https://w3id.org/np/RAEH40u-6bYaYLSe_kW08A6CYxn6qCJNzDqiaCclQmJWI
created: 2026-05-28T12:10:28.509Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
has nanopub type: isRelevantFor
was created at: nanodash.knowledgepixels.com
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo

sig
has algorithm: RSA
signed by: Erik Schultes

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

FAIR Digital Twins of COVID Spike variants
type: NewsArticle
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

FAIR Digital Twins of COVID Spike variants
created: 2026-05-28T12:06:20.125Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
introduces: FAIR Digital Twins of COVID Spike variants
was created at: nanodash.knowledgepixels.com
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo

sig
has algorithm: RSA
signed by: Erik Schultes

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

Qualification of: RADAF56NSX
created: 2026-05-28T11:43:18.388Z
creator: Barbara Magagna
data usage license: Attribution 4.0 International (CC BY 4.0)
was created at: nanodash.knowledgepixels.com
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo

sig
has algorithm: RSA
signed by: Barbara Magagna

https://w3id.org/np/RAz6NiRXfQ0EeMaPhvCzmWP9vvcPN1VCNfcCIUM6fzLb0
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T11:20:04.543Z
creator: Cyril Matthey-Doret
data usage license: Attribution 4.0 International (CC 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
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T11:14:23.095Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
embeds: display
was created at: nanodash.knowledgepixels.com

sig
has algorithm: RSA
signed by: Erik Schultes

MAC FDT — Alpha variant digital twin (knowlet)
has pin group tag: Digital twin (worked example)
created: 2026-05-28T10:51:46Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
introduces: MAC FDT — Alpha variant digital twin (knowlet)
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo

Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs has pinned query: MAC FDT — Alpha variant digital twin (knowlet)
created: 2026-05-28T10:53:17Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
has nanopub type: hasPinnedQuery
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo

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
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T10:53:17Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
has nanopub type: hasPinnedQuery

MAC FDT — catalogue summary by type
has pin group tag: Catalogue overview
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T10:51:46Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC 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
created: 2026-05-28T10:53:17Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
has nanopub type: hasPinnedQuery
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo

sig
has algorithm: RSA
signed by: Erik Schultes

MAC FDT — observations per method
has pin group tag: Situational dashboards
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T10:51:46Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
introduces: MAC FDT — observations per method

MAC FDT — variants by WHO classification
has pin group tag: Situational dashboards
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T10:51:46Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
introduces: MAC FDT — variants by WHO classification

Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs has pinned query: MAC FDT — variants by WHO classification
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T10:53:17Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
has nanopub type: hasPinnedQuery

sig
has algorithm: RSA
signed by: Erik Schultes

sig
has algorithm: RSA
signed by: Erik Schultes

MAC FDT — Alpha variant digital twin (knowlet)
type: grlc-query
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.
data usage license: LICENSE-2.0
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
type: grlc-query
description: Counts of MAC FDT FDOs grouped by their specific type (variants, observations, methods). Bounded summary view of the full catalogue.
data usage license: LICENSE-2.0
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)

MAC FDT — observations per method
type: grlc-query
description: Counts of observation FDOs grouped by the method (computational, experimental, or surveillance) that produced them — demonstrating multi-source decentralized attribution.
data usage license: LICENSE-2.0
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
type: grlc-query
description: Counts of Spike RBD variants grouped by WHO risk designation (VOC / VOI / VUM), via their WHO classification observation FDOs.
data usage license: LICENSE-2.0
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
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T10:05:46.347Z
creator: Cyril Matthey-Doret
data usage license: Attribution 4.0 International (CC BY 4.0)
was created at: nanodash.knowledgepixels.com

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

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

User: Cyril Matthey-Doret
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T10:03:15.710Z
creator: Cyril Matthey-Doret
data usage license: Attribution 4.0 International (CC BY 4.0)
has nanopub type: declaredBy
introduces: Cyril Matthey-Doret
was created at: nanodash.knowledgepixels.com

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

Participation in: Demo session for Swiss Data Science Center
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T09:44:19.287Z
creator: Irene Keller
data usage license: Attribution 4.0 International (CC BY 4.0)
was created at: nanodash.knowledgepixels.com

Irene Keller
P1344: Demo session for Swiss Data Science Center

sig
has algorithm: RSA
signed by: Irene Keller

User: Irene Keller
type: Nanopublication
has assertion: assertion
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has publication info: pubinfo
created: 2026-05-28T09:24:18.151Z
creator: Irene Keller
data usage license: Attribution 4.0 International (CC 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

Stefan Milosavljevic
P1344: Demo session for Swiss Data Science Center

https://w3id.org/np/RA-IJTTitx2KdCPmBqFOvLU9UlFlfxMGcvurLM_4fZSgU
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T09:22:47.599Z
creator: Stefan Milosavljevic
data usage license: Attribution 4.0 International (CC BY 4.0)
was created at: nanodash.knowledgepixels.com

sig
has algorithm: RSA
signed by: Stefan Milosavljevic

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

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

Demo session for Swiss Data Science Center
has label from api: Demo session for Swiss Data Science Center
P823: Tobias Kuhn
has role: participantRole
has role: speakerRole
type: Event
type: Space
description: During this interactive session, Nanodash and nanopublications will be demoed.
end date: 2026-05-28T12:00:00.0+02:00
start date: 2026-05-28T11:00:00.0+02:00
has admin: Tobias Kuhn

https://w3id.org/np/RAdtTOqZNz30RR4HxcfHQ_-wiqM-0mk65AOH0VX_2WYy4
type: Nanopublication
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has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T09:21:16.457Z
creator: Stefan Milosavljevic
data usage license: Attribution 4.0 International (CC 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
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T09:21:16.395Z
creator: Sabine Maennel
data usage license: Attribution 4.0 International (CC BY 4.0)
was created at: nanodash.knowledgepixels.com

Sabine Maennel
P1344: Demo session for Swiss Data Science Center

sig
has algorithm: RSA
signed by: Sabine Maennel

Tobias Kuhn is participant in Demo session for Swiss Data Science Center
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T09:19:57.992Z
creator: Tobias Kuhn
data usage license: https://creativecommons.org/publicdomain/zero/1.0/
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Tobias Kuhn
P1344: Demo session for Swiss Data Science Center

sig
has algorithm: RSA
signed by: Tobias Kuhn

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

User: Stefan Milosavljevic
type: Nanopublication
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has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T09:19:44.131Z
creator: Stefan Milosavljevic
data usage license: Attribution 4.0 International (CC BY 4.0)
has nanopub type: declaredBy
introduces: Stefan Milosavljevic
was created at: nanodash.knowledgepixels.com

sig
has algorithm: RSA
signed by: Stefan Milosavljevic

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

User: Sabine Maennel
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T09:19:29.307Z
creator: Sabine Maennel
data usage license: Attribution 4.0 International (CC BY 4.0)
has nanopub type: declaredBy
introduces: Sabine Maennel
was created at: 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
created: 2026-05-28T09:17:05.107Z
creator: Stefan Milosavljevic
data usage license: Attribution 4.0 International (CC BY 4.0)
was created at: nanodash.knowledgepixels.com
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo

sig
has algorithm: RSA
signed by: Stefan Milosavljevic

Nanopublication website
comment: The site of the nanopublication community
is relevant for: Demo session for Swiss Data Science Center

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

sig
has algorithm: RSA
signed by: Tobias Kuhn

https://w3id.org/np/RAzxtMpFooETDACI4RAQSws5GwsxVjkXxfQt6qEtKuabA
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T09:04:44.018Z
creator: Tobias Kuhn
data usage 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: Demo session for Swiss Data Science Center

sig
has algorithm: RSA
signed by: Tobias Kuhn

Knowledge Pixels
comment: Our start-up focussed on nanopublications
is relevant for: Demo session for Swiss Data Science Center

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

sig
has algorithm: RSA
signed by: Tobias Kuhn

Demo session for Swiss Data Science Center displays view: Relevant resources view
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T09:00:51.692Z
creator: Tobias Kuhn
data usage 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
data usage license: Attribution 4.0 International (CC BY 4.0)
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: Alpha AgMata = 0.7004717948717948 — Bio2Byte
created: 2026-05-28T08:20:53Z
creator: Erik Schultes
introduces: Alpha AgMata = 0.7004717948717948 — Bio2Byte
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo

Alpha AgMata = 0.7004717948717948 — Bio2Byte
type: FAIR Digital Object (FDO)
type: Computational Prediction — AgMata
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
has source: FAIR² Data Package DOI
has source: esm wuhan 1step v1
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 AgMata score (aggregation propensity): 0.7004717948717948
has prediction method: Bio2Byte AgMata — aggregation propensity predictor
is observation of: Spike RBD Variant Alpha (N169Y)

sig
has algorithm: RSA
signed by: Erik Schultes

Alpha DMS observation — Bloom Lab (bind=9.81374, expr=10.05266)
data usage license: Attribution 4.0 International (CC BY 4.0)
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: Alpha DMS observation — Bloom Lab (bind=9.81374, expr=10.05266)
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
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)
type: FAIR Digital Object (FDO)
type: Experimental DMS Observation
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
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 (binding affinity, log KD, unitless): 9.81374
has confidence_bind (unitless): 0.0732354593527125
has confidence_expr (unitless): 0.0713853600674372
has delta_bind (vs. wild-type, unitless): 1.04213
has delta_expr (vs. wild-type, unitless): -0.13322
has experimental method: Deep mutational scanning — Bloom Lab SARS-CoV-2 RBD
has expr (expression level, log MFI, unitless): 10.05266
is observation of: Spike RBD Variant Alpha (N169Y)

sig
has algorithm: RSA
signed by: Erik Schultes

Alpha real-world occurrence — England (late 2020-2021)
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T08:20:53Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
introduces: Alpha real-world occurrence — England (late 2020-2021)
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: Alpha real-world occurrence — England (late 2020-2021)

sig
has algorithm: RSA
signed by: Erik Schultes

Alpha real-world occurrence — England (late 2020-2021)
type: FAIR Digital Object (FDO)
type: Real-World Occurrence
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
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 number: EPI_ISL_601443
has occurrence date: late 2020-2021
has surveillance method: GISAID — Global Initiative on Sharing All Influenza Data
is observation of: Spike RBD Variant Alpha (N169Y)

Alpha — WHO Variant of Concern (2020-12-18)
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T08:20:53Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
introduces: Alpha — WHO Variant of Concern (2020-12-18)
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: Alpha — WHO Variant of Concern (2020-12-18)

sig
has algorithm: RSA
signed by: Erik Schultes

Alpha — WHO Variant of Concern (2020-12-18)
type: FAIR Digital Object (FDO)
type: WHO Variant Classification
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
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 WHO classification date: 2020-12-18
has WHO variant classification: VOC
is observation of: Spike RBD Variant Alpha (N169Y)

Epsilon AgMata = 0.7194974358974362 — Bio2Byte
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
data usage license: Attribution 4.0 International (CC BY 4.0)
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: Epsilon AgMata = 0.7194974358974362 — Bio2Byte
created: 2026-05-28T08:20:53Z
creator: Erik Schultes
introduces: Epsilon AgMata = 0.7194974358974362 — Bio2Byte

Epsilon AgMata = 0.7194974358974362 — Bio2Byte
type: FAIR Digital Object (FDO)
type: Computational Prediction — AgMata
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
has source: FAIR² Data Package DOI
has source: esm wuhan 1step v1
comment: Computational prediction of AgMata aggregation propensity score (0.7194974358974362, unitless) for SARS-CoV-2 Spike RBD variant Epsilon (L120R) using the Bio2Byte AgMata predictor. Sequence-derived: one FDO per variant.
has AgMata score (aggregation propensity): 0.7194974358974362
has prediction method: Bio2Byte AgMata — aggregation propensity predictor
is observation of: Spike RBD Variant Epsilon (L120R)

sig
has algorithm: RSA
signed by: Erik Schultes

Epsilon DMS observation — Bloom Lab (bind=8.93862, expr=10.25356)
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T08:20:53Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
introduces: Epsilon DMS observation — Bloom Lab (bind=8.93862, expr=10.25356)
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: Epsilon DMS observation — Bloom Lab (bind=8.93862, expr=10.25356)

sig
has algorithm: RSA
signed by: Erik Schultes

Epsilon DMS observation — Bloom Lab (bind=8.93862, expr=10.25356)
type: FAIR Digital Object (FDO)
type: Experimental DMS Observation
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
comment: Deep mutational scanning measurements (Bloom Lab) for SARS-CoV-2 Spike RBD variant Epsilon (L120R). Six values: bind=8.93862, delta_bind=0.16701, expr=10.25356, delta_expr=0.06768, confidence_bind=0.0729917177063099, confidence_expr=0.0705230077448188. All unitless.
has bind (binding affinity, log KD, unitless): 8.93862
has confidence_bind (unitless): 0.0729917177063099
has confidence_expr (unitless): 0.0705230077448188
has delta_bind (vs. wild-type, unitless): 0.16701
has delta_expr (vs. wild-type, unitless): 0.06768
has experimental method: Deep mutational scanning — Bloom Lab SARS-CoV-2 RBD
has expr (expression level, log MFI, unitless): 10.25356
is observation of: Spike RBD Variant Epsilon (L120R)

Epsilon real-world occurrence — United States (2021-01-13)
created: 2026-05-28T08:20:53Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
introduces: Epsilon real-world occurrence — United States (2021-01-13)
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: Epsilon real-world occurrence — United States (2021-01-13)

sig
has algorithm: RSA
signed by: Erik Schultes

Epsilon real-world occurrence — United States (2021-01-13)
type: FAIR Digital Object (FDO)
type: Real-World Occurrence
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
comment: Real-world detection of SARS-CoV-2 Spike variant Epsilon (B.1.427 + B.1.429) in the United States on 2021-01-13, as reported in GISAID (accession EPI_ISL_2295356).
has collection location: https://sws.geonames.org/6252001/
has GISAID accession number: EPI_ISL_2295356
has occurrence date: 2021-01-13
has surveillance method: GISAID — Global Initiative on Sharing All Influenza Data
is observation of: Spike RBD Variant Epsilon (L120R)

Epsilon — WHO Variant of Interest (2021-03-05)
created: 2026-05-28T08:20:53Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
introduces: Epsilon — WHO Variant of Interest (2021-03-05)
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: Epsilon — WHO Variant of Interest (2021-03-05)

sig
has algorithm: RSA
signed by: Erik Schultes

Epsilon — WHO Variant of Interest (2021-03-05)
type: FAIR Digital Object (FDO)
type: WHO Variant Classification
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
comment: WHO classification of SARS-CoV-2 Spike variant Epsilon (B.1.427 + B.1.429) as a Variant of Interest (VOI) on 2021-03-05.
has WHO classification date: 2021-03-05
has WHO variant classification: VOI
is observation of: Spike RBD Variant Epsilon (L120R)

Eta AgMata = 0.680579487179487 — Bio2Byte
created: 2026-05-28T08:20:53Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
introduces: Eta AgMata = 0.680579487179487 — Bio2Byte
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: Eta AgMata = 0.680579487179487 — Bio2Byte

sig
has algorithm: RSA
signed by: Erik Schultes

Eta AgMata = 0.680579487179487 — Bio2Byte
type: FAIR Digital Object (FDO)
type: Computational Prediction — AgMata
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
has source: FAIR² Data Package DOI
has source: esm wuhan 1step v1
comment: Computational prediction of AgMata aggregation propensity score (0.680579487179487, unitless) for SARS-CoV-2 Spike RBD variant Eta (E152K) using the Bio2Byte AgMata predictor. Sequence-derived: one FDO per variant.
has AgMata score (aggregation propensity): 0.680579487179487
has prediction method: Bio2Byte AgMata — aggregation propensity predictor
is observation of: Spike RBD Variant Eta (E152K)

Eta DMS observation — Bloom Lab (bind=9.01256, expr=10.21898)
data usage license: Attribution 4.0 International (CC BY 4.0)
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: Eta DMS observation — Bloom Lab (bind=9.01256, expr=10.21898)
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T08:20:53Z
creator: Erik Schultes
introduces: Eta DMS observation — Bloom Lab (bind=9.01256, expr=10.21898)

Eta DMS observation — Bloom Lab (bind=9.01256, expr=10.21898)
type: FAIR Digital Object (FDO)
type: Experimental DMS Observation
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
comment: Deep mutational scanning measurements (Bloom Lab) for SARS-CoV-2 Spike RBD variant Eta (E152K). Six values: bind=9.01256, delta_bind=0.24095, expr=10.21898, delta_expr=0.03311, confidence_bind=0.0722604927671021, confidence_expr=0.0697838486111459. All unitless.
has bind (binding affinity, log KD, unitless): 9.01256
has confidence_bind (unitless): 0.0722604927671021
has confidence_expr (unitless): 0.0697838486111459
has delta_bind (vs. wild-type, unitless): 0.24095
has delta_expr (vs. wild-type, unitless): 0.03311
has experimental method: Deep mutational scanning — Bloom Lab SARS-CoV-2 RBD
has expr (expression level, log MFI, unitless): 10.21898
is observation of: Spike RBD Variant Eta (E152K)

sig
has algorithm: RSA
signed by: Erik Schultes

Eta real-world occurrence — Nigeria (2020-12-15)
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T08:20:53Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
introduces: Eta real-world occurrence — Nigeria (2020-12-15)
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: Eta real-world occurrence — Nigeria (2020-12-15)

sig
has algorithm: RSA
signed by: Erik Schultes

Eta real-world occurrence — Nigeria (2020-12-15)
type: FAIR Digital Object (FDO)
type: Real-World Occurrence
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
comment: Real-world detection of SARS-CoV-2 Spike variant Eta (B.1.525) in Nigeria on 2020-12-15, as reported in GISAID (accession EPI_ISL_941290).
has collection location: https://sws.geonames.org/2328926/
has GISAID accession number: EPI_ISL_941290
has occurrence date: 2020-12-15
has surveillance method: GISAID — Global Initiative on Sharing All Influenza Data
is observation of: Spike RBD Variant Eta (E152K)

Eta — WHO Variant of Interest (2021-03-05)
data usage license: Attribution 4.0 International (CC BY 4.0)
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: Eta — WHO Variant of Interest (2021-03-05)
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T08:20:53Z
creator: Erik Schultes
introduces: Eta — WHO Variant of Interest (2021-03-05)

Eta — WHO Variant of Interest (2021-03-05)
type: FAIR Digital Object (FDO)
type: WHO Variant Classification
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
comment: WHO classification of SARS-CoV-2 Spike variant Eta (B.1.525) as a Variant of Interest (VOI) on 2021-03-05.
has WHO classification date: 2021-03-05
has WHO variant classification: VOI
is observation of: Spike RBD Variant Eta (E152K)

sig
has algorithm: RSA
signed by: Erik Schultes

FAIR Connect displays view: View of FIP domains
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T10:09:51.167+02:00
creator: Tobias Kuhn
data usage license: Attribution 4.0 International (CC BY 4.0)
embeds: display
was created at: localhost:37373

fip-domains
has label from api: View of FIP domains

sig
has algorithm: RSA
signed by: Tobias Kuhn

fairconnect
has label from api: FAIR Connect - This is the Space for FAIR Connect.

FAIR Connect displays view: View of FAIR-Enabling Resource types
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T08:09:23.708Z
creator: Tobias Kuhn
data usage license: Attribution 4.0 International (CC BY 4.0)
embeds: display
was created at: nanodash.knowledgepixels.com

fer-types
has label from api: View of FAIR-Enabling Resource types

sig
has algorithm: RSA
has signature target: FAIR Connect displays view: View of FAIR-Enabling Resource types
signed by: Tobias Kuhn

Alpha RMSD = 13.378861773140596 Å — ESM2
created: 2026-05-28T08:02:29Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
introduces: Alpha RMSD = 13.378861773140596 Å — ESM2
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: Alpha RMSD = 13.378861773140596 Å — ESM2

sig
has algorithm: RSA
signed by: Erik Schultes

Alpha RMSD = 13.378861773140596 Å — ESM2
type: FAIR Digital Object (FDO)
type: Computational Prediction — RMSD
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
has source: FAIR² Data Package DOI
has source: esm wuhan 1step v1
comment: Computational prediction of RMSD (13.378861773140596 Angstroms) for SARS-CoV-2 Spike RBD variant Alpha (N169Y) using ESM2.
has prediction method: ESM2 — Meta AI protein language model
has RMSD (Root Mean Square Deviation): 13.378861773140596
is observation of: Spike RBD Variant Alpha (N169Y)

Alpha RMSD = 2.277628683231952 Å — AlphaFold 2
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T08:02:29Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
introduces: Alpha RMSD = 2.277628683231952 Å — AlphaFold 2
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: Alpha RMSD = 2.277628683231952 Å — AlphaFold 2

sig
has algorithm: RSA
signed by: Erik Schultes

Alpha RMSD = 2.277628683231952 Å — AlphaFold 2
type: FAIR Digital Object (FDO)
type: Computational Prediction — RMSD
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
has source: FAIR² Data Package DOI
has source: af wuhan 1step v1
comment: Computational prediction of RMSD (2.277628683231952 Angstroms) for SARS-CoV-2 Spike RBD variant Alpha (N169Y) using AlphaFold 2.
has prediction method: AlphaFold 2 — DeepMind structure predictor
has RMSD (Root Mean Square Deviation): 2.277628683231952
is observation of: Spike RBD Variant Alpha (N169Y)

Alpha SASA = 10141.236988525969 Å² — AlphaFold 2
data usage license: Attribution 4.0 International (CC BY 4.0)
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: Alpha SASA = 10141.236988525969 Å² — AlphaFold 2
created: 2026-05-28T08:02:29Z
creator: Erik Schultes
introduces: Alpha SASA = 10141.236988525969 Å² — AlphaFold 2
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo

Alpha SASA = 10141.236988525969 Å² — AlphaFold 2
type: FAIR Digital Object (FDO)
type: Computational Prediction — SASA
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
has source: FAIR² Data Package DOI
has source: af wuhan 1step v1
comment: Computational prediction of SASA (10141.236988525969 square Angstroms) for SARS-CoV-2 Spike RBD variant Alpha (N169Y) using AlphaFold 2.
has prediction method: AlphaFold 2 — DeepMind structure predictor
has SASA (Solvent Accessible Surface Area): 10141.236988525969
is observation of: Spike RBD Variant Alpha (N169Y)

sig
has algorithm: RSA
signed by: Erik Schultes

Alpha SASA = 16494.878394358453 Å² — ESM2
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T08:02:29Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
introduces: Alpha SASA = 16494.878394358453 Å² — ESM2
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: Alpha SASA = 16494.878394358453 Å² — ESM2

sig
has algorithm: RSA
signed by: Erik Schultes

Alpha SASA = 16494.878394358453 Å² — ESM2
type: FAIR Digital Object (FDO)
type: Computational Prediction — SASA
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
has source: FAIR² Data Package DOI
has source: esm wuhan 1step v1
comment: Computational prediction of SASA (16494.878394358453 square Angstroms) for SARS-CoV-2 Spike RBD variant Alpha (N169Y) using ESM2.
has prediction method: ESM2 — Meta AI protein language model
has SASA (Solvent Accessible Surface Area): 16494.878394358453
is observation of: Spike RBD Variant Alpha (N169Y)

Alpha pLDDT = 23.673561732385306 — ESM2
data usage license: Attribution 4.0 International (CC BY 4.0)
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: Alpha pLDDT = 23.673561732385306 — ESM2
created: 2026-05-28T08:02:29Z
creator: Erik Schultes
introduces: Alpha pLDDT = 23.673561732385306 — ESM2
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo

Alpha pLDDT = 23.673561732385306 — ESM2
type: FAIR Digital Object (FDO)
type: Computational Prediction — pLDDT
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
has source: FAIR² Data Package DOI
has source: esm wuhan 1step v1
comment: Computational prediction of pLDDT (23.673561732385306 unitless, 0-100) for SARS-CoV-2 Spike RBD variant Alpha (N169Y) using ESM2.
has prediction method: ESM2 — Meta AI protein language model
has pLDDT score (0-100, unitless): 23.673561732385306
is observation of: Spike RBD Variant Alpha (N169Y)

sig
has algorithm: RSA
signed by: Erik Schultes

Alpha pLDDT = 93.74392833444035 — AlphaFold 2
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
data usage license: Attribution 4.0 International (CC BY 4.0)
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: Alpha pLDDT = 93.74392833444035 — AlphaFold 2
created: 2026-05-28T08:02:29Z
creator: Erik Schultes
introduces: Alpha pLDDT = 93.74392833444035 — AlphaFold 2

Alpha pLDDT = 93.74392833444035 — AlphaFold 2
type: FAIR Digital Object (FDO)
type: Computational Prediction — pLDDT
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
has source: FAIR² Data Package DOI
has source: af wuhan 1step v1
comment: Computational prediction of pLDDT (93.74392833444035 unitless, 0-100) for SARS-CoV-2 Spike RBD variant Alpha (N169Y) using AlphaFold 2.
has prediction method: AlphaFold 2 — DeepMind structure predictor
has pLDDT score (0-100, unitless): 93.74392833444035
is observation of: Spike RBD Variant Alpha (N169Y)

sig
has algorithm: RSA
signed by: Erik Schultes

Epsilon RMSD = 12.801648143493145 Å — ESM2
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
data usage license: Attribution 4.0 International (CC BY 4.0)
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: Epsilon RMSD = 12.801648143493145 Å — ESM2
created: 2026-05-28T08:02:29Z
creator: Erik Schultes
introduces: Epsilon RMSD = 12.801648143493145 Å — ESM2

Epsilon RMSD = 12.801648143493145 Å — ESM2
type: FAIR Digital Object (FDO)
type: Computational Prediction — RMSD
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
has source: FAIR² Data Package DOI
has source: esm wuhan 1step v1
comment: Computational prediction of RMSD (12.801648143493145 Angstroms) for SARS-CoV-2 Spike RBD variant Epsilon (L120R) using ESM2.
has prediction method: ESM2 — Meta AI protein language model
has RMSD (Root Mean Square Deviation): 12.801648143493145
is observation of: Spike RBD Variant Epsilon (L120R)

sig
has algorithm: RSA
signed by: Erik Schultes

Epsilon RMSD = 2.975776098053212 Å — AlphaFold 2
created: 2026-05-28T08:02:29Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
introduces: Epsilon RMSD = 2.975776098053212 Å — AlphaFold 2
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: Epsilon RMSD = 2.975776098053212 Å — AlphaFold 2
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo

sig
has algorithm: RSA
signed by: Erik Schultes

Epsilon RMSD = 2.975776098053212 Å — AlphaFold 2
type: FAIR Digital Object (FDO)
type: Computational Prediction — RMSD
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
has source: FAIR² Data Package DOI
has source: af wuhan 1step v1
comment: Computational prediction of RMSD (2.975776098053212 Angstroms) for SARS-CoV-2 Spike RBD variant Epsilon (L120R) using AlphaFold 2.
has prediction method: AlphaFold 2 — DeepMind structure predictor
has RMSD (Root Mean Square Deviation): 2.975776098053212
is observation of: Spike RBD Variant Epsilon (L120R)

Epsilon SASA = 10181.968717666516 Å² — AlphaFold 2
created: 2026-05-28T08:02:29Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
introduces: Epsilon SASA = 10181.968717666516 Å² — AlphaFold 2
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: Epsilon SASA = 10181.968717666516 Å² — AlphaFold 2

sig
has algorithm: RSA
signed by: Erik Schultes

Epsilon SASA = 10181.968717666516 Å² — AlphaFold 2
type: FAIR Digital Object (FDO)
type: Computational Prediction — SASA
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
has source: FAIR² Data Package DOI
has source: af wuhan 1step v1
comment: Computational prediction of SASA (10181.968717666516 square Angstroms) for SARS-CoV-2 Spike RBD variant Epsilon (L120R) using AlphaFold 2.
has prediction method: AlphaFold 2 — DeepMind structure predictor
has SASA (Solvent Accessible Surface Area): 10181.968717666516
is observation of: Spike RBD Variant Epsilon (L120R)

Epsilon SASA = 17620.862527029858 Å² — ESM2
data usage license: Attribution 4.0 International (CC BY 4.0)
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: Epsilon SASA = 17620.862527029858 Å² — ESM2
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T08:02:29Z
creator: Erik Schultes
introduces: Epsilon SASA = 17620.862527029858 Å² — ESM2

Epsilon SASA = 17620.862527029858 Å² — ESM2
type: FAIR Digital Object (FDO)
type: Computational Prediction — SASA
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
has source: FAIR² Data Package DOI
has source: esm wuhan 1step v1
comment: Computational prediction of SASA (17620.862527029858 square Angstroms) for SARS-CoV-2 Spike RBD variant Epsilon (L120R) using ESM2.
has prediction method: ESM2 — Meta AI protein language model
has SASA (Solvent Accessible Surface Area): 17620.862527029858
is observation of: Spike RBD Variant Epsilon (L120R)

sig
has algorithm: RSA
signed by: Erik Schultes

Epsilon pLDDT = 23.73609314359643 — ESM2
data usage license: Attribution 4.0 International (CC BY 4.0)
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: Epsilon pLDDT = 23.73609314359643 — ESM2
created: 2026-05-28T08:02:29Z
creator: Erik Schultes
introduces: Epsilon pLDDT = 23.73609314359643 — ESM2
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo

Epsilon pLDDT = 23.73609314359643 — ESM2
type: FAIR Digital Object (FDO)
type: Computational Prediction — pLDDT
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
has source: FAIR² Data Package DOI
has source: esm wuhan 1step v1
comment: Computational prediction of pLDDT (23.73609314359643 unitless, 0-100) for SARS-CoV-2 Spike RBD variant Epsilon (L120R) using ESM2.
has prediction method: ESM2 — Meta AI protein language model
has pLDDT score (0-100, unitless): 23.73609314359643
is observation of: Spike RBD Variant Epsilon (L120R)

sig
has algorithm: RSA
signed by: Erik Schultes

Epsilon pLDDT = 94.19297808764844 — AlphaFold 2
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T08:02:29Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
introduces: Epsilon pLDDT = 94.19297808764844 — AlphaFold 2
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: Epsilon pLDDT = 94.19297808764844 — AlphaFold 2

sig
has algorithm: RSA
signed by: Erik Schultes

Epsilon pLDDT = 94.19297808764844 — AlphaFold 2
type: FAIR Digital Object (FDO)
type: Computational Prediction — pLDDT
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
has source: FAIR² Data Package DOI
has source: af wuhan 1step v1
comment: Computational prediction of pLDDT (94.19297808764844 unitless, 0-100) for SARS-CoV-2 Spike RBD variant Epsilon (L120R) using AlphaFold 2.
has prediction method: AlphaFold 2 — DeepMind structure predictor
has pLDDT score (0-100, unitless): 94.19297808764844
is observation of: Spike RBD Variant Epsilon (L120R)

Eta RMSD = 2.476768477258109 Å — ESM2
created: 2026-05-28T08:02:29Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
introduces: Eta RMSD = 2.476768477258109 Å — ESM2
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: Eta RMSD = 2.476768477258109 Å — ESM2

sig
has algorithm: RSA
signed by: Erik Schultes

Eta RMSD = 2.476768477258109 Å — ESM2
type: FAIR Digital Object (FDO)
type: Computational Prediction — RMSD
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
has source: FAIR² Data Package DOI
has source: esm wuhan 1step v1
comment: Computational prediction of RMSD (2.476768477258109 Angstroms) for SARS-CoV-2 Spike RBD variant Eta (E152K) using ESM2.
has prediction method: ESM2 — Meta AI protein language model
has RMSD (Root Mean Square Deviation): 2.476768477258109
is observation of: Spike RBD Variant Eta (E152K)

Eta RMSD = 2.7195180252543003 Å — AlphaFold 2
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T08:02:29Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
introduces: Eta RMSD = 2.7195180252543003 Å — AlphaFold 2
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: Eta RMSD = 2.7195180252543003 Å — AlphaFold 2

sig
has algorithm: RSA
signed by: Erik Schultes

Eta RMSD = 2.7195180252543003 Å — AlphaFold 2
type: FAIR Digital Object (FDO)
type: Computational Prediction — RMSD
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
has source: FAIR² Data Package DOI
has source: af wuhan 1step v1
comment: Computational prediction of RMSD (2.7195180252543003 Angstroms) for SARS-CoV-2 Spike RBD variant Eta (E152K) using AlphaFold 2.
has prediction method: AlphaFold 2 — DeepMind structure predictor
has RMSD (Root Mean Square Deviation): 2.7195180252543003
is observation of: Spike RBD Variant Eta (E152K)

Eta SASA = 10226.641288430395 Å² — AlphaFold 2
created: 2026-05-28T08:02:29Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
introduces: Eta SASA = 10226.641288430395 Å² — AlphaFold 2
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: Eta SASA = 10226.641288430395 Å² — AlphaFold 2

sig
has algorithm: RSA
signed by: Erik Schultes

Eta SASA = 10226.641288430395 Å² — AlphaFold 2
type: FAIR Digital Object (FDO)
type: Computational Prediction — SASA
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
has source: FAIR² Data Package DOI
has source: af wuhan 1step v1
comment: Computational prediction of SASA (10226.641288430395 square Angstroms) for SARS-CoV-2 Spike RBD variant Eta (E152K) using AlphaFold 2.
has prediction method: AlphaFold 2 — DeepMind structure predictor
has SASA (Solvent Accessible Surface Area): 10226.641288430395
is observation of: Spike RBD Variant Eta (E152K)

Eta SASA = 18026.596842240684 Å² — ESM2
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
data usage license: Attribution 4.0 International (CC BY 4.0)
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: Eta SASA = 18026.596842240684 Å² — ESM2
created: 2026-05-28T08:02:29Z
creator: Erik Schultes
introduces: Eta SASA = 18026.596842240684 Å² — ESM2

Eta SASA = 18026.596842240684 Å² — ESM2
type: FAIR Digital Object (FDO)
type: Computational Prediction — SASA
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
has source: FAIR² Data Package DOI
has source: esm wuhan 1step v1
comment: Computational prediction of SASA (18026.596842240684 square Angstroms) for SARS-CoV-2 Spike RBD variant Eta (E152K) using ESM2.
has prediction method: ESM2 — Meta AI protein language model
has SASA (Solvent Accessible Surface Area): 18026.596842240684
is observation of: Spike RBD Variant Eta (E152K)

sig
has algorithm: RSA
signed by: Erik Schultes

Eta pLDDT = 23.15035644847704 — ESM2
data usage license: Attribution 4.0 International (CC BY 4.0)
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: Eta pLDDT = 23.15035644847704 — ESM2
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T08:02:29Z
creator: Erik Schultes
introduces: Eta pLDDT = 23.15035644847704 — ESM2

Eta pLDDT = 23.15035644847704 — ESM2
type: FAIR Digital Object (FDO)
type: Computational Prediction — pLDDT
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
has source: FAIR² Data Package DOI
has source: esm wuhan 1step v1
comment: Computational prediction of pLDDT (23.15035644847704 unitless, 0-100) for SARS-CoV-2 Spike RBD variant Eta (E152K) using ESM2.
has prediction method: ESM2 — Meta AI protein language model
has pLDDT score (0-100, unitless): 23.15035644847704
is observation of: Spike RBD Variant Eta (E152K)

sig
has algorithm: RSA
signed by: Erik Schultes

Eta pLDDT = 94.05421698739244 — AlphaFold 2
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T08:02:29Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
introduces: Eta pLDDT = 94.05421698739244 — AlphaFold 2
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: Eta pLDDT = 94.05421698739244 — AlphaFold 2

sig
has algorithm: RSA
signed by: Erik Schultes

Eta pLDDT = 94.05421698739244 — AlphaFold 2
type: FAIR Digital Object (FDO)
type: Computational Prediction — pLDDT
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
has source: FAIR² Data Package DOI
has source: af wuhan 1step v1
comment: Computational prediction of pLDDT (94.05421698739244 unitless, 0-100) for SARS-CoV-2 Spike RBD variant Eta (E152K) using AlphaFold 2.
has prediction method: AlphaFold 2 — DeepMind structure predictor
has pLDDT score (0-100, unitless): 94.05421698739244
is observation of: Spike RBD Variant Eta (E152K)

AlphaFold 2 — DeepMind structure predictor
data usage license: Attribution 4.0 International (CC BY 4.0)
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: AlphaFold 2 — DeepMind structure predictor
created: 2026-05-28T07:46:35Z
creator: Erik Schultes
introduces: AlphaFold 2 — DeepMind structure predictor
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo

AlphaFold 2 — DeepMind structure predictor
type: FAIR Digital Object (FDO)
type: Computational Method
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
cites as authority: s41586-021-03819-2
comment: AlphaFold 2 (DeepMind) protein structure prediction system.

sig
has algorithm: RSA
signed by: Erik Schultes

Bio2Byte AgMata — aggregation propensity predictor
data usage license: Attribution 4.0 International (CC BY 4.0)
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: Bio2Byte AgMata — aggregation propensity predictor
created: 2026-05-28T07:46:35Z
creator: Erik Schultes
introduces: Bio2Byte AgMata — aggregation propensity predictor
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo

Bio2Byte AgMata — aggregation propensity predictor
type: FAIR Digital Object (FDO)
type: Computational Method
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
cites as authority: btac149
comment: AgMata aggregation propensity predictor, Bio2Byte toolkit.

sig
has algorithm: RSA
signed by: Erik Schultes

Deep mutational scanning — Bloom Lab SARS-CoV-2 RBD
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
data usage license: Attribution 4.0 International (CC BY 4.0)
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: Deep mutational scanning — Bloom Lab SARS-CoV-2 RBD
created: 2026-05-28T07:46:35Z
creator: Erik Schultes
introduces: Deep mutational scanning — Bloom Lab SARS-CoV-2 RBD

Deep mutational scanning — Bloom Lab SARS-CoV-2 RBD
type: FAIR Digital Object (FDO)
type: Experimental Method
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
cites as authority: j.cell.2020.08.012
comment: Deep mutational scanning of SARS-CoV-2 RBD binding and expression, Bloom Lab.

sig
has algorithm: RSA
signed by: Erik Schultes

ESM2 — Meta AI protein language model
data usage license: Attribution 4.0 International (CC BY 4.0)
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: ESM2 — Meta AI protein language model
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T07:46:35Z
creator: Erik Schultes
introduces: ESM2 — Meta AI protein language model

ESM2 — Meta AI protein language model
type: FAIR Digital Object (FDO)
type: Computational Method
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
cites as authority: science.ade2574
comment: ESM2 protein language model (Meta AI) for structure and property prediction from sequence.

sig
has algorithm: RSA
signed by: Erik Schultes

GISAID — Global Initiative on Sharing All Influenza Data
data usage license: Attribution 4.0 International (CC BY 4.0)
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: GISAID — Global Initiative on Sharing All Influenza Data
created: 2026-05-28T07:46:35Z
creator: Erik Schultes
introduces: GISAID — Global Initiative on Sharing All Influenza Data
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo

GISAID — Global Initiative on Sharing All Influenza Data
type: FAIR Digital Object (FDO)
type: Observational Method
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
cites as authority: 1560-7917.ES.2017.22.13.30494
cites as authority: ccdcw2021.255
comment: GISAID SARS-CoV-2 genomic surveillance platform.

sig
has algorithm: RSA
signed by: Erik Schultes

Spike RBD Variant Alpha (N169Y)
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
data usage license: Attribution 4.0 International (CC BY 4.0)
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: Spike RBD Variant Alpha (N169Y)
created: 2026-05-28T07:38:32Z
creator: Erik Schultes
introduces: Spike RBD Variant Alpha (N169Y)

Spike RBD Variant Alpha (N169Y)
type: FAIR Digital Object (FDO)
type: SpikeRBDVariant
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
references: FAIR² data article (Frontiers in Bioinformatics)
has source: FAIR² Data Package DOI
comment: SARS-CoV-2 Spike RBD variant Alpha, carrying the N169Y substitution (corresponding to N501Y in the full Spike numbering). Pango lineage B.1.1.7. Designated a Variant of Concern (VOC) by the WHO. RBD anchor FDO for the MAC FAIR Digital Twin observation cluster — all Type 2-8 observation FDOs of this variant link back here via mac:isObservationOf.
has GISAID accession number: EPI_ISL_601443
has GISAID seq id: N501Y
has MAC seq id: N169Y
has pango lineage: B.1.1.7
has parent protein: P0DTC2
has RBD sequence: TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCGP
has WHO variant name: Alpha

sig
has algorithm: RSA
signed by: Erik Schultes

Spike RBD Variant Epsilon (L120R)
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T07:38:32Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
introduces: Spike RBD Variant Epsilon (L120R)
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: Spike RBD Variant Epsilon (L120R)

sig
has algorithm: RSA
signed by: Erik Schultes

Spike RBD Variant Epsilon (L120R)
type: FAIR Digital Object (FDO)
type: SpikeRBDVariant
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
references: FAIR² data article (Frontiers in Bioinformatics)
has source: FAIR² Data Package DOI
comment: SARS-CoV-2 Spike RBD variant Epsilon, carrying the L120R substitution (corresponding to L452R in the full Spike numbering — Epsilon's canonical defining mutation). Pango lineage B.1.427 + B.1.429 (composite). RBD anchor FDO for the MAC FAIR Digital Twin observation cluster — all Type 2-8 observation FDOs of this variant link back here via mac:isObservationOf.
has GISAID accession number: EPI_ISL_2295356
has GISAID seq id: L452R
has MAC seq id: L120R
has pango lineage: B.1.427 + B.1.429
has parent protein: P0DTC2
has RBD sequence: TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGP
has WHO variant name: Epsilon

Spike RBD Variant Eta (E152K)
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
data usage license: Attribution 4.0 International (CC BY 4.0)
has format: TriG (RDF named-graph serialization)
is a concrete materialization of: Spike RBD Variant Eta (E152K)
created: 2026-05-28T07:38:32Z
creator: Erik Schultes
introduces: Spike RBD Variant Eta (E152K)

Spike RBD Variant Eta (E152K)
type: FAIR Digital Object (FDO)
type: SpikeRBDVariant
creator: Erik Schultes
is part of: StayAhead-Project
publisher: 027bh9e22
references: FAIR² data article (Frontiers in Bioinformatics)
has source: FAIR² Data Package DOI
comment: SARS-CoV-2 Spike RBD variant Eta, carrying the E152K substitution (corresponding to E484K in the full Spike numbering). Pango lineage B.1.525. Designated a Variant of Interest (VOI) by the WHO. RBD anchor FDO for the MAC FAIR Digital Twin observation cluster — all Type 2-8 observation FDOs of this variant link back here via mac:isObservationOf.
has GISAID accession number: EPI_ISL_941290
has GISAID seq id: E484K
has MAC seq id: E152K
has pango lineage: B.1.525
has parent protein: P0DTC2
has RBD sequence: TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVKGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGP
has WHO variant name: Eta

sig
has algorithm: RSA
signed by: Erik Schultes

Demo session for Swiss Data Science Center has speaker Tobias Kuhn
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T07:16:55.481Z
creator: Tobias Kuhn
data usage license: https://creativecommons.org/publicdomain/zero/1.0/
was created at: nanodash.knowledgepixels.com

sig
has algorithm: RSA
signed by: Tobias Kuhn

Demo session for Swiss Data Science Center has role: General participant role
created: 2026-05-28T07:16:36.693Z
creator: Tobias Kuhn
data usage license: https://creativecommons.org/publicdomain/zero/1.0/
has nanopub type: SpaceMemberRole
was created at: nanodash.knowledgepixels.com
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo

sig
has algorithm: RSA
signed by: Tobias Kuhn

participantRole
has label from api: General participant role

Demo session for Swiss Data Science Center has role: Speaker role
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T07:16:17.911Z
creator: Tobias Kuhn
data usage license: https://creativecommons.org/publicdomain/zero/1.0/
has nanopub type: SpaceMemberRole
was created at: nanodash.knowledgepixels.com

speakerRole
has label from api: Speaker role

sig
has algorithm: RSA
signed by: Tobias Kuhn

Demo session for Swiss Data Science Center displays view: simple message view
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T07:14:56.731Z
creator: Tobias Kuhn
data usage license: https://creativecommons.org/publicdomain/zero/1.0/
embeds: display
was created at: nanodash.knowledgepixels.com

sig
has algorithm: RSA
signed by: Tobias Kuhn

https://w3id.org/np/RAoVM91LtmP42OKUYTEVamcZghSS-7poDTuWYFhqw1fSM
created: 2026-05-28T07:14:23.851Z
creator: Tobias Kuhn
data usage license: https://creativecommons.org/publicdomain/zero/1.0/
introduces: Demo session for Swiss Data Science Center
was created at: nanodash.knowledgepixels.com
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo

sig
has algorithm: RSA
signed by: Tobias Kuhn

Test Group A displays view: Status updates for event view
created: 2026-05-28T09:08:51.304+02:00
creator: Tobias Kuhn
data usage license: https://creativecommons.org/publicdomain/zero/1.0/
embeds: display
was created at: localhost:37373
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo

sig
has algorithm: RSA
signed by: Tobias Kuhn

status-updates-for-event-view
has label from api: Status updates for event view

group
has label from api: Test Group A

Get view displays
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T06:48:52Z
creator: Tobias Kuhn
data usage license: Attribution 4.0 International (CC BY 4.0)
embeds: Get view displays

sig
has algorithm: RSA
signed by: Tobias Kuhn

Get view displays
type: grlc-query
description: Returns the view displays declared for a given resource. If the resource is a Space or is maintained by a Space, results are filtered server-side to only those signed by a trust-state-validated admin of that Space (sourced from the spaces repo's current state graph joined to npa:AccountState). If the resource has no Space association (e.g. an individual agent profile), no signer filter is applied, matching the prior client-side gate's behaviour where space==null skipped the check.
data usage license: LICENSE-2.0
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 distinct ?display ?view (coalesce(?viewKindOptional, ?view) as ?viewKind) ?label ?displayType ?displayMode ?np ?pubkey ?date where { values ?_resource_multi_iri {} service <https://w3id.org/np/l/nanopub-query-1.1/repo/spaces> { graph npa:graph { npa:thisRepo npa:hasCurrentSpaceState ?stateG . } { graph ?stateG { { ?_resource_multi_iri npa:isMaintainedBy ?space . } union { bind(?_resource_multi_iri as ?space) } ?ri a gen:RoleInstantiation ; npa:inverseProperty gen:hasAdmin ; npa:forSpace ?space ; npa:forAgent ?adminAgent . ?acct a npa:AccountState ; npa:agent ?adminAgent ; npa:pubkey ?pubkey . } } union { filter not exists { graph ?stateG { { ?_resource_multi_iri npa:isMaintainedBy [] } union { [] a gen:RoleInstantiation ; npa:forSpace ?_resource_multi_iri } } } } } graph npa:graph { ?np npx:hasNanopubType gen:ViewDisplay . ?np npa:hasValidSignatureForPublicKeyHash ?pubkey . filter not exists { ?npx npx:invalidates ?np ; npa:hasValidSignatureForPublicKeyHash ?pubkey . } ?np dct:created ?date . ?np npx:embeds ?display . ?np np:hasAssertion ?a . optional { ?np rdfs:label ?label } } graph ?a { ?display gen:isDisplayOfView ?view . ?display gen:isDisplayFor ?_resource_multi_iri . optional { values ?displayType { gen:PartLevelViewDisplay gen:TopLevelViewDisplay } ?display a ?displayType . } optional { values ?displayMode { gen:ActivatedViewDisplay gen:DeactivatedViewDisplay } ?display a ?displayMode . } } optional { service <https://w3id.org/np/l/nanopub-query-1.1/repo/type/ec6722efa3b44e0a18aa63afe5964158a1fdb7f0413ea5f23bfddf5c03ca0221> { select ?view ?viewKindOptional { graph npa:graph { ?np npx:hasNanopubType gen:ResourceView . ?np npa:hasValidSignatureForPublicKeyHash ?pubkey . filter not exists…

Nanopublications
comment: The nanopublication community space
is relevant for: home

https://w3id.org/np/RAn9U_NOZbNGhlLPag09C8w5tXXPCgrozRMiypStlCXnM
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-28T08:12:21.786+02:00
creator: Tobias Kuhn
data usage license: https://creativecommons.org/publicdomain/zero/1.0/
has nanopub type: isRelevantFor
was created at: localhost:37373

sig
has algorithm: RSA
signed by: Tobias Kuhn

Template: Declaring an Observational Method (MAC FDT Type 11)
has label from api: Template: Declaring an Observational Method (MAC FDT Type 11) - An epidemiological surveillance system or data collection platform through wh...
has pin group tag: Declaring an Observational Method
type: Nanopublication
has assertion: Declaring an Observational Method (MAC FDT Type 11)
has provenance: provenance
has publication info: pubinfo
created: 2026-05-27T20:44:44Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)

Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs has pinned template: Template: Declaring an Observational Method (MAC FDT Type 11)
created: 2026-05-27T21:03:55.412Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
has nanopub type: hasPinnedTemplate
was created at: nanodash.petapico.org
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo

sig
has algorithm: RSA
signed by: Erik Schultes

Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs has pinned template: Template: Declaring an Experimental Method (MAC FDT Type 10)
created: 2026-05-27T21:03:23.017Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
has nanopub type: hasPinnedTemplate
was created at: nanodash.petapico.org
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo

sig
has algorithm: RSA
signed by: Erik Schultes

Template: Declaring an Experimental Method (MAC FDT Type 10)
has label from api: Template: Declaring an Experimental Method (MAC FDT Type 10) - An experimental assay or measurement protocol producing empirical observation...
has pin group tag: Declaring an Experimental Method
type: Nanopublication
has assertion: Declaring an Experimental Method (MAC FDT Type 10)
has provenance: provenance
has publication info: pubinfo
created: 2026-05-27T20:44:44Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)

Template: Declaring a Computational Method (MAC FDT Type 9)
has label from api: Template: Declaring a Computational Method (MAC FDT Type 9) - A computational method, tool, or algorithm producing predictions or scores fr...
has pin group tag: Declaring a Computational Method
created: 2026-05-27T20:44:44Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
type: Nanopublication
has assertion: Declaring a Computational Method (MAC FDT Type 9)
has provenance: provenance
has publication info: pubinfo

Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs has pinned template: Template: Declaring a Computational Method (MAC FDT Type 9)
created: 2026-05-27T21:02:31.585Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
has nanopub type: hasPinnedTemplate
was created at: nanodash.petapico.org
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo

sig
has algorithm: RSA
signed by: Erik Schultes

Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs has pinned template: Template: Declaring a WHO Variant Classification (MAC FDT Type 8)
type: Nanopublication
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has provenance: provenance
has publication info: pubinfo
created: 2026-05-27T21:01:54.520Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
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Template: Declaring a WHO Variant Classification (MAC FDT Type 8)
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has label from api: Template: Declaring a WHO Variant Classification (MAC FDT Type 8) - Classification of a SARS-CoV-2 lineage according to the WHO risk framework — ...
type: Nanopublication
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data usage license: Attribution 4.0 International (CC BY 4.0)

sig
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Template: Declaring a Deep Mutational Scanning Observation (MAC FDT Type 7)
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has pin group tag: Declaring a Deep Mutational Scanning Observation
created: 2026-05-27T20:31:37Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
type: Nanopublication
has assertion: Declaring a Deep Mutational Scanning Observation (MAC FDT Type 7)
has provenance: provenance
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Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs has pinned template: Template: Declaring a Deep Mutational Scanning Observation (MAC FDT Type 7)
created: 2026-05-27T21:00:58.451Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
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type: Nanopublication
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has publication info: pubinfo

sig
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Template: Declaring a Computational Prediction — AgMata (MAC FDT Type 6)
has pin group tag: Declaring a Computational Prediction — AgMata
has label from api: Template: Declaring a Computational Prediction — AgMata (MAC FDT Type 6) - Computational prediction of the AgMata aggregation propensity score (unitless...
created: 2026-05-27T20:27:36Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
type: Nanopublication
has assertion: Declaring a Computational Prediction — AgMata (MAC FDT Type 6)
has provenance: provenance
has publication info: pubinfo

Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs has pinned template: Template: Declaring a Computational Prediction — AgMata (MAC FDT Type 6)
type: Nanopublication
has assertion: assertion
has provenance: provenance
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creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
has nanopub type: hasPinnedTemplate
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sig
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Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs has pinned template: Template: Declaring a Computational Prediction — pLDDT (MAC FDT Type 5)
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-27T20:59:37.386Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
has nanopub type: hasPinnedTemplate
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Template: Declaring a Computational Prediction — pLDDT (MAC FDT Type 5)
has pin group tag: Declaring a Computational Prediction — pLDDT
has label from api: Template: Declaring a Computational Prediction — pLDDT (MAC FDT Type 5) - Computational prediction of the per-residue confidence score (pLDDT, unitless...
type: Nanopublication
has assertion: Declaring a Computational Prediction — pLDDT (MAC FDT Type 5)
has provenance: provenance
has publication info: pubinfo
created: 2026-05-27T20:19:06Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)

sig
has algorithm: RSA
signed by: Erik Schultes

Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs has pinned template: Template: Declaring a Computational Prediction — SASA (MAC FDT Type 4)
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-27T20:59:00.045Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
has nanopub type: hasPinnedTemplate
was created at: nanodash.petapico.org

Template: Declaring a Computational Prediction — SASA (MAC FDT Type 4)
has label from api: Template: Declaring a Computational Prediction — SASA (MAC FDT Type 4) - Computational prediction of the Solvent Accessible Surface Area (SASA, in squ...
has pin group tag: Declaring a Computational Prediction — SASA
type: Nanopublication
has assertion: Declaring a Computational Prediction — SASA (MAC FDT Type 4)
has provenance: provenance
has publication info: pubinfo
created: 2026-05-27T20:19:06Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)

sig
has algorithm: RSA
signed by: Erik Schultes

Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs has pinned template: Template: Declaring a Computational Prediction — RMSD (MAC FDT Type 3)
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-27T20:58:18.418Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
has nanopub type: hasPinnedTemplate
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Template: Declaring a Computational Prediction — RMSD (MAC FDT Type 3)
has pin group tag: Declaring a Computational Prediction — RMSD
has label from api: Template: Declaring a Computational Prediction — RMSD (MAC FDT Type 3) - Computational prediction of the Root Mean Square Deviation (RMSD, in Angstrom...
type: Nanopublication
has assertion: Declaring a Computational Prediction — RMSD (MAC FDT Type 3)
has provenance: provenance
has publication info: pubinfo
created: 2026-05-27T20:19:06Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)

sig
has algorithm: RSA
signed by: Erik Schultes

Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs has pinned template: Template: Declaring a Real-World Occurrence (MAC FDT Type 2)
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-27T20:57:16.817Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
has nanopub type: hasPinnedTemplate
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Template: Declaring a Real-World Occurrence (MAC FDT Type 2)
has label from api: Template: Declaring a Real-World Occurrence (MAC FDT Type 2) - Real-world detection of a SARS-CoV-2 Spike variant, as reported in GISAID. Ca...
has pin group tag: Declaring a Real-World Occurrence
type: Nanopublication
has assertion: Declaring a Real-World Occurrence (MAC FDT Type 2)
has provenance: provenance
has publication info: pubinfo
created: 2026-05-27T20:07:27Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)

sig
has algorithm: RSA
signed by: Erik Schultes

https://w3id.org/np/RADOnITa1gjGIQtuENvlB2I7hykzrASzake1bIjGLiAtM
has label from api: Template: Declaring a Spike RBD Variant (MAC FDT Type 1) - Template for the central anchor of a MAC FAIR Digital Twin: a SARS-CoV-2 Spik...
has pin group tag: Declaring a Spike RBD Variant

Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs has pinned template: Template: Declaring a Spike RBD Variant (MAC FDT Type 1)
created: 2026-05-27T20:55:37.218Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
has nanopub type: hasPinnedTemplate
was created at: nanodash.petapico.org
type: Nanopublication
has assertion: assertion
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has publication info: pubinfo

sig
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signed by: Erik Schultes

Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs displays view: Pinned templates view
created: 2026-05-27T20:52:36.218Z
creator: Erik Schultes
data usage license: Attribution 4.0 International (CC BY 4.0)
embeds: display
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type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo

sig
has algorithm: RSA
signed by: Erik Schultes

pinned-templates-view
has label from api: Pinned templates view

Declaring a Computational Method (MAC FDT Type 9)
was attributed to: Erik Schultes
type: AssertionTemplate
description: A computational method, tool, or algorithm producing predictions or scores from biological sequence or structure data. Referenced by computational-prediction observation FDOs (Types 3-6) via mac:hasPredictionMethod. Carries one or more cito:citesAsAuthority URIs identifying the published method descriptions, and an optional schema:url for the software resource. The nanopublication self-materializes (assertion graph is the FDO).
has nanopub label pattern: Computational method (${label})
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has contributor

has creator

is part of

data usage license

has publisher

references

has source

has domain

cites as authority

has URL

is a

has description

has the label

implements

has format

has its metadata in

is a concrete materialization of

published method authority (DOI or URL)
type: ExternalUriPlaceholder

contact email
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ORCID of contributor
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ORCID of creator
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free-text description of this method
type: LongLiteralPlaceholder

domain
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full URI or short suffix for this computational method FDO
type: IntroducedResource
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FAIR Implementation Profile
type: GuidedChoicePlaceholder
possible values from api: http://purl.org/nanopub/api/find_signed_things

label for this method (e.g. "ESM2 — Meta AI protein language model")
type: LiteralPlaceholder

project
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possible values from api: https://w3id.org/np/l/nanopub-query-1.1/api/RAFTZ8GqPOOJQOBcEo5IB8lg5vZCFiIyr_RVLKZDQBHMk/get-projects

ROR of the publishing entity
type: ExternalUriPlaceholder

has access URL

has contact point

software URL
type: ExternalUriPlaceholder

sig
has algorithm: RSA
signed by: Erik Schultes

Declaring an Experimental Method (MAC FDT Type 10)
type: AssertionTemplate
description: An experimental assay or measurement protocol producing empirical observations about biological entities. Referenced by experimental observation FDOs (Type 7) via mac:hasExperimentalMethod. Carries one or more cito:citesAsAuthority URIs identifying the published assay descriptions, and an optional schema:url for the data resource. The nanopublication self-materializes (assertion graph is the FDO).
has nanopub label pattern: Experimental method (${label})
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published method authority (DOI or URL)
type: ExternalUriPlaceholder

contact email
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ORCID of contributor
type: AgentPlaceholder

ORCID of creator
type: AgentPlaceholder
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free-text description of this method
type: LongLiteralPlaceholder

domain
type: RestrictedChoicePlaceholder

full URI or short suffix for this experimental method FDO
type: IntroducedResource
type: LocalResource
type: UriPlaceholder

FAIR Implementation Profile
type: GuidedChoicePlaceholder
possible values from api: http://purl.org/nanopub/api/find_signed_things

label for this method (e.g. "Deep mutational scanning — Bloom Lab SARS-CoV-2 RBD")
type: LiteralPlaceholder

project
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possible values from api: https://w3id.org/np/l/nanopub-query-1.1/api/RAFTZ8GqPOOJQOBcEo5IB8lg5vZCFiIyr_RVLKZDQBHMk/get-projects

ROR of the publishing entity
type: ExternalUriPlaceholder

data resource URL
type: ExternalUriPlaceholder

sig
has algorithm: RSA
signed by: Erik Schultes

Declaring an Observational Method (MAC FDT Type 11)
was attributed to: Erik Schultes
type: AssertionTemplate
description: An epidemiological surveillance system or data collection platform through which real-world occurrences of biological entities are documented. Referenced by real-world observation FDOs (Type 2) via mac:hasSurveillanceMethod. Carries one or more cito:citesAsAuthority URIs identifying the published descriptions of the system, and an optional schema:url for the platform. The nanopublication self-materializes (assertion graph is the FDO).
has nanopub label pattern: Observational method (${label})
has statement: st0
has statement: st1
has statement: st2
has statement: st3
has statement: st4
has statement: st5
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has statement: st7
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has statement: st95
has statement: st ci
has statement: st pp
has statement: st su
has tag: MAC

published method authority (DOI or URL)
type: ExternalUriPlaceholder

contact email
type: LiteralPlaceholder

ORCID of contributor
type: AgentPlaceholder

ORCID of creator
type: AgentPlaceholder
has default value: CREATOR

free-text description of this method
type: LongLiteralPlaceholder

domain
type: RestrictedChoicePlaceholder

full URI or short suffix for this observational method FDO
type: IntroducedResource
type: LocalResource
type: UriPlaceholder

FAIR Implementation Profile
type: GuidedChoicePlaceholder
possible values from api: http://purl.org/nanopub/api/find_signed_things

label for this method (e.g. "GISAID — Global Initiative on Sharing All Influenza Data")
type: LiteralPlaceholder

project
type: GuidedChoicePlaceholder
possible values from api: https://w3id.org/np/l/nanopub-query-1.1/api/RAFTZ8GqPOOJQOBcEo5IB8lg5vZCFiIyr_RVLKZDQBHMk/get-projects

ROR of the publishing entity
type: ExternalUriPlaceholder

platform URL
type: ExternalUriPlaceholder

sig
has algorithm: RSA
signed by: Erik Schultes

Declaring a WHO Variant Classification (MAC FDT Type 8)
was attributed to: Erik Schultes
type: AssertionTemplate
description: Classification of a SARS-CoV-2 lineage according to the WHO risk framework — Variant of Concern (VOC), Variant of Interest (VOI), or Variant Under Monitoring (VUM) — based on assessed public-health risk and virological characteristics. Time-stamped because designation status changes over time. Links via mac:isObservationOf to the Spike RBD Variant FDO it observes. The nanopublication self-materializes (assertion graph is the FDO).
has nanopub label pattern: WHO classification: ${classification} (${classificationDate})
has statement: st0
has statement: st1
has statement: st2
has statement: st3
has statement: st4
has statement: st5
has statement: st5b
has statement: st5c
has statement: st5d
has statement: st6
has statement: st7
has statement: st8
has statement: st91
has statement: st92
has statement: st95
has statement: st cd
has statement: st cr
has statement: st obs
has statement: st oc
has statement: st pp
has statement: st wc
has tag: MAC

sig
has algorithm: RSA
signed by: Erik Schultes

observation-specific authority (DOI or URL)
type: ExternalUriPlaceholder

WHO variant classification
type: RestrictedChoicePlaceholder
possible value: VOC
possible value: VOI
possible value: VUM

WHO classification date (date)
type: LiteralPlaceholder

WHO classification reference URL
type: ExternalUriPlaceholder

contact email
type: LiteralPlaceholder

ORCID of contributor
type: AgentPlaceholder

ORCID of creator
type: AgentPlaceholder
has default value: CREATOR

free-text description of this WHO classification
type: LongLiteralPlaceholder

domain
type: RestrictedChoicePlaceholder

full URI or short suffix for this WHO classification FDO
type: IntroducedResource
type: LocalResource
type: UriPlaceholder

FAIR Implementation Profile
type: GuidedChoicePlaceholder
possible values from api: http://purl.org/nanopub/api/find_signed_things

label for this classification (e.g. "Alpha WHO classification: VOC")
type: LiteralPlaceholder

project
type: GuidedChoicePlaceholder
possible values from api: https://w3id.org/np/l/nanopub-query-1.1/api/RAFTZ8GqPOOJQOBcEo5IB8lg5vZCFiIyr_RVLKZDQBHMk/get-projects

ROR of the publishing entity
type: ExternalUriPlaceholder

has WHO classification date

has WHO classification reference URL

Spike RBD Variant FDO referent URI
type: ExternalUriPlaceholder

is observation of

has WHO variant classification

Declaring a Deep Mutational Scanning Observation (MAC FDT Type 7)
type: AssertionTemplate
description: Experimental binding affinity and expression level measurements for a SARS-CoV-2 Spike RBD variant determined by deep mutational scanning (Bloom Lab). One FDO per variant. Carries six measured values: bind (log KD, unitless), delta_bind (vs. wild-type), expr (log MFI, unitless), delta_expr, and confidence scores for bind and expr. Links via mac:isObservationOf to the variant FDO it observes and via mac:hasExperimentalMethod to the Bloom Lab DMS Method FDO (Type 10). The nanopublication self-materializes (assertion graph is the FDO).
has nanopub label pattern: DMS observation (bind=${bind}, expr=${expr})
has statement: st0
has statement: st1
has statement: st2
has statement: st3
has statement: st4
has statement: st5
has statement: st5b
has statement: st5c
has statement: st5d
has statement: st6
has statement: st7
has statement: st8
has statement: st91
has statement: st92
has statement: st95
has statement: st bi
has statement: st cb
has statement: st ce
has statement: st db
has statement: st de
has statement: st em
has statement: st ex
has statement: st obs
has statement: st oc
has statement: st pp
has statement: st src
has tag: MAC
was attributed to: Erik Schultes

observation-specific authority (DOI or URL)
type: ExternalUriPlaceholder

bind (binding affinity, log KD, unitless)
type: LiteralPlaceholder

confidence_bind (unitless)
type: LiteralPlaceholder

confidence_expr (unitless)
type: LiteralPlaceholder

contact email
type: LiteralPlaceholder

ORCID of contributor
type: AgentPlaceholder

ORCID of creator
type: AgentPlaceholder
has default value: CREATOR

delta_bind (change vs. wild-type, unitless)
type: LiteralPlaceholder

delta_expr (change vs. wild-type, unitless)
type: LiteralPlaceholder

free-text description of this DMS observation
type: LongLiteralPlaceholder

domain
type: RestrictedChoicePlaceholder

Experimental Method FDO referent URI (Type 10)
type: ExternalUriPlaceholder

expr (expression level, log MFI, unitless)
type: LiteralPlaceholder

full URI or short suffix for this DMS observation FDO
type: IntroducedResource
type: LocalResource
type: UriPlaceholder

FAIR Implementation Profile
type: GuidedChoicePlaceholder
possible values from api: http://purl.org/nanopub/api/find_signed_things

label for this observation (e.g. "Alpha DMS - Bloom Lab")
type: LiteralPlaceholder

project
type: GuidedChoicePlaceholder
possible values from api: https://w3id.org/np/l/nanopub-query-1.1/api/RAFTZ8GqPOOJQOBcEo5IB8lg5vZCFiIyr_RVLKZDQBHMk/get-projects

ROR of the publishing entity
type: ExternalUriPlaceholder

FAIR² Package DOI, FAIR² resource URL, or OSF URL
type: ExternalUriPlaceholder

has bind (binding affinity, log KD, unitless)

has confidence_bind (unitless)

has confidence_expr (unitless)

has delta_bind (vs. wild-type, unitless)

has delta_expr (vs. wild-type, unitless)

has experimental method

has expr (expression level, log MFI, unitless)

Spike RBD Variant FDO referent URI
type: ExternalUriPlaceholder

sig
has algorithm: RSA
signed by: Erik Schultes

Declaring a Computational Prediction — AgMata (MAC FDT Type 6)
was attributed to: Erik Schultes
type: AssertionTemplate
description: Computational prediction of the AgMata aggregation propensity score (unitless) of a SARS-CoV-2 Spike RBD variant, produced by the Bio2Byte AgMata predictor. Sequence-derived: one FDO per variant. Links via mac:isObservationOf to the variant FDO it observes and via mac:hasPredictionMethod to the Bio2Byte Computational Method FDO (Type 9). The nanopublication self-materializes (assertion graph is the FDO).
has nanopub label pattern: AgMata = ${value}
has statement: st0
has statement: st1
has statement: st2
has statement: st3
has statement: st4
has statement: st5
has statement: st5b
has statement: st5c
has statement: st5d
has statement: st6
has statement: st7
has statement: st8
has statement: st91
has statement: st92
has statement: st95
has statement: st obs
has statement: st oc
has statement: st pm
has statement: st pp
has statement: st src
has statement: st val
has tag: MAC

sig
has algorithm: RSA
signed by: Erik Schultes

observation-specific authority (DOI or URL)
type: ExternalUriPlaceholder

contact email
type: LiteralPlaceholder

ORCID of contributor
type: AgentPlaceholder

ORCID of creator
type: AgentPlaceholder
has default value: CREATOR

free-text description of this AgMata observation
type: LongLiteralPlaceholder

domain
type: RestrictedChoicePlaceholder

full URI or short suffix for this AgMata observation FDO
type: IntroducedResource
type: LocalResource
type: UriPlaceholder

FAIR Implementation Profile
type: GuidedChoicePlaceholder
possible values from api: http://purl.org/nanopub/api/find_signed_things

label for this observation (e.g. "Alpha AgMata")
type: LiteralPlaceholder

Computational Method FDO referent URI (Bio2Byte AgMata, Type 9)
type: ExternalUriPlaceholder

project
type: GuidedChoicePlaceholder
possible values from api: https://w3id.org/np/l/nanopub-query-1.1/api/RAFTZ8GqPOOJQOBcEo5IB8lg5vZCFiIyr_RVLKZDQBHMk/get-projects

ROR of the publishing entity
type: ExternalUriPlaceholder

FAIR² Package DOI or FAIR² ESM resource URL or OSF URL
type: ExternalUriPlaceholder

Spike RBD Variant FDO referent URI
type: ExternalUriPlaceholder

has prediction method

AgMata score (unitless)
type: LiteralPlaceholder

has AgMata score (aggregation propensity)

Declaring a Computational Prediction — RMSD (MAC FDT Type 3)
type: AssertionTemplate
description: Computational prediction of the Root Mean Square Deviation (RMSD, in Angstroms) of a SARS-CoV-2 Spike RBD variant relative to the wild-type structure, produced by a named computational method (e.g., ESM, AlphaFold II). Links via mac:isObservationOf to the variant FDO it observes and via mac:hasPredictionMethod to the Type 9 method FDO. The nanopublication self-materializes (assertion graph is the FDO).
has nanopub label pattern: RMSD = ${value} A (${predictionMethod})
has statement: st0
has statement: st1
has statement: st2
has statement: st3
has statement: st4
has statement: st5
has statement: st5b
has statement: st5c
has statement: st5d
has statement: st6
has statement: st7
has statement: st8
has statement: st91
has statement: st92
has statement: st95
has statement: st obs
has statement: st oc
has statement: st pm
has statement: st pp
has statement: st src
has statement: st val
has tag: MAC
was attributed to: Erik Schultes

observation-specific authority (DOI or URL)
type: ExternalUriPlaceholder

contact email
type: LiteralPlaceholder

ORCID of contributor
type: AgentPlaceholder

ORCID of creator
type: AgentPlaceholder
has default value: CREATOR

free-text description of this RMSD observation
type: LongLiteralPlaceholder

domain
type: RestrictedChoicePlaceholder

full URI or short suffix for this RMSD observation FDO
type: IntroducedResource
type: LocalResource
type: UriPlaceholder

FAIR Implementation Profile
type: GuidedChoicePlaceholder
possible values from api: http://purl.org/nanopub/api/find_signed_things

label for this observation (e.g. "Alpha RMSD - AlphaFold II")
type: LiteralPlaceholder

Computational Method FDO referent URI (Type 9)
type: ExternalUriPlaceholder

project
type: GuidedChoicePlaceholder
possible values from api: https://w3id.org/np/l/nanopub-query-1.1/api/RAFTZ8GqPOOJQOBcEo5IB8lg5vZCFiIyr_RVLKZDQBHMk/get-projects

ROR of the publishing entity
type: ExternalUriPlaceholder

FAIR² Package DOI or FAIR² resource URL or OSF URL
type: ExternalUriPlaceholder

Spike RBD Variant FDO referent URI
type: ExternalUriPlaceholder

RMSD value (Angstroms)
type: LiteralPlaceholder

has RMSD (Root Mean Square Deviation)

sig
has algorithm: RSA
signed by: Erik Schultes

Declaring a Computational Prediction — SASA (MAC FDT Type 4)
was attributed to: Erik Schultes
type: AssertionTemplate
description: Computational prediction of the Solvent Accessible Surface Area (SASA, in square Angstroms) of a SARS-CoV-2 Spike RBD variant, produced by a named computational method (e.g., ESM, AlphaFold II). Links via mac:isObservationOf to the variant FDO it observes and via mac:hasPredictionMethod to the Type 9 method FDO. The nanopublication self-materializes (assertion graph is the FDO).
has nanopub label pattern: SASA = ${value} A^2 (${predictionMethod})
has statement: st0
has statement: st1
has statement: st2
has statement: st3
has statement: st4
has statement: st5
has statement: st5b
has statement: st5c
has statement: st5d
has statement: st6
has statement: st7
has statement: st8
has statement: st91
has statement: st92
has statement: st95
has statement: st obs
has statement: st oc
has statement: st pm
has statement: st pp
has statement: st src
has statement: st val
has tag: MAC

sig
has algorithm: RSA
signed by: Erik Schultes

observation-specific authority (DOI or URL)
type: ExternalUriPlaceholder

contact email
type: LiteralPlaceholder

ORCID of contributor
type: AgentPlaceholder

ORCID of creator
type: AgentPlaceholder
has default value: CREATOR

free-text description of this SASA observation
type: LongLiteralPlaceholder

domain
type: RestrictedChoicePlaceholder

full URI or short suffix for this SASA observation FDO
type: IntroducedResource
type: LocalResource
type: UriPlaceholder

FAIR Implementation Profile
type: GuidedChoicePlaceholder
possible values from api: http://purl.org/nanopub/api/find_signed_things

label for this observation (e.g. "Alpha SASA - ESM")
type: LiteralPlaceholder

Computational Method FDO referent URI (Type 9)
type: ExternalUriPlaceholder

project
type: GuidedChoicePlaceholder
possible values from api: https://w3id.org/np/l/nanopub-query-1.1/api/RAFTZ8GqPOOJQOBcEo5IB8lg5vZCFiIyr_RVLKZDQBHMk/get-projects

ROR of the publishing entity
type: ExternalUriPlaceholder

FAIR² Package DOI or FAIR² resource URL or OSF URL
type: ExternalUriPlaceholder

Spike RBD Variant FDO referent URI
type: ExternalUriPlaceholder

SASA value (square Angstroms)
type: LiteralPlaceholder

has SASA (Solvent Accessible Surface Area)

Declaring a Computational Prediction — pLDDT (MAC FDT Type 5)
type: AssertionTemplate
description: Computational prediction of the per-residue confidence score (pLDDT, unitless, 0-100) of a SARS-CoV-2 Spike RBD variant structure, produced by a named computational method (typically AlphaFold II). Links via mac:isObservationOf to the variant FDO it observes and via mac:hasPredictionMethod to the Type 9 method FDO. The nanopublication self-materializes (assertion graph is the FDO).
has nanopub label pattern: pLDDT = ${value} (${predictionMethod})
has statement: st0
has statement: st1
has statement: st2
has statement: st3
has statement: st4
has statement: st5
has statement: st5b
has statement: st5c
has statement: st5d
has statement: st6
has statement: st7
has statement: st8
has statement: st91
has statement: st92
has statement: st95
has statement: st obs
has statement: st oc
has statement: st pm
has statement: st pp
has statement: st src
has statement: st val
has tag: MAC
was attributed to: Erik Schultes

observation-specific authority (DOI or URL)
type: ExternalUriPlaceholder

contact email
type: LiteralPlaceholder

ORCID of contributor
type: AgentPlaceholder

ORCID of creator
type: AgentPlaceholder
has default value: CREATOR

free-text description of this pLDDT observation
type: LongLiteralPlaceholder

domain
type: RestrictedChoicePlaceholder

full URI or short suffix for this pLDDT observation FDO
type: IntroducedResource
type: LocalResource
type: UriPlaceholder

FAIR Implementation Profile
type: GuidedChoicePlaceholder
possible values from api: http://purl.org/nanopub/api/find_signed_things

label for this observation (e.g. "Alpha pLDDT - AlphaFold II")
type: LiteralPlaceholder

Computational Method FDO referent URI (Type 9)
type: ExternalUriPlaceholder

project
type: GuidedChoicePlaceholder
possible values from api: https://w3id.org/np/l/nanopub-query-1.1/api/RAFTZ8GqPOOJQOBcEo5IB8lg5vZCFiIyr_RVLKZDQBHMk/get-projects

ROR of the publishing entity
type: ExternalUriPlaceholder

FAIR² Package DOI or FAIR² resource URL or OSF URL
type: ExternalUriPlaceholder

Spike RBD Variant FDO referent URI
type: ExternalUriPlaceholder

pLDDT score (0-100, unitless)
type: LiteralPlaceholder

has pLDDT score (0-100, unitless)

sig
has algorithm: RSA
signed by: Erik Schultes

sig
has algorithm: RSA
signed by: Erik Schultes

Declaring a Real-World Occurrence (MAC FDT Type 2)
type: AssertionTemplate
description: Real-world detection of a SARS-CoV-2 Spike variant, as reported in GISAID. Carries the occurrence date and the collection location (GeoNames URI), and optionally the canonical GISAID accession. Links via mac:isObservationOf to the Spike RBD Variant FDO it observes, and optionally via mac:hasSurveillanceMethod to the surveillance system (Type 11 FDO). The nanopublication self-materializes (assertion graph is the FDO).
has nanopub label pattern: Real-world occurrence (${occurrenceDate})
has statement: st0
has statement: st1
has statement: st2
has statement: st3
has statement: st4
has statement: st5
has statement: st5b
has statement: st5c
has statement: st5d
has statement: st6
has statement: st7
has statement: st8
has statement: st91
has statement: st92
has statement: st95
has statement: st d
has statement: st gi
has statement: st l
has statement: st obs
has statement: st oc
has statement: st pp
has statement: st sm
has tag: MAC
was attributed to: Erik Schultes

observation-specific authority (DOI or URL)
type: ExternalUriPlaceholder

contact email
type: LiteralPlaceholder

ORCID of contributor
type: AgentPlaceholder

ORCID of creator
type: AgentPlaceholder
has default value: CREATOR

free-text description of this occurrence
type: LongLiteralPlaceholder

domain
type: RestrictedChoicePlaceholder

full URI (e.g. handle.net) or short suffix for this occurrence FDO
type: IntroducedResource
type: LocalResource
type: UriPlaceholder

FAIR Implementation Profile
type: GuidedChoicePlaceholder
possible values from api: http://purl.org/nanopub/api/find_signed_things

canonical GISAID accession (EPI_ISL_XXXXXXX)
type: LiteralPlaceholder
has regex: ^EPI_ISL_\d+$

label or name for this occurrence (e.g. "Alpha first detected, UK Sept 2020")
type: LiteralPlaceholder

GeoNames feature URI (e.g. https://sws.geonames.org/6269131/)
type: ExternalUriPlaceholder

GISAID-reported collection date
type: LiteralPlaceholder

project
type: GuidedChoicePlaceholder
possible values from api: https://w3id.org/np/l/nanopub-query-1.1/api/RAFTZ8GqPOOJQOBcEo5IB8lg5vZCFiIyr_RVLKZDQBHMk/get-projects

ROR of the publishing entity
type: ExternalUriPlaceholder

has occurrence date

has GISAID accession number

has collection location

Spike RBD Variant FDO referent URI
type: ExternalUriPlaceholder

surveillance method FDO referent URI
type: ExternalUriPlaceholder

has surveillance method

Morphological Feature Observation
type: Class
part of: ontology
definition: A specific observation of a morphological feature in an image, linking the feature instance to its spatial location (image region with coordinates) and the taxon or organism being observed.

https://w3id.org/np/RAfocFeUWOny3cKBSJ7rW3OV8stqC6-URDCgdkSfxJ-0A
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
created: 2026-05-27T15:09:00.559Z
creator: Tobias Kuhn
data usage license: https://creativecommons.org/publicdomain/zero/1.0/
introduces: Morphological Feature Observation
was created at: nanodash.knowledgepixels.com

sig
has algorithm: RSA
signed by: Tobias Kuhn

ontology
has label from api: Biodiversity Ontology