[ { "@id": "https://w3id.org/np/RAP3Yiccarf5sBGkDPI0iiAwtrlCUOhfNSVEGQNgoRiR8/assertion", "@graph": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/ComputationalPredictionSASA", "@type": [ "http://www.w3.org/2002/07/owl#Class" ], "http://purl.org/dc/terms/partOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/MAC-Ontology" } ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "A computed prediction of the Solvent Accessible Surface Area of a Spike RBD variant's predicted structure, produced by a named computational structure-prediction method." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Computational Prediction SASA" } ], "http://www.w3.org/2000/01/rdf-schema#subClassOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/ComputationalPrediction" } ] } ] }, { "@id": "https://w3id.org/np/RAin3nSs_QMqqkVJXnW2Mpt0A8VjSQjctVeZwknZd31TA/assertion", "@graph": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/Method", "@type": [ "http://www.w3.org/2002/07/owl#Class" ], "http://purl.org/dc/terms/partOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/MAC-Ontology" } ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "An abstract parent class for methods, tools, assays, or surveillance platforms that produce observations within the MAC FAIR Digital Twin substrate. Concrete subclasses distinguish computational methods (`mac:ComputationalMethod`), experimental methods (`mac:ExperimentalMethod`), and observational/surveillance methods (`mac:ObservationalMethod`). Instances of any concrete subclass carry one or more `cito:citesAsAuthority` URIs identifying the published descriptions of the method. This class is abstract: all instances belong to one of its concrete subclasses." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Method" } ] } ] }, { "@id": "https://w3id.org/np/RAS0UvFZif7dVx1hqlKodgcWeZiQ-8LR7lptPoW_uS0E4/assertion", "@graph": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/has_I_uncertainty_estimate", "@type": [ "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property", "http://www.w3.org/2002/07/owl#DatatypeProperty" ], "http://purl.org/dc/terms/partOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/MAC-Ontology" } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "has I uncertainty estimate" } ], "http://www.w3.org/2004/02/skos/core#definition": [ { "@value": "Links a dataset to its I uncertainty estimate." } ] } ] }, { "@id": "https://w3id.org/np/RALrwDOAWiIPVr1uNQyNf43gRhcSkgFKDFm0jhn2pB0F8/assertion", "@graph": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/ObservationalMethod", "@type": [ "http://www.w3.org/2002/07/owl#Class" ], "http://purl.org/dc/terms/partOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/MAC-Ontology" } ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "An epidemiological surveillance system or data-collection platform through which real-world occurrences of biological entities are documented. Referenced by Type 2 observation FDOs via `mac:hasSurveillanceMethod`. Instances carry one or more `cito:citesAsAuthority` URIs identifying the published descriptions of the surveillance platform." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Observational Method" } ], "http://www.w3.org/2000/01/rdf-schema#subClassOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/Method" } ] } ] }, { "@id": "https://w3id.org/np/RAeF7IC3vCsSnUMoLcojSbvRnIJIth-fa2ehyadTjS1CM/assertion", "@graph": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/has_mz_uncertainty_estimate", "@type": [ "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property", "http://www.w3.org/2002/07/owl#DatatypeProperty" ], "http://purl.org/dc/terms/partOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/MAC-Ontology" } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "has m/z uncertainty estimate" } ], "http://www.w3.org/2004/02/skos/core#definition": [ { "@value": "Links a dataset to its m/z uncertainty estimate." } ] } ] }, { "@id": "https://w3id.org/np/RAYOlJ43EmeoJ8lLRjS9cv5pn1PKNy0udeS36KfWSRCPk/assertion", "@graph": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/VOC", "@type": [ "http://www.w3.org/2002/07/owl#Class" ], "http://purl.org/dc/terms/partOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/MAC-Ontology" } ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "A SARS-CoV-2 variant designated by the WHO as carrying evidence of increased transmissibility, increased disease severity, or significant reduction in vaccine or therapeutic effectiveness." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Variant of Concern" } ], "http://www.w3.org/2000/01/rdf-schema#subClassOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/WHODesignation" } ] } ] }, { "@id": "https://w3id.org/np/RAKAogouhVXFZUSbqSZ_AUAIeUnz24jzGQ3u8FKRVf0Ks/assertion", "@graph": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/WHOVariantClassification", "@type": [ "http://www.w3.org/2002/07/owl#Class" ], "http://purl.org/dc/terms/partOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/MAC-Ontology" } ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "A classification of a SARS-CoV-2 lineage according to the WHO risk framework (VOC / VOI / VUM), with a specified assignment date and reference URL. Time-stamped because designation status changes over time." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "WHO Variant Classification" } ], "http://www.w3.org/2000/01/rdf-schema#subClassOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/Observation" } ] } ] }, { "@id": "https://w3id.org/np/RAG1yQSjgjX2cH7UA2fgm5UE5JMOgZ9XNx8GpdHVF5aww/assertion", "@graph": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/SpikeRBDVariant", "@type": [ "http://www.w3.org/2002/07/owl#Class" ], "http://purl.org/dc/terms/partOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/MAC-Ontology" } ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "A variant of the SARS-CoV-2 Spike receptor-binding domain (RBD, 195 residues) produced by one or more amino-acid substitutions from the wild-type Wuhan isolate (UniProt P0DTC2). This class is the type of the anchor FDO (A_r) of a FAIR Digital Twin; all observation FDOs link to it via `mac:isObservationOf` and collectively constitute the FDT." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Spike RBD Variant" } ] } ] }, { "@id": "https://w3id.org/np/RAiwK1L9NkB_qPZpdFoaIGISRB7-kO3xB3J3m3z_AkXR4/assertion", "@graph": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/VOI", "@type": [ "http://www.w3.org/2002/07/owl#Class" ], "http://purl.org/dc/terms/partOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/MAC-Ontology" } ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "A SARS-CoV-2 variant designated by the WHO as carrying genetic markers associated with phenotypic changes and demonstrated epidemiological impact warranting enhanced monitoring." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Variant of Interest" } ], "http://www.w3.org/2000/01/rdf-schema#subClassOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/WHODesignation" } ] } ] }, { "@id": "https://w3id.org/np/RAKoHwHclGn7vPxzwP5MWvsYcetSDXXaRMBa8pikYm_-A/assertion", "@graph": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/ComputationalPrediction", "@type": [ "http://www.w3.org/2002/07/owl#Class" ], "http://purl.org/dc/terms/partOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/MAC-Ontology" } ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "An abstract parent class for computational predictions about a Spike RBD variant, produced by a named computational method. Concrete subclasses cover specific predicted quantities (`mac:ComputationalPredictionRMSD`, `…SASA`, `…PLDDT`, `…AgMata`). Anticipates additional computational prediction types as siblings without restructuring the hierarchy. This class is abstract: all instances belong to one of its concrete subclasses." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Computational Prediction" } ], "http://www.w3.org/2000/01/rdf-schema#subClassOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/Observation" } ] } ] }, { "@id": "https://w3id.org/np/RA86GQCvCKP7tMt4cjZEroNkL4103kw1TlFH-nR_0trIM/assertion", "@graph": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/RealWorldOccurrence", "@type": [ "http://www.w3.org/2002/07/owl#Class" ], "http://purl.org/dc/terms/partOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/MAC-Ontology" } ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "A documented detection of a SARS-CoV-2 Spike variant in the real world, as reported in a surveillance database (typically GISAID). The occurrence is anchored to a specific collection date and to a GeoNames-identified location." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Real-World Occurrence" } ], "http://www.w3.org/2000/01/rdf-schema#subClassOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/Observation" } ] } ] }, { "@id": "https://w3id.org/np/RAwWafsvm-XuaeWXIfIkmY7-25TeGmLAxyb8baj0aUDGA/assertion", "@graph": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/VUM", "@type": [ "http://www.w3.org/2002/07/owl#Class" ], "http://purl.org/dc/terms/partOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/MAC-Ontology" } ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "A SARS-CoV-2 variant for which the WHO has identified evidence of growth advantage or immune escape and that is being monitored precautionarily pending further characterisation." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Variant Under Monitoring" } ], "http://www.w3.org/2000/01/rdf-schema#subClassOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/WHODesignation" } ] } ] }, { "@id": "https://w3id.org/np/RAopqX_RYM3fl5sAzy2pEOWQb4Qp4szll01XzilsakLDQ/assertion", "@graph": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/ComputationalPredictionRMSD", "@type": [ "http://www.w3.org/2002/07/owl#Class" ], "http://purl.org/dc/terms/partOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/MAC-Ontology" } ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "A computed prediction of the Root Mean Square Deviation between a predicted structure of a Spike RBD variant and a reference structure, produced by a named computational structure-prediction method." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Computational Prediction RMSD" } ], "http://www.w3.org/2000/01/rdf-schema#subClassOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/ComputationalPrediction" } ] } ] }, { "@id": "https://w3id.org/np/RAp5U-AAKn_oJZQM0bXcCHQX7KE4AseYLER3EBPCQVUCI/assertion", "@graph": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/Observation", "@type": [ "http://www.w3.org/2002/07/owl#Class" ], "http://purl.org/dc/terms/partOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/MAC-Ontology" } ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "An abstract parent class for all observation-layer FDOs in a MAC FAIR Digital Twin. Concrete subclasses include `mac:RealWorldOccurrence` (Type 2), `mac:ComputationalPrediction` and its sub-hierarchy (Types 3–6), `mac:ExperimentalObservation` and its sub-hierarchy (Type 7), and `mac:WHOVariantClassification` (Type 8). Every member links to the FDT's anchor (a `mac:SpikeRBDVariant`) via `mac:isObservationOf`. This class is abstract: it carries no direct instances; all instances belong to one of its concrete subclasses." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Observation" } ] } ] }, { "@id": "https://w3id.org/np/RAKKVsMYy26YhHVjTV2a9UVmm7TALoC8cIbkfuhQdccQs/assertion", "@graph": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/ComputationalPredictionAgMata", "@type": [ "http://www.w3.org/2002/07/owl#Class" ], "http://purl.org/dc/terms/partOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/MAC-Ontology" } ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "A computed prediction of the aggregation propensity of a Spike RBD variant, produced by the Bio2Byte AgMata method. The score is sequence-derived and is therefore predicted once per variant rather than once per structural-prediction method." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Computational Prediction AgMata" } ], "http://www.w3.org/2000/01/rdf-schema#subClassOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/ComputationalPrediction" } ] } ] }, { "@id": "https://w3id.org/np/RAK2Vc5pEBq3fak5RrbPFqLs_MkEuabVI1yesaxyUTp5U/assertion", "@graph": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/has_RT_uncertainty_estimate", "@type": [ "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property", "http://www.w3.org/2002/07/owl#DatatypeProperty" ], "http://purl.org/dc/terms/partOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/MAC-Ontology" } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "has RT uncertainty estimate" } ], "http://www.w3.org/2004/02/skos/core#definition": [ { "@value": "Links a dataset to its RT uncertainty estimate." } ] } ] }, { "@id": "https://w3id.org/np/RAG9wYbx-rdz06t_tIbMmZQUx1408kbuCIEedmitWrpuY/assertion", "@graph": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/MAC-Ontology", "@type": [ "http://www.w3.org/2002/07/owl#Ontology", "https://w3id.org/kpxl/gen/terms/MaintainedResource" ], "http://purl.org/dc/terms/description": [ { "@value": "This is the ontology of the MAC group." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "MAC Ontology" } ], "https://w3id.org/kpxl/gen/terms/hasNamespace": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/" } ], "https://w3id.org/kpxl/gen/terms/isMaintainedBy": [ { "@id": "https://w3id.org/spaces/mac" } ] } ] }, { "@id": "https://w3id.org/np/RA-PiBGB7iMOT16-M3gpGUajoKFi6kWSXfRy2hrvWp5Sk/assertion", "@graph": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/ComputationalPredictionPLDDT", "@type": [ "http://www.w3.org/2002/07/owl#Class" ], "http://purl.org/dc/terms/partOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/MAC-Ontology" } ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "A computed prediction confidence score (predicted Local Distance Difference Test) for the structural prediction of a Spike RBD variant, produced by a named computational structure-prediction method." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Computational Prediction pLDDT" } ], "http://www.w3.org/2000/01/rdf-schema#subClassOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/ComputationalPrediction" } ] } ] }, { "@id": "https://w3id.org/np/RAmVAWWz3ixLjoBjdQFi25QOfZvz0X2ZCYuJ7lYeSvetA/assertion", "@graph": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/WHODesignation", "@type": [ "http://www.w3.org/2002/07/owl#Class" ], "http://purl.org/dc/terms/partOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/MAC-Ontology" } ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "An abstract parent class for the World Health Organization's controlled-vocabulary risk designations applied to SARS-CoV-2 variants: Variant of Concern (`mac:VOC`), Variant of Interest (`mac:VOI`), and Variant Under Monitoring (`mac:VUM`). Used as the range of `mac:hasWHOClassification`. This class is abstract: all instances belong to one of its concrete subclasses." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "WHO Designation" } ] } ] }, { "@id": "https://w3id.org/np/RAnxnqy2hDygtFwC0w7EtRCyh4mQtiCGIG31iS8QT8O5Q/assertion", "@graph": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/ComputationalMethod", "@type": [ "http://www.w3.org/2002/07/owl#Class" ], "http://purl.org/dc/terms/partOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/MAC-Ontology" } ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "A computational method, tool, or algorithm that produces predictions or scores from biological sequence or structure data. Referenced by observation FDOs of Types 3–6 via `mac:hasPredictionMethod`. Instances carry one or more `cito:citesAsAuthority` URIs identifying the published descriptions of the method." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Computational Method" } ], "http://www.w3.org/2000/01/rdf-schema#subClassOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/Method" } ] } ] }, { "@id": "https://w3id.org/np/RAfSBNcdUBXznN0NooBOgeDPIkogXRzZVFwzyPG8_QYgc/assertion", "@graph": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/ExperimentalObservation", "@type": [ "http://www.w3.org/2002/07/owl#Class" ], "http://purl.org/dc/terms/partOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/MAC-Ontology" } ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "An abstract parent class for empirical observations produced by laboratory assays on a Spike RBD variant. Currently has one concrete child (`mac:ExperimentalDMSObservation`, deep mutational scanning); the forthcoming Bosch extension adds `mac:ExperimentalCellSortingObservation` as a sibling. This class is abstract: all instances belong to one of its concrete subclasses." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Experimental Observation" } ], "http://www.w3.org/2000/01/rdf-schema#subClassOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/Observation" } ] } ] }, { "@id": "https://w3id.org/np/RAO8JPqfCsnqamN5V7O8ytb4Rb43xBrQEi7UpYb9_MNRM/assertion", "@graph": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/uncertainty_model", "@type": [ "http://www.w3.org/2002/07/owl#Class" ], "http://purl.org/dc/terms/partOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/MAC-Ontology" } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Uncertainty Model" } ], "http://www.w3.org/2004/02/skos/core#definition": [ { "@value": "Documentation of the model used to compute or estimate uncertainty." } ] } ] }, { "@id": "https://w3id.org/np/RA4W7BTjZqyFF7yHyNBPXKwqfoFFBlC1-OLYw-U6jy1S4/assertion", "@graph": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/ExperimentalDMSObservation", "@type": [ "http://www.w3.org/2002/07/owl#Class" ], "http://purl.org/dc/terms/partOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/MAC-Ontology" } ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "An experimental observation of binding affinity and expression level measurements for a Spike RBD variant, determined by deep mutational scanning (Bloom Lab protocol). One FDO records all six DMS metrics (`bind`, `delta_bind`, `expr`, `delta_expr`, `confidence_bind`, `confidence_expr`) for a single variant." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Experimental DMS Observation" } ], "http://www.w3.org/2000/01/rdf-schema#subClassOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/ExperimentalObservation" } ] } ] }, { "@id": "https://w3id.org/np/RAZ6oFtmR_aeSfjBD634RS-VhRP1k__3u_tWgziHbW1JU/assertion", "@graph": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/ExperimentalMethod", "@type": [ "http://www.w3.org/2002/07/owl#Class" ], "http://purl.org/dc/terms/partOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/MAC-Ontology" } ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "An experimental assay or measurement protocol that produces empirical observations about biological entities. Referenced by Type 7 observation FDOs via `mac:hasExperimentalMethod`. Instances carry one or more `cito:citesAsAuthority` URIs identifying the published descriptions of the assay." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Experimental Method" } ], "http://www.w3.org/2000/01/rdf-schema#subClassOf": [ { "@id": "https://w3id.org/spaces/mac/r/ontology/Method" } ] } ] } ]