Table 3.
List of the SAF elements, descriptions, mappings and data types with examples that apply to the KINOMEscan assay.
| SAF Element | Element Description | SAF Example | HMS mapping | BAO mapping | Data type |
|---|---|---|---|---|---|
| safVersion | Version of SAF, tightly bound to ontology annotations | “safVersion”:“0.1”, | Numeric value | ||
| bioAssay | Bioassay is defined by the assay (design) method, detection, biology / target, format perturbagen, and reported endpoint | “bioAssay”:“KINOMEscan”, | bioassay | bioassay | controlled vocabulary |
| hmsDatasetiD | Identification of the bioassay | “hmsDatasetiD”:“20020”, | HMS Dataset ID | has bioassay ID | local ID |
| screeningLablinwestigator | Screening facility laboratory investigator | “sereeningLabInvestigator”: “Qingsong Liu”, | Screening Lab Investigator | has screening lab Investigator | free text |
| screeningPrincipalInvestigator | Screening facility principal investigator or head of the laboratory | “screeningPrincipalInvestigator”: “Nathanael Gray”, | Screening Principal Investigator | has screening principal Investigator | free text |
| assayProtocol | Methodology to perform a bioassay | “assayProtocol”: “1 T7 kinase-tagged phage strains are grown in parallel in 24-well or 96 well block in… | Assay Protocol | has assay protocol | free text |
| assayProtocolReference | Reference (publications, urls…) for the assay protocol | “ assayProtocolReference”: “KINOMEscan website: http://kinomescan.com/Techno1ogy/How-it-Works… | Assay Protocol Reference | has PMID | global ID |
| screeningFacility | Screening facility where the assay was performed | “ sereeningFacility”:“HMS”, | research institute | controlled vocabulary | |
| assayDescription | Background information to perform the bioassay | “assayDescription”: “The KINOMEscan assay platform is based on a competition binding assay that is… | Assay Description | has assay narrative | free text |
| assayTitle | Name of a bioassay | “assayTitle”:“Sorafenib KINOMEscan”, | AssayTitle | has assay title | free text |
| smCenterCompoundID | Center specific compound ID, for the parent structure. | smCenterCompoundID:“10008”, | Small Mol HMS LINCS ID | local ID | |
| smSalt | Reference to counter-ions and other addends present in the compound’s formulation | smSalt:“101”, | Salt ID | local ID | |
| smCenterSamplelD | Sample ID of the tested compound, referring to of the tested sample; assigned after local registry of the compound (center specific) | “smCenterSamplelD”:“10008–101-1”, | Small Mol HMS LINCS ID | local ID | |
| smLincsID | Small molecule LINCS ID | smLincsID: “LSM- 1008”, | LINCS ID | has small molecule ID | global ID |
| smName | The primary name for the (parent) compound. | smName: “BAY- 439006”, | SM Name | small molecule | controlled vocabulary |
| ppName | The primary name of the protein. | ppName: “ABL1(E255K) phosphorylated”, | Protein Name | protein | controlled vocabulary |
| ppCenterProteinID | LINCS center-specific protein ID | ppCenterProteinID:“200004”, | HMS Protein ID | has UniProtlD | global ID |
| concUnit | Standardized quantity in which the concentration is expressed/measured | datapointName: “concUnit”, “datapointValue”: “uM” | Concunit | concentration unit | controlled vocabulary |
| assayCompoundConcentration | The concentration of the perturbagen used in the assay to elicit the biological effect or perturbation | datapointName:” assay CompoundConcentration”, “datapointValue”: “10” | Assay compound conc; | has concentration value | numeric value |
| percentControl | Percent control is the response relative to a reference state, typically to a high control | datapointName:“percentControl”,“datapointValue”: “100” | % Control | has percent response value | numeric value |