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).
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
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).
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
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).
Get the classes assigned to a thing (view)
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
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).
Get the templates using given URI (view)
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
Citations for: RAsPjEImfZaXsIri0ny4j_s_k_6wyOlC6tkocl6w2y7f4
Coverage-based rarefaction does not restore agreement between GBIF richness hotspots and the EU Article 12 expert-rangemap gold standard (Iberian birds, HEALPix-NESTED)
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.
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
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.
Coverage-based effort correction of Iberian-bird richness hotspots (HEALPix-NESTED)
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.
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.
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).
Coverage-based rarefaction restores GBIF-vs-expert-rangemap hotspot agreement (Iberian birds, HEALPix-NESTED)
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.
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.
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.
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.
OSPARK output - Managing Outreach on Open Research Material to Heterogeneous Groups
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.
Read: OSPARK output - Managing Outreach on Open Research Material to Heterogeneous Groups
From Waste to Worth cites Chakhmouradian & Wall (2012) as evidence
From Waste to Worth cites Jowitt et al. (2018) as evidence
From Waste to Worth cites de Boer & Lammertsma (2013) as evidence
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.
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
Given a resource, this query returns the claims (AIDA sentences) it covers via gen:coversClaim.
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
Biodiversity Ontology displays view: simple message view
Explorative use case: from waste to worth displays view: Claims view
Explorative use case: from waste to worth
Explorative use case: from waste to worth displays view: Cited papers view
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).
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)
Exploring how we can apply nanopubs for science-related blog posts.
An informal group where Reatch and Knowledge Pixels discuss nanopublication applications.
AIDA sentence - an English sentence that is Atomic, Independent, Declarative, and Absolute
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)
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.
Expressing a literature-derived statement as an AIDA sentence
DOI (https://doi.org/10...) or URL of the source the sentence is derived from
identifier of concept or topic the sentence is about
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.
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
Rare Earth Elements: Minerals, Mines, Magnets (and More)
Article: Rare Earth Elements: Minerals, Mines, Magnets (and More)
Current Opinion in Green and Sustainable Chemistry
Article: Recycling of the rare earth elements
Article: Scarcity of Rare Earth Elements
From waste to worth, let's reconcile the world through a new bio-recycling way!
From Waste to Worth (Reatch overview article)
Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs displays view: fdt-alpha-knowlet-view
Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs displays view: fdt-catalogue-summary-view
Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs displays view: fdt-observations-per-method-view
Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs displays view: fdt-variants-by-who-view
MAC FDT — Alpha variant digital twin view
MAC FDT — catalogue summary by type view
MAC FDT — variants by WHO classification
MAC FDT — variants by WHO classification view
Wrong mechanism: used npx:invalidates rather than the publisher-facing npx:retracts. Superseded by an npx:retracts-based retraction in the same fix branch.
Retraction of RA0aGsMc41L (mistaken npx:invalidates nanopub, alpha-knowlet)
Conflated mechanism: ViewDisplay (gen:isDisplayOfView) requires a gen:View wrapper, not a bare grlc-query.
Retraction of RAD5G7Z3kY14 (broken ViewDisplay, alpha-knowlet)
Retraction of RAUVFxrhms_ (mistaken npx:invalidates nanopub, catalogue-summary)
Retraction of RAq9o-TF0vcy (broken ViewDisplay, catalogue-summary)
Showing the decentralized network, including links to the Registry and Query instances
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.
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))
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).
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)
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.
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)
Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs displays view: RAecvUbvUW
Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs
FIP.38.T.8 | FAIR Implementation Profile Training Session 8
FIP.38.T.6 | FAIR Implementation Profile Training Session 6
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).
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
FAIR Digital Twins of COVID Spike variants
Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs displays view: RAGlsCUDZr
Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs has pinned query: MAC FDT — Alpha variant digital twin (knowlet)
Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs has pinned query: MAC FDT — catalogue summary by type
Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs has pinned query: MAC FDT — observations per method
Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs has pinned query: MAC FDT — variants by WHO classification
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.
MAC FDT — Alpha variant digital twin (knowlet)
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
Counts of MAC FDT FDOs grouped by their specific type (variants, observations, methods). Bounded summary view of the full catalogue.
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)
Counts of observation FDOs grouped by the method (computational, experimental, or surveillance) that produced them — demonstrating multi-source decentralized attribution.
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)
Counts of Spike RBD variants grouped by WHO risk designation (VOC / VOI / VUM), via their WHO classification observation FDOs.
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)
Participation in: Demo session for Swiss Data Science Center
0009-0000-5571-5036 is participant in Demo session for Swiss Data Science Center
Demo session for Swiss Data Science Center
Sabine Maennel is participant in Demo session for Swiss Data Science Center
Tobias Kuhn is participant in Demo session for Swiss Data Science Center
0000-0002-9135-1353 is participant in Demo session for Swiss Data Science Center
The site of the nanopublication community
Our start-up focussed on nanopublications
Demo session for Swiss Data Science Center displays view: Relevant resources view
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.
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.
Alpha DMS observation — Bloom Lab (bind=9.81374, expr=10.05266)
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).
Alpha real-world occurrence — England (late 2020-2021)
WHO classification of SARS-CoV-2 Spike variant Alpha (B.1.1.7) as a Variant of Concern (VOC) on 2020-12-18.
Alpha — WHO Variant of Concern (2020-12-18)