 5.1.fdt-catalogue-summary
has view query target field: resource

sig
has algorithm: RSA
signed by: Erik Schultes

MAC FDT — observations per method view
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T08:51:39Z
creator: Erik Schultes
license: https://creativecommons.org/licenses/by/4.0/
embeds: MAC FDT — observations per method
introduces: fdt-observations-per-method-view-kind

MAC FDT — observations per method
is version of: fdt-observations-per-method-view-kind
type: ResourceView
type: TabularView
label: MAC FDT — observations per method view
applies to instances of: Space
has structural position: 5.3.fdt-observations-per-method
has view query target field: resource

sig
has algorithm: RSA
signed by: Erik Schultes

MAC FDT — variants by WHO classification view
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T08:51:39Z
creator: Erik Schultes
license: https://creativecommons.org/licenses/by/4.0/
embeds: MAC FDT — variants by WHO classification
introduces: fdt-variants-by-who-view-kind

MAC FDT — variants by WHO classification
is version of: fdt-variants-by-who-view-kind
type: ResourceView
type: TabularView
label: MAC FDT — variants by WHO classification view
applies to instances of: Space
has structural position: 5.2.fdt-variants-by-who
has view query target field: resource

sig
has algorithm: RSA
signed by: Erik Schultes

Retraction of RA0aGsMc41L (mistaken npx:invalidates nanopub, alpha-knowlet)
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T08:18:16Z
creator: Erik Schultes
license: https://creativecommons.org/licenses/by/4.0/
has nanopub type: retracts

assertion
comment: Wrong mechanism: used npx:invalidates rather than the publisher-facing npx:retracts. Superseded by an npx:retracts-based retraction in the same fix branch.
was attributed to: Erik Schultes

sig
has algorithm: RSA
signed by: Erik Schultes

Retraction of RAD5G7Z3kY14 (broken ViewDisplay, alpha-knowlet)
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T08:18:16Z
creator: Erik Schultes
license: https://creativecommons.org/licenses/by/4.0/
has nanopub type: retracts

assertion
comment: Conflated mechanism: ViewDisplay (gen:isDisplayOfView) requires a gen:View wrapper, not a bare grlc-query.
was attributed to: Erik Schultes

sig
has algorithm: RSA
signed by: Erik Schultes

Retraction of RAUVFxrhms_ (mistaken npx:invalidates nanopub, catalogue-summary)
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T08:18:16Z
creator: Erik Schultes
license: https://creativecommons.org/licenses/by/4.0/
has nanopub type: retracts

assertion
comment: Wrong mechanism: used npx:invalidates rather than the publisher-facing npx:retracts. Superseded by an npx:retracts-based retraction in the same fix branch.
was attributed to: Erik Schultes

sig
has algorithm: RSA
signed by: Erik Schultes

Retraction of RAq9o-TF0vcy (broken ViewDisplay, catalogue-summary)
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T08:18:16Z
creator: Erik Schultes
license: https://creativecommons.org/licenses/by/4.0/
has nanopub type: retracts

assertion
comment: Conflated mechanism: ViewDisplay (gen:isDisplayOfView) requires a gen:View wrapper, not a bare grlc-query.
was attributed to: Erik Schultes

sig
has algorithm: RSA
signed by: Erik Schultes

RAsWrjiZLAWCROtwebUG-fAHvmvUM2ye ZCgZyc2vj9ek
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-29T06:09:33.034Z
creator: Tobias Kuhn
license: https://creativecommons.org/publicdomain/zero/1.0/
has nanopub type: isRelevantFor
was created at: nanodash.knowledgepixels.com

Nanopub Monitor
comment: Showing the decentralized network, including links to the Registry and Query instances
is relevant for: sdsc-demo-20260528

sig
has algorithm: RSA
has signature target: RAsWrjiZLAWCROtwebUG-fAHvmvUM2ye ZCgZyc2vj9ek
signed by: Tobias Kuhn

https://w3id.org/np/RAS8OVZaJPIGC9HoVRAU4zdXYOK64ssGYURx_f_b3NOpA
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T19:48:15Z
creator: Tobias Kuhn
license: https://creativecommons.org/licenses/by/4.0/
embeds: All Spaces
introduces: all-spaces-view-kind

All Spaces
is version of: all-spaces-view-kind
type: ResourceView
type: TabularView
label: All spaces view
has structural position: 5.5.all-spaces
has view query: Get all spaces

sig
has algorithm: RSA
signed by: Tobias Kuhn

https://w3id.org/np/RAlSgMFS1RJc1z7DM69BQ6HT2FEo46fm9JER7bQ6q1TA8
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T19:48:15Z
creator: Tobias Kuhn
license: https://creativecommons.org/licenses/by/4.0/
introduces: Get all spaces
was created from template: RARuOLDzf45L wBceBownrcLLvAKP-2yB-uwJJx8H7IWI

Get all spaces
description: Returns one row per known space with its label, type IRI and short type name, ordered alphabetically by space label. Intended for the /spaces table view.
license: LICENSE-2.0
type: grlc-query
endpoint: spaces
sparql: prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> prefix npa: <http://purl.org/nanopub/admin/> prefix npx: <http://purl.org/nanopub/x/> prefix gen: <https://w3id.org/kpxl/gen/terms/> select ?space_iri (sample(?lbl) as ?space_iri_label) (sample(?t) as ?type) (sample(?tlbl) as ?type_label) where { graph npa:spacesGraph { ?spaceRef a npa:SpaceRef ; npa:spaceIri ?space_iri . ?def a npa:SpaceDefinition ; npa:forSpaceRef ?spaceRef ; npa:viaNanopub ?np . } graph npa:graph { ?np rdfs:label ?lbl . ?np npx:hasNanopubType ?t . filter(strstarts(str(?t), "https://w3id.org/kpxl/gen/terms/")) filter(?t != gen:Space) } filter not exists { graph npa:graph { ?invNp npx:invalidates ?np . } } bind(strafter(str(?t), "https://w3id.org/kpxl/gen/terms/") as ?tlbl) } group by ?space_iri order by lcase(sample(?lbl))

sig
has algorithm: RSA
signed by: Tobias Kuhn

https://w3id.org/np/RAxGboS_juHuMyJQghGV3elEgZmQTew5oyw_aC9O9FFQI
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T18:48:29Z
creator: Tobias Kuhn
license: https://creativecommons.org/licenses/by/4.0/
embeds: Get spaces (v2)

Get spaces (v2)
description: Returns the latest non-invalidated SpaceDefinition per space from the server-materialised spaces repo, joined to the declaring nanopublication for its label and type. View-friendly columns (space_iri / type_label / np).
license: LICENSE-2.0
type: grlc-query
endpoint: spaces
sparql: 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 gen: <https://w3id.org/kpxl/gen/terms/> select ?space_iri ?space_iri_label ?type ?type_label ?date ?np ("^" as ?np_label) where { graph npa:spacesGraph { ?spaceRef a npa:SpaceRef ; npa:spaceIri ?space_iri . ?def a npa:SpaceDefinition ; npa:forSpaceRef ?spaceRef ; npa:viaNanopub ?np ; dct:created ?date . } graph npa:graph { ?np rdfs:label ?space_iri_label . ?np npx:hasNanopubType ?type . filter(strstarts(str(?type), "https://w3id.org/kpxl/gen/terms/")) filter(?type != gen:Space) } filter not exists { graph npa:graph { ?invNp npx:invalidates ?np . } } bind(strafter(str(?type), "https://w3id.org/kpxl/gen/terms/") as ?type_label) } order by desc(?date)

sig
has algorithm: RSA
signed by: Tobias Kuhn

https://w3id.org/np/RAHfLCMk5jF0yaamDU9d0tQAaKKRZaYwWFH1HdbW35Qwo
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T18:20:05Z
creator: Tobias Kuhn
license: https://creativecommons.org/licenses/by/4.0/
embeds: 🔍 All Queries
introduces: queries-view-kind

🔍 All Queries
is version of: queries-view-kind
type: ListView
type: ResourceView
label: All Queries View
has structural position: 5.5.queries
has view query: Get all grlc query nanopubs (v2)

sig
has algorithm: RSA
signed by: Tobias Kuhn

https://w3id.org/np/RAYEV8FlQFlZvSQ2Qctl5FU8OW0vTNU3HYyG10t_jEIc4
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T18:20:05Z
creator: Tobias Kuhn
license: https://creativecommons.org/licenses/by/4.0/
introduces: Get all grlc query nanopubs (v2)
was created from template: RARuOLDzf45L wBceBownrcLLvAKP-2yB-uwJJx8H7IWI

Get all grlc query nanopubs (v2)
description: Returns all nanopublications that declare a grlc query, with the query IRI, its label, its creator, the creation date, and the nanopublication IRI. Designed for rendering as a list/table view.
license: LICENSE-2.0
type: grlc-query
endpoint: full
sparql: 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 grlc: <https://w3id.org/kpxl/grlc/> select ?query_iri ?query_iri_label ?creator ?date ?np ("^" as ?np_label) where { graph npa:graph { ?np npa:hasValidSignatureForPublicKeyHash ?pubkeyhash . filter not exists { ?npx npx:invalidates ?np ; npa:hasValidSignatureForPublicKeyHash ?pubkeyhash . } ?np dct:created ?date . ?np npx:introduces|npx:embeds ?query . ?np np:hasAssertion ?a . ?np npx:hasNanopubType grlc:grlc-query . optional { ?np rdfs:label ?query_iri_label } optional { ?np npx:signedBy ?creator . } } graph ?a { ?query grlc:endpoint ?endpoint . filter(strstarts(str(?endpoint), "https://w3id.org/np/l/nanopub-query")) } bind(?query as ?query_iri) } order by desc(?date)

sig
has algorithm: RSA
signed by: Tobias Kuhn

Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs displays view: RAecvUbvUW
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T17:56:54.662Z
creator: Erik Schultes
license: https://creativecommons.org/licenses/by/4.0/
embeds: display
was created at: nanodash.knowledgepixels.com

sig
has algorithm: RSA
signed by: Erik Schultes

project4
has label from api: Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs

https://w3id.org/np/RA6e2ALDGvVBPLAGPwkQ0C-qxVtXqw2WZ1BwsMJsOBzys
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T14:35:38.314Z
creator: Eftychia Tzafesta
license: https://creativecommons.org/licenses/by/4.0/
was created at: nanodash.knowledgepixels.com

Eftychia Tzafesta
participated as participant in: FIP.38.T.8
participated as participant in: FIP.38.T.7
participated as participant in: FIP.38.T.6

FIP.38.T.8
has label from api: FIP.38.T.8 | FAIR Implementation Profile Training Session 8

sig
has algorithm: RSA
signed by: Eftychia Tzafesta

https://w3id.org/np/RAD75B_8wpHfP_89Xgn3VE7qAtriJIXjN1P0seC_IKLMQ
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T14:35:07.846Z
creator: Eftychia Tzafesta
license: https://creativecommons.org/licenses/by/4.0/
was created at: nanodash.knowledgepixels.com

FIP.38.T.7
has label from api: FIP.38.T.7| FAIR2Adapt FIP training

sig
has algorithm: RSA
signed by: Eftychia Tzafesta

https://w3id.org/np/RAbcMl_rXcu0CHMdXmiKN96y21iBQVxelQqpVJIMZL4CQ
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T14:34:14.146Z
creator: Eftychia Tzafesta
license: https://creativecommons.org/licenses/by/4.0/
was created at: nanodash.knowledgepixels.com

FIP.38.T.6
has label from api: FIP.38.T.6 | FAIR Implementation Profile Training Session 6

sig
has algorithm: RSA
signed by: Eftychia Tzafesta

https://w3id.org/np/RAEH40u-6bYaYLSe_kW08A6CYxn6qCJNzDqiaCclQmJWI
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T12:10:28.509Z
creator: Erik Schultes
license: https://creativecommons.org/licenses/by/4.0/
has nanopub type: isRelevantFor
was created at: nanodash.knowledgepixels.com

Mac-fdt-staging GitHub Repo
comment: Staging materials for minting the 38 nanopublication-based FAIR Digital Twins of SARS-CoV-2 Spike RBD variants (Alpha, Epsilon, Eta) reported in Schultes et al. (in preparation). MAC / Leiden University LACDR. Project StayAhead (LSHM22038).
is relevant for: project4

sig
has algorithm: RSA
signed by: Erik Schultes

FAIR Digital Twins of COVID Spike variants
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T12:06:20.125Z
creator: Erik Schultes
license: https://creativecommons.org/licenses/by/4.0/
introduces: FAIR Digital Twins of COVID Spike variants
was created at: nanodash.knowledgepixels.com

FAIR Digital Twins of COVID Spike variants
article body: The MAC FDT demonstration is complete and fully version-controlled all live on the nanopub network : 3 FDTs for COVID Spike protein variants are realized using nanopub-based FDOs representing 45 vocabulary terms + 11 templates --> 38 instances
is part of: project4
type: NewsArticle

sig
has algorithm: RSA
signed by: Erik Schultes

Qualification of: RADAF56NSX
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T11:43:18.388Z
creator: Barbara Magagna
license: https://creativecommons.org/licenses/by/4.0/
was created at: nanodash.knowledgepixels.com

sig
has algorithm: RSA
signed by: Barbara Magagna

https://w3id.org/np/RAz6NiRXfQ0EeMaPhvCzmWP9vvcPN1VCNfcCIUM6fzLb0
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T11:20:04.543Z
creator: Cyril Matthey-Doret
license: https://creativecommons.org/licenses/by/4.0/
was created at: nanodash.knowledgepixels.com

sig
has algorithm: RSA
signed by: Cyril Matthey-Doret

Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs displays view: RAGlsCUDZr
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T11:14:23.095Z
creator: Erik Schultes
license: https://creativecommons.org/licenses/by/4.0/
embeds: display
was created at: nanodash.knowledgepixels.com

sig
has algorithm: RSA
signed by: Erik Schultes

Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs has pinned query: MAC FDT — Alpha variant digital twin (knowlet)
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T10:53:17Z
creator: Erik Schultes
license: https://creativecommons.org/licenses/by/4.0/
has nanopub type: hasPinnedQuery

MAC FDT — Alpha variant digital twin (knowlet)
has pin group tag: Digital twin (worked example)
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T10:51:46Z
creator: Erik Schultes
license: https://creativecommons.org/licenses/by/4.0/
introduces: MAC FDT — Alpha variant digital twin (knowlet)

sig
has algorithm: RSA
signed by: Erik Schultes

Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs has pinned query: MAC FDT — catalogue summary by type
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T10:53:17Z
creator: Erik Schultes
license: https://creativecommons.org/licenses/by/4.0/
has nanopub type: hasPinnedQuery

MAC FDT — catalogue summary by type
has pin group tag: Catalogue overview
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T10:51:46Z
creator: Erik Schultes
license: https://creativecommons.org/licenses/by/4.0/
introduces: MAC FDT — catalogue summary by type

sig
has algorithm: RSA
signed by: Erik Schultes

Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs has pinned query: MAC FDT — observations per method
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T10:53:17Z
creator: Erik Schultes
license: https://creativecommons.org/licenses/by/4.0/
has nanopub type: hasPinnedQuery

MAC FDT — observations per method
has pin group tag: Situational dashboards
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T10:51:46Z
creator: Erik Schultes
license: https://creativecommons.org/licenses/by/4.0/
introduces: MAC FDT — observations per method

sig
has algorithm: RSA
signed by: Erik Schultes

Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs has pinned query: MAC FDT — variants by WHO classification
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T10:53:17Z
creator: Erik Schultes
license: https://creativecommons.org/licenses/by/4.0/
has nanopub type: hasPinnedQuery

MAC FDT — variants by WHO classification
has pin group tag: Situational dashboards
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T10:51:46Z
creator: Erik Schultes
license: https://creativecommons.org/licenses/by/4.0/
introduces: MAC FDT — variants by WHO classification

sig
has algorithm: RSA
signed by: Erik Schultes

MAC FDT — Alpha variant digital twin (knowlet)
description: All observation FDOs about the Alpha Spike RBD variant — real-world occurrence, computational predictions, experimental DMS, and WHO classification — forming the FAIR Digital Twin knowlet for Alpha. Worked example of a single FDT.
license: LICENSE-2.0
type: grlc-query
endpoint: full
sparql: PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX np: <http://www.nanopub.org/nschema#> PREFIX npa: <http://purl.org/nanopub/admin/> PREFIX npx: <http://purl.org/nanopub/x/> PREFIX dct: <http://purl.org/dc/terms/> PREFIX fdof: <https://w3id.org/fdof/ontology#> PREFIX mac: <https://w3id.org/spaces/mac/r/ontology/> SELECT ?obs ?type ?label WHERE { GRAPH npa:graph { ?n1 npa:hasValidSignatureForPublicKey ?pubkey . filter not exists { ?np2 npx:invalidates ?n1 ; npa:hasValidSignatureForPublicKey ?pubkey . } ?n1 np:hasAssertion ?a . } graph ?a { ?obs mac:isObservationOf <https://w3id.org/np/RA4BHII2Bz7HfpUkaSJqNmhjF8F7hyWpCJnvXYkA4EP_M/Alpha-RBD-Variant> . ?obs a ?type . FILTER(?type != fdof:FAIRDigitalObject) OPTIONAL { ?obs rdfs:label ?label . } } } ORDER BY ?type

sig
has algorithm: RSA
signed by: Erik Schultes

MAC FDT — catalogue summary by type
description: Counts of MAC FDT FDOs grouped by their specific type (variants, observations, methods). Bounded summary view of the full catalogue.
license: LICENSE-2.0
type: grlc-query
endpoint: full
sparql: PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX np: <http://www.nanopub.org/nschema#> PREFIX npa: <http://purl.org/nanopub/admin/> PREFIX npx: <http://purl.org/nanopub/x/> PREFIX dct: <http://purl.org/dc/terms/> PREFIX fdof: <https://w3id.org/fdof/ontology#> PREFIX mac: <https://w3id.org/spaces/mac/r/ontology/> SELECT ?type (COUNT(?thing) AS ?count) WHERE { GRAPH npa:graph { ?n1 npa:hasValidSignatureForPublicKey ?pubkey . filter not exists { ?np2 npx:invalidates ?n1 ; npa:hasValidSignatureForPublicKey ?pubkey . } ?n1 np:hasAssertion ?a . } graph ?a { ?thing a fdof:FAIRDigitalObject . ?thing a ?type . FILTER(?type != fdof:FAIRDigitalObject) FILTER(STRSTARTS(STR(?type), "https://w3id.org/spaces/mac/r/ontology/")) } } GROUP BY ?type ORDER BY DESC(?count)

sig
has algorithm: RSA
signed by: Erik Schultes

MAC FDT — observations per method
description: Counts of observation FDOs grouped by the method (computational, experimental, or surveillance) that produced them — demonstrating multi-source decentralized attribution.
license: LICENSE-2.0
type: grlc-query
endpoint: full
sparql: PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX np: <http://www.nanopub.org/nschema#> PREFIX npa: <http://purl.org/nanopub/admin/> PREFIX npx: <http://purl.org/nanopub/x/> PREFIX dct: <http://purl.org/dc/terms/> PREFIX fdof: <https://w3id.org/fdof/ontology#> PREFIX mac: <https://w3id.org/spaces/mac/r/ontology/> SELECT ?method (COUNT(?obs) AS ?count) WHERE { GRAPH npa:graph { ?n1 npa:hasValidSignatureForPublicKey ?pubkey . filter not exists { ?np2 npx:invalidates ?n1 ; npa:hasValidSignatureForPublicKey ?pubkey . } ?n1 np:hasAssertion ?a . } graph ?a { ?obs ?methodPred ?method . VALUES ?methodPred { mac:hasPredictionMethod mac:hasExperimentalMethod mac:hasSurveillanceMethod } } } GROUP BY ?method ORDER BY DESC(?count)

sig
has algorithm: RSA
signed by: Erik Schultes

MAC FDT — variants by WHO classification
description: Counts of Spike RBD variants grouped by WHO risk designation (VOC / VOI / VUM), via their WHO classification observation FDOs.
license: LICENSE-2.0
type: grlc-query
endpoint: full
sparql: PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX np: <http://www.nanopub.org/nschema#> PREFIX npa: <http://purl.org/nanopub/admin/> PREFIX npx: <http://purl.org/nanopub/x/> PREFIX dct: <http://purl.org/dc/terms/> PREFIX fdof: <https://w3id.org/fdof/ontology#> PREFIX mac: <https://w3id.org/spaces/mac/r/ontology/> SELECT ?whoClass (COUNT(?variant) AS ?count) WHERE { GRAPH npa:graph { ?n1 npa:hasValidSignatureForPublicKey ?pubkey . filter not exists { ?np2 npx:invalidates ?n1 ; npa:hasValidSignatureForPublicKey ?pubkey . } ?n1 np:hasAssertion ?a . } graph ?a { ?obs a mac:WHOVariantClassification . ?obs mac:hasWHOClassification ?whoClass . ?obs mac:isObservationOf ?variant . } } GROUP BY ?whoClass ORDER BY DESC(?count)

sig
has algorithm: RSA
signed by: Erik Schultes

https://w3id.org/np/RA2IHnDRfYvauH_dwY9HG3Sy4uQ0kg4saSKSJfLsYUVAM
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T10:05:46.347Z
creator: Cyril Matthey-Doret
license: https://creativecommons.org/licenses/by/4.0/
was created at: nanodash.knowledgepixels.com

sig
has algorithm: RSA
signed by: Cyril Matthey-Doret

User: Cyril Matthey-Doret
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T10:03:15.710Z
creator: Cyril Matthey-Doret
license: https://creativecommons.org/licenses/by/4.0/
has nanopub type: declaredBy
introduces: Cyril Matthey-Doret
was created at: nanodash.knowledgepixels.com

M..AQEA3..
declared by: Cyril Matthey-Doret
has algorithm: RSA
has key location: nanodash.knowledgepixels.com

sig
has algorithm: RSA
signed by: Cyril Matthey-Doret

Participation in: Demo session for Swiss Data Science Center
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T09:44:19.287Z
creator: Irene Keller
license: https://creativecommons.org/licenses/by/4.0/
was created at: nanodash.knowledgepixels.com

Irene Keller
P1344: sdsc-demo-20260528

sig
has algorithm: RSA
signed by: Irene Keller

User: Irene Keller
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T09:24:18.151Z
creator: Irene Keller
license: https://creativecommons.org/licenses/by/4.0/
has nanopub type: declaredBy
introduces: Irene Keller
was created at: nanodash.knowledgepixels.com

M..AQEAj..
declared by: Irene Keller
has algorithm: RSA
has key location: nanodash.knowledgepixels.com

sig
has algorithm: RSA
signed by: Irene Keller

https://w3id.org/np/RA-IJTTitx2KdCPmBqFOvLU9UlFlfxMGcvurLM_4fZSgU
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T09:22:47.599Z
creator: Stefan Milosavljevic
license: https://creativecommons.org/licenses/by/4.0/
was created at: nanodash.knowledgepixels.com

Stefan Milosavljevic
P1344: sdsc-demo-20260528

sig
has algorithm: RSA
signed by: Stefan Milosavljevic

0009-0000-5571-5036 is participant in Demo session for Swiss Data Science Center
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T09:21:47.563Z
creator: https://orcid.org/0009-0000-5571-5036
license: https://creativecommons.org/licenses/by/4.0/
was created at: nanodash.knowledgepixels.com

sig
has algorithm: RSA
signed by: https://orcid.org/0009-0000-5571-5036

sdsc-demo-20260528
has label from api: Demo session for Swiss Data Science Center

https://w3id.org/np/RAdtTOqZNz30RR4HxcfHQ_-wiqM-0mk65AOH0VX_2WYy4
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T09:21:16.457Z
creator: Stefan Milosavljevic
license: https://creativecommons.org/licenses/by/4.0/
was created at: nanodash.knowledgepixels.com

sig
has algorithm: RSA
signed by: Stefan Milosavljevic

Sabine Maennel is participant in Demo session for Swiss Data Science Center
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T09:21:16.395Z
creator: Sabine Maennel
license: https://creativecommons.org/licenses/by/4.0/
was created at: nanodash.knowledgepixels.com

Sabine Maennel
P1344: sdsc-demo-20260528

sig
has algorithm: RSA
signed by: Sabine Maennel

Tobias Kuhn is participant in Demo session for Swiss Data Science Center
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T09:19:57.992Z
creator: Tobias Kuhn
license: https://creativecommons.org/publicdomain/zero/1.0/
was created at: nanodash.knowledgepixels.com

sig
has algorithm: RSA
signed by: Tobias Kuhn

User: Stefan Milosavljevic
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T09:19:44.131Z
creator: Stefan Milosavljevic
license: https://creativecommons.org/licenses/by/4.0/
has nanopub type: declaredBy
introduces: Stefan Milosavljevic
was created at: nanodash.knowledgepixels.com

M..AQEAi..
declared by: Stefan Milosavljevic
has algorithm: RSA
has key location: nanodash.knowledgepixels.com

sig
has algorithm: RSA
signed by: Stefan Milosavljevic

User: Sabine Maennel
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T09:19:29.307Z
creator: Sabine Maennel
license: https://creativecommons.org/licenses/by/4.0/
has nanopub type: declaredBy
introduces: Sabine Maennel
was created at: nanodash.knowledgepixels.com

M..AQEAr..
declared by: Sabine Maennel
has algorithm: RSA
has key location: nanodash.knowledgepixels.com

sig
has algorithm: RSA
signed by: Sabine Maennel

0000-0002-9135-1353 is participant in Demo session for Swiss Data Science Center
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T09:17:05.107Z
creator: Stefan Milosavljevic
license: https://creativecommons.org/licenses/by/4.0/
was created at: nanodash.knowledgepixels.com

sig
has algorithm: RSA
signed by: Stefan Milosavljevic

https://w3id.org/np/RAesdcYnmctEQyLs-kCBbstTnY-QuKCjt5yGHVXJvRZjU
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T09:11:25.732Z
creator: Tobias Kuhn
license: https://creativecommons.org/publicdomain/zero/1.0/
has nanopub type: isRelevantFor
was created at: nanodash.knowledgepixels.com

Nanopublication website
comment: The site of the nanopublication community
is relevant for: sdsc-demo-20260528

sig
has algorithm: RSA
signed by: Tobias Kuhn

https://w3id.org/np/RAzxtMpFooETDACI4RAQSws5GwsxVjkXxfQt6qEtKuabA
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T09:04:44.018Z
creator: Tobias Kuhn
license: https://creativecommons.org/publicdomain/zero/1.0/
has nanopub type: isRelevantFor
was created at: nanodash.knowledgepixels.com

Try out Nanodash GIF
is relevant for: sdsc-demo-20260528

sig
has algorithm: RSA
signed by: Tobias Kuhn

https://w3id.org/np/RAKbXsGD6rAjQyxxqZZPMbC7Zo5xb6ylIdrKSmAaJ1STA
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T09:03:00.889Z
creator: Tobias Kuhn
license: https://creativecommons.org/publicdomain/zero/1.0/
has nanopub type: isRelevantFor
was created at: nanodash.knowledgepixels.com

Knowledge Pixels
comment: Our start-up focussed on nanopublications
is relevant for: sdsc-demo-20260528

sig
has algorithm: RSA
signed by: Tobias Kuhn

Demo session for Swiss Data Science Center displays view: Relevant resources view
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-05-28T09:00:51.692Z
creator: Tobias Kuhn
license: https://creativecommons.org/publicdomain/zero/1.0/
embeds: display
was created at: nanodash.knowledgepixels.com

relevant-resource-view
has label from api: Relevant resources view

sig
has algorithm: RSA
signed by: Tobias Kuhn

Alpha AgMata = 0.7004717948717948 — Bio2Byte
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
license: https://creativecommons.org/licenses/by/4.0/
has encoding format: trig
materializes: Alpha AgMata = 0.7004717948717948 — Bio2Byte
created: 2026-05-28T08:20:53Z
creator: Erik Schultes
introduces: Alpha AgMata = 0.7004717948717948 — Bio2Byte

Alpha AgMata = 0.7004717948717948 — Bio2Byte
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
source: hw56-vj34
source: esm wuhan 1step v1
type: FAIRDigitalObject
type: ComputationalPredictionAgMata
comment: Computational prediction of AgMata aggregation propensity score (0.7004717948717948, unitless) for SARS-CoV-2 Spike RBD variant Alpha (N169Y) using the Bio2Byte AgMata predictor. Sequence-derived: one FDO per variant.
has ag mata score: 0.7004717948717948
has prediction method: AgMata-Method
is observation of: Alpha-RBD-Variant

sig
has algorithm: RSA
signed by: Erik Schultes

Alpha DMS observation — Bloom Lab (bind=9.81374, expr=10.05266)
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
license: https://creativecommons.org/licenses/by/4.0/
has encoding format: trig
materializes: Alpha DMS observation — Bloom Lab (bind=9.81374, expr=10.05266)
created: 2026-05-28T08:20:53Z
creator: Erik Schultes
introduces: Alpha DMS observation — Bloom Lab (bind=9.81374, expr=10.05266)

Alpha DMS observation — Bloom Lab (bind=9.81374, expr=10.05266)
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
type: FAIRDigitalObject
type: ExperimentalDMSObservation
comment: Deep mutational scanning measurements (Bloom Lab) for SARS-CoV-2 Spike RBD variant Alpha (N169Y). Six values: bind=9.81374, delta_bind=1.04213, expr=10.05266, delta_expr=-0.13322, confidence_bind=0.0732354593527125, confidence_expr=0.0713853600674372. All unitless.
has bind: 9.81374
has confidence bind: 0.0732354593527125
has confidence expr: 0.0713853600674372
has delta bind: 1.04213
has delta expr: -0.13322
has experimental method: BloomLab-DMS-Method
has expr: 10.05266
is observation of: Alpha-RBD-Variant

sig
has algorithm: RSA
signed by: Erik Schultes

Alpha real-world occurrence — England (late 2020-2021)
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
license: https://creativecommons.org/licenses/by/4.0/
has encoding format: trig
materializes: Alpha real-world occurrence — England (late 2020-2021)
created: 2026-05-28T08:20:53Z
creator: Erik Schultes
introduces: Alpha real-world occurrence — England (late 2020-2021)

Alpha real-world occurrence — England (late 2020-2021)
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
type: FAIRDigitalObject
type: RealWorldOccurrence
comment: Real-world detection of SARS-CoV-2 Spike variant Alpha (B.1.1.7) in England during late 2020-2021, as reported in GISAID (accession EPI_ISL_601443).
has collection location: https://sws.geonames.org/6269131/
has GISAID accession: EPI_ISL_601443
has occurrence date: late 2020-2021
has surveillance method: GISAID-Method
is observation of: Alpha-RBD-Variant

sig
has algorithm: RSA
signed by: Erik Schultes

Alpha — WHO Variant of Concern (2020-12-18)
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
license: https://creativecommons.org/licenses/by/4.0/
has encoding format: trig
materializes: Alpha — WHO Variant of Concern (2020-12-18)
created: 2026-05-28T08:20:53Z
creator: Erik Schultes
introduces: Alpha — WHO Variant of Concern (2020-12-18)

Alpha — WHO Variant of Concern (2020-12-18)
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
type: FAIRDigitalObject
type: WHOVariantClassification
comment: WHO classification of SARS-CoV-2 Spike variant Alpha (B.1.1.7) as a Variant of Concern (VOC) on 2020-12-18.
has classification date: 2020-12-18
has WHO classification: VOC
is observation of: Alpha-RBD-Variant

sig
has algorithm: RSA
signed by: Erik Schultes