Staging materials for minting the 38 nanopublication-based FAIR Digital Twins of SARS-CoV-2 Spike RBD variants (Alpha, Epsilon, Eta) reported in Schultes et al. (in preparation). MAC / Leiden University LACDR. Project StayAhead (LSHM22038).
The MAC FDT demonstration is complete and fully version-controlled all live on the nanopub network : 3 FDTs for COVID Spike protein variants are realized using nanopub-based FDOs representing 45 vocabulary terms + 11 templates --> 38 instances
FAIR Digital Twins of COVID Spike variants
Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs
Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs displays view: RAGlsCUDZr
Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs has pinned query: MAC FDT — Alpha variant digital twin (knowlet)
Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs has pinned query: MAC FDT — catalogue summary by type
Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs has pinned query: MAC FDT — observations per method
Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs has pinned query: MAC FDT — variants by WHO classification
MAC FDT — Alpha variant digital twin (knowlet)
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.
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX np: <http://www.nanopub.org/nschema#> PREFIX npa: <http://purl.org/nanopub/admin/> PREFIX npx: <http://purl.org/nanopub/x/> PREFIX dct: <http://purl.org/dc/terms/> PREFIX fdof: <https://w3id.org/fdof/ontology#> PREFIX mac: <https://w3id.org/spaces/mac/r/ontology/> SELECT ?obs ?type ?label WHERE { GRAPH npa:graph { ?n1 npa:hasValidSignatureForPublicKey ?pubkey . filter not exists { ?np2 npx:invalidates ?n1 ; npa:hasValidSignatureForPublicKey ?pubkey . } ?n1 np:hasAssertion ?a . } graph ?a { ?obs mac:isObservationOf <https://w3id.org/np/RA4BHII2Bz7HfpUkaSJqNmhjF8F7hyWpCJnvXYkA4EP_M/Alpha-RBD-Variant> . ?obs a ?type . FILTER(?type != fdof:FAIRDigitalObject) OPTIONAL { ?obs rdfs:label ?label . } } } ORDER BY ?type
Counts of MAC FDT FDOs grouped by their specific type (variants, observations, methods). Bounded summary view of the full catalogue.
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX np: <http://www.nanopub.org/nschema#> PREFIX npa: <http://purl.org/nanopub/admin/> PREFIX npx: <http://purl.org/nanopub/x/> PREFIX dct: <http://purl.org/dc/terms/> PREFIX fdof: <https://w3id.org/fdof/ontology#> PREFIX mac: <https://w3id.org/spaces/mac/r/ontology/> SELECT ?type (COUNT(?thing) AS ?count) WHERE { GRAPH npa:graph { ?n1 npa:hasValidSignatureForPublicKey ?pubkey . filter not exists { ?np2 npx:invalidates ?n1 ; npa:hasValidSignatureForPublicKey ?pubkey . } ?n1 np:hasAssertion ?a . } graph ?a { ?thing a fdof:FAIRDigitalObject . ?thing a ?type . FILTER(?type != fdof:FAIRDigitalObject) FILTER(STRSTARTS(STR(?type), "https://w3id.org/spaces/mac/r/ontology/")) } } GROUP BY ?type ORDER BY DESC(?count)
Counts of observation FDOs grouped by the method (computational, experimental, or surveillance) that produced them — demonstrating multi-source decentralized attribution.
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX np: <http://www.nanopub.org/nschema#> PREFIX npa: <http://purl.org/nanopub/admin/> PREFIX npx: <http://purl.org/nanopub/x/> PREFIX dct: <http://purl.org/dc/terms/> PREFIX fdof: <https://w3id.org/fdof/ontology#> PREFIX mac: <https://w3id.org/spaces/mac/r/ontology/> SELECT ?method (COUNT(?obs) AS ?count) WHERE { GRAPH npa:graph { ?n1 npa:hasValidSignatureForPublicKey ?pubkey . filter not exists { ?np2 npx:invalidates ?n1 ; npa:hasValidSignatureForPublicKey ?pubkey . } ?n1 np:hasAssertion ?a . } graph ?a { ?obs ?methodPred ?method . VALUES ?methodPred { mac:hasPredictionMethod mac:hasExperimentalMethod mac:hasSurveillanceMethod } } } GROUP BY ?method ORDER BY DESC(?count)
Counts of Spike RBD variants grouped by WHO risk designation (VOC / VOI / VUM), via their WHO classification observation FDOs.
MAC FDT — variants by WHO classification
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX np: <http://www.nanopub.org/nschema#> PREFIX npa: <http://purl.org/nanopub/admin/> PREFIX npx: <http://purl.org/nanopub/x/> PREFIX dct: <http://purl.org/dc/terms/> PREFIX fdof: <https://w3id.org/fdof/ontology#> PREFIX mac: <https://w3id.org/spaces/mac/r/ontology/> SELECT ?whoClass (COUNT(?variant) AS ?count) WHERE { GRAPH npa:graph { ?n1 npa:hasValidSignatureForPublicKey ?pubkey . filter not exists { ?np2 npx:invalidates ?n1 ; npa:hasValidSignatureForPublicKey ?pubkey . } ?n1 np:hasAssertion ?a . } graph ?a { ?obs a mac:WHOVariantClassification . ?obs mac:hasWHOClassification ?whoClass . ?obs mac:isObservationOf ?variant . } } GROUP BY ?whoClass ORDER BY DESC(?count)
Participation in: Demo session for Swiss Data Science Center
0009-0000-5571-5036 is participant in Demo session for Swiss Data Science Center
Demo session for Swiss Data Science Center
Sabine Maennel is participant in Demo session for Swiss Data Science Center
Tobias Kuhn is participant in Demo session for Swiss Data Science Center
0000-0002-9135-1353 is participant in Demo session for Swiss Data Science Center
The site of the nanopublication community
Our start-up focussed on nanopublications
Demo session for Swiss Data Science Center displays view: Relevant resources view
Computational prediction of AgMata aggregation propensity score (0.7004717948717948, unitless) for SARS-CoV-2 Spike RBD variant Alpha (N169Y) using the Bio2Byte AgMata predictor. Sequence-derived: one FDO per variant.
Deep mutational scanning measurements (Bloom Lab) for SARS-CoV-2 Spike RBD variant Alpha (N169Y). Six values: bind=9.81374, delta_bind=1.04213, expr=10.05266, delta_expr=-0.13322, confidence_bind=0.0732354593527125, confidence_expr=0.0713853600674372. All unitless.
Alpha DMS observation — Bloom Lab (bind=9.81374, expr=10.05266)
Alpha real-world occurrence — England (late 2020-2021)
Real-world detection of SARS-CoV-2 Spike variant Alpha (B.1.1.7) in England during late 2020-2021, as reported in GISAID (accession EPI_ISL_601443).
Alpha — WHO Variant of Concern (2020-12-18)
WHO classification of SARS-CoV-2 Spike variant Alpha (B.1.1.7) as a Variant of Concern (VOC) on 2020-12-18.
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.
Epsilon DMS observation — Bloom Lab (bind=8.93862, expr=10.25356)
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.
Epsilon real-world occurrence — United States (2021-01-13)
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).
Epsilon — WHO Variant of Interest (2021-03-05)
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.
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.
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.
Eta DMS observation — Bloom Lab (bind=9.01256, expr=10.21898)
Eta real-world occurrence — Nigeria (2020-12-15)
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).
WHO classification of SARS-CoV-2 Spike variant Eta (B.1.525) as a Variant of Interest (VOI) on 2021-03-05.
Eta — WHO Variant of Interest (2021-03-05)
FAIR Connect displays view: View of FIP domains
FAIR Connect - This is the Space for FAIR Connect.
FAIR Connect displays view: View of FAIR-Enabling Resource types
Computational prediction of RMSD (13.378861773140596 Angstroms) for SARS-CoV-2 Spike RBD variant Alpha (N169Y) using ESM2.
Computational prediction of RMSD (2.277628683231952 Angstroms) for SARS-CoV-2 Spike RBD variant Alpha (N169Y) using AlphaFold 2.
Computational prediction of SASA (10141.236988525969 square Angstroms) for SARS-CoV-2 Spike RBD variant Alpha (N169Y) using AlphaFold 2.
Computational prediction of SASA (16494.878394358453 square Angstroms) for SARS-CoV-2 Spike RBD variant Alpha (N169Y) using ESM2.
Computational prediction of pLDDT (23.673561732385306 unitless, 0-100) for SARS-CoV-2 Spike RBD variant Alpha (N169Y) using ESM2.
Computational prediction of pLDDT (93.74392833444035 unitless, 0-100) for SARS-CoV-2 Spike RBD variant Alpha (N169Y) using AlphaFold 2.
Computational prediction of RMSD (12.801648143493145 Angstroms) for SARS-CoV-2 Spike RBD variant Epsilon (L120R) using ESM2.
Epsilon RMSD = 2.975776098053212 Å — AlphaFold 2
Computational prediction of RMSD (2.975776098053212 Angstroms) for SARS-CoV-2 Spike RBD variant Epsilon (L120R) using AlphaFold 2.
Computational prediction of SASA (10181.968717666516 square Angstroms) for SARS-CoV-2 Spike RBD variant Epsilon (L120R) using AlphaFold 2.
Computational prediction of SASA (17620.862527029858 square Angstroms) for SARS-CoV-2 Spike RBD variant Epsilon (L120R) using ESM2.
Computational prediction of pLDDT (23.73609314359643 unitless, 0-100) for SARS-CoV-2 Spike RBD variant Epsilon (L120R) using ESM2.
Epsilon pLDDT = 94.19297808764844 — AlphaFold 2
Computational prediction of pLDDT (94.19297808764844 unitless, 0-100) for SARS-CoV-2 Spike RBD variant Epsilon (L120R) using AlphaFold 2.
Computational prediction of RMSD (2.476768477258109 Angstroms) for SARS-CoV-2 Spike RBD variant Eta (E152K) using ESM2.
Computational prediction of RMSD (2.7195180252543003 Angstroms) for SARS-CoV-2 Spike RBD variant Eta (E152K) using AlphaFold 2.
Computational prediction of SASA (10226.641288430395 square Angstroms) for SARS-CoV-2 Spike RBD variant Eta (E152K) using AlphaFold 2.
Computational prediction of SASA (18026.596842240684 square Angstroms) for SARS-CoV-2 Spike RBD variant Eta (E152K) using ESM2.
Computational prediction of pLDDT (23.15035644847704 unitless, 0-100) for SARS-CoV-2 Spike RBD variant Eta (E152K) using ESM2.
Computational prediction of pLDDT (94.05421698739244 unitless, 0-100) for SARS-CoV-2 Spike RBD variant Eta (E152K) using AlphaFold 2.
AlphaFold 2 (DeepMind) protein structure prediction system.
AlphaFold 2 — DeepMind structure predictor
AgMata aggregation propensity predictor, Bio2Byte toolkit.
Bio2Byte AgMata — aggregation propensity predictor
Deep mutational scanning of SARS-CoV-2 RBD binding and expression, Bloom Lab.
Deep mutational scanning — Bloom Lab SARS-CoV-2 RBD
ESM2 protein language model (Meta AI) for structure and property prediction from sequence.
GISAID SARS-CoV-2 genomic surveillance platform.
GISAID — Global Initiative on Sharing All Influenza Data
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.
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.
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.
Demo session for Swiss Data Science Center has speaker Tobias Kuhn
Demo session for Swiss Data Science Center has role: General participant role
Demo session for Swiss Data Science Center has role: Speaker role
Demo session for Swiss Data Science Center displays view: simple message view
During this interactive session, Nanodash and nanopublications will be demoed.
Test Group A displays view: Status updates for event view
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.
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 { ?npx npx:invalidates ?np ; npa:hasValidSignatureForPublicKeyHash ?pubkey . } ?np npx:embeds ?view . ?np np:hasAssertion ?a . } graph ?a { ?view a gen:ResourceView . ?view dct:isVersionOf ?viewKindOptional . } } } } } order by desc(?date)
Template: Declaring an Observational Method (MAC FDT Type 11) - An epidemiological surveillance system or data collection platform through wh...
Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs has pinned template: Template: Declaring an Observational Method (MAC FDT Type 11)
Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs has pinned template: Template: Declaring an Experimental Method (MAC FDT Type 10)
Template: Declaring an Experimental Method (MAC FDT Type 10) - An experimental assay or measurement protocol producing empirical observation...
Template: Declaring a Computational Method (MAC FDT Type 9) - A computational method, tool, or algorithm producing predictions or scores fr...
Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs has pinned template: Template: Declaring a Computational Method (MAC FDT Type 9)
Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs has pinned template: Template: Declaring a WHO Variant Classification (MAC FDT Type 8)
Template: Declaring a WHO Variant Classification (MAC FDT Type 8) - Classification of a SARS-CoV-2 lineage according to the WHO risk framework — ...
Template: Declaring a Deep Mutational Scanning Observation (MAC FDT Type 7) - Experimental binding affinity and expression level measurements for a SARS-Co...
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)
Declaring a Deep Mutational Scanning Observation
Declaring a Computational Prediction — AgMata
Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs has pinned template: Template: Declaring a Computational Prediction — AgMata (MAC FDT Type 6)
Template: Declaring a Computational Prediction — AgMata (MAC FDT Type 6) - Computational prediction of the AgMata aggregation propensity score (unitless...
Declaring a Computational Prediction — pLDDT
Template: Declaring a Computational Prediction — pLDDT (MAC FDT Type 5) - Computational prediction of the per-residue confidence score (pLDDT, unitless...
Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs has pinned template: Template: Declaring a Computational Prediction — pLDDT (MAC FDT Type 5)
Template: Declaring a Computational Prediction — SASA (MAC FDT Type 4) - Computational prediction of the Solvent Accessible Surface Area (SASA, in squ...
Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs has pinned template: Template: Declaring a Computational Prediction — SASA (MAC FDT Type 4)
Declaring a Computational Prediction — SASA
Declaring a Computational Prediction — RMSD
Template: Declaring a Computational Prediction — RMSD (MAC FDT Type 3) - Computational prediction of the Root Mean Square Deviation (RMSD, in Angstrom...
Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs has pinned template: Template: Declaring a Computational Prediction — RMSD (MAC FDT Type 3)
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...
Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs has pinned template: Template: Declaring a Real-World Occurrence (MAC FDT Type 2)
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...
Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs has pinned template: Template: Declaring a Spike RBD Variant (MAC FDT Type 1)
Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs displays view: Pinned templates view
Attribution 4.0 International (CC BY 4.0)
FAIR² data article (Frontiers in Bioinformatics)
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).
Declaring a Computational Method (MAC FDT Type 9)
full URI or short suffix for this computational method FDO
label for this method (e.g. "ESM2 — Meta AI protein language model")
Template: Declaring a Computational Method (MAC FDT Type 9)
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).
Declaring an Experimental Method (MAC FDT Type 10)
full URI or short suffix for this experimental method FDO
label for this method (e.g. "Deep mutational scanning — Bloom Lab SARS-CoV-2 RBD")
Template: Declaring an Experimental Method (MAC FDT Type 10)
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).
Declaring an Observational Method (MAC FDT Type 11)
full URI or short suffix for this observational method FDO
label for this method (e.g. "GISAID — Global Initiative on Sharing All Influenza Data")
Template: Declaring an Observational Method (MAC FDT Type 11)
Template: Declaring a WHO Variant Classification (MAC FDT Type 8)
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).
Declaring a WHO Variant Classification (MAC FDT Type 8)
WHO classification: ${classification} (${classificationDate})
observation-specific authority (DOI or URL)
free-text description of this WHO classification
full URI or short suffix for this WHO classification FDO
label for this classification (e.g. "Alpha WHO classification: VOC")
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).
Declaring a Deep Mutational Scanning Observation (MAC FDT Type 7)
DMS observation (bind=${bind}, expr=${expr})
bind (binding affinity, log KD, unitless)
delta_bind (change vs. wild-type, unitless)
delta_expr (change vs. wild-type, unitless)
free-text description of this DMS observation
Experimental Method FDO referent URI (Type 10)
expr (expression level, log MFI, unitless)
full URI or short suffix for this DMS observation FDO
label for this observation (e.g. "Alpha DMS - Bloom Lab")
FAIR² Package DOI, FAIR² resource URL, or OSF URL
has bind (binding affinity, log KD, unitless)
has delta_bind (vs. wild-type, unitless)
has delta_expr (vs. wild-type, unitless)
has expr (expression level, log MFI, unitless)
Template: Declaring a Deep Mutational Scanning Observation (MAC FDT Type 7)
Template: Declaring a Computational Prediction — AgMata (MAC FDT Type 6)
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).
Declaring a Computational Prediction — AgMata (MAC FDT Type 6)
free-text description of this AgMata observation
full URI or short suffix for this AgMata observation FDO
label for this observation (e.g. "Alpha AgMata")
Computational Method FDO referent URI (Bio2Byte AgMata, Type 9)
FAIR² Package DOI or FAIR² ESM resource URL or OSF URL
has AgMata score (aggregation propensity)
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).
Declaring a Computational Prediction — RMSD (MAC FDT Type 3)
free-text description of this RMSD observation
full URI or short suffix for this RMSD observation FDO
label for this observation (e.g. "Alpha RMSD - AlphaFold II")
Computational Method FDO referent URI (Type 9)
FAIR² Package DOI or FAIR² resource URL or OSF URL
Template: Declaring a Computational Prediction — RMSD (MAC FDT Type 3)
Template: Declaring a Computational Prediction — SASA (MAC FDT Type 4)
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).
Declaring a Computational Prediction — SASA (MAC FDT Type 4)
SASA = ${value} A^2 (${predictionMethod})
free-text description of this SASA observation
full URI or short suffix for this SASA observation FDO
label for this observation (e.g. "Alpha SASA - ESM")
has SASA (Solvent Accessible Surface Area)
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).
Declaring a Computational Prediction — pLDDT (MAC FDT Type 5)
free-text description of this pLDDT observation
full URI or short suffix for this pLDDT observation FDO
label for this observation (e.g. "Alpha pLDDT - AlphaFold II")
Template: Declaring a Computational Prediction — pLDDT (MAC FDT Type 5)
Template: Declaring a Real-World Occurrence (MAC FDT Type 2)
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).
Declaring a Real-World Occurrence (MAC FDT Type 2)
Real-world occurrence (${occurrenceDate})
free-text description of this occurrence
full URI (e.g. handle.net) or short suffix for this occurrence FDO
canonical GISAID accession (EPI_ISL_XXXXXXX)
label or name for this occurrence (e.g. "Alpha first detected, UK Sept 2020")
GeoNames feature URI (e.g. https://sws.geonames.org/6269131/)
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.