assay metabolomics template
Template for Metabolomics [Source]
| Attribute | Description | Required | columnType | DependsOn | Source | Parent | Valid Values |
|---|---|---|---|---|---|---|---|
| acquisitionBatchID | Acquisition batch identifier, provided by the data contributor to Sage Bionetworks. The batch identifier(s) must be stored in a data dictionary .csv file uploaded to Synapse | False | STRING | ManifestColumn | |||
| acquisitionBatchSize | The number of samples | False | STRING | ManifestColumn | |||
| acquisitionBatchSizeUnit | The unit of measurement for number of samples in a batch | False | STRING | ManifestColumn | |||
| acquisitionMode | The specific aspect of a mass spectrometer method by which mass ranges are selected and possibly dissociated (full scan, MSn, SIM, MRM, etc.). Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | ManifestColumn | |||
| acquisitionSoftware | The name of the acquisition software used. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | ManifestColumn | |||
| batchID | ID used to identify a batch, provided by the data contributor to Sage Bionetworks. The batch identifier(s) must be stored in a data dictionary .csv file uploaded to Synapse | False | STRING | ManifestColumn | |||
| batchLabel | Used to supply batch label information with any string value | False | STRING | ManifestColumn | |||
| dataFile | Name of additional file(s) accompanying the data. The file(s) provide, for example, the name of any raw files generated by the instrument, generated reports from a vendor, an Rscript, or an instructions document. The files can be instrument raw files, converted peak lists such as mzML, MGF, or result files like mzIdentML. The files can be additional documentation submitted alongside the data needed for reuse and sharing purposes. Provide the file names of any additional files submitted alongside the data (ex., an ADAT file). Multiple file names can be separated by (;)Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | ManifestColumn | |||
| databaseName | The name of the search database (nr, SwissProt or est_human, and/or mass spectral library). Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | ManifestColumn | |||
| databaseSource | The name of the organization, project, or laboratory from where the database is obtained (UniProt, NCBI, EBI, other). | True | STRING | ManifestColumn | |||
| databaseWeblink | An internet address that may provide details of a database or software search, as well as for labs that generate their own search method (web link). Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | ManifestColumn | |||
| experimentalBatchSizeUnit | The unit of measurement for number of samples in a experimental batch | False | STRING | ManifestColumn | |||
| extractionMethod | The name of the process used to separate a desired component of an input material from the remainder. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | ManifestColumn | |||
| gasFlowTemperature | e.g., nebulization gas, cone gas, etc.Unit of measure-C, F, K, Not specified | False | NUMBER | ManifestColumn | |||
| gasFlowTemperatureUnit | Unit of gas flow temperature | False | STRING | ManifestColumn | C,F,K | ||
| hasAssayControl | Boolean flag indicating whether or not a specimen is a technical or assay control. Examples include study pools or reference pools, blanks, or internal standards. | False | BOOLEAN | ManifestColumn | |||
| hasIonizationSource | Were the ionization conditions recorded to enable reproduction of the experiment? | False | BOOLEAN | ManifestColumn | No,Yes | ||
| instrumentModel | The model of the instrument used. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | ManifestColumn | |||
| ionProperty | Ion charge state (positive or negative-ion analysis) | False | STRING | ManifestColumn | Negative,Positive | ||
| lensVoltages | The skimmer/focusing lens voltages e.g., capillary voltage, etc. | False | NUMBER | ManifestColumn | |||
| lensVoltagesUnit | Unit of lens voltages | False | STRING | ManifestColumn | |||
| measurementTechnique | The name of the measurement technique describing the assay method. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | ManifestColumn | |||
| msAnalyteType | The type of biospecimen subjected to analysis (ex., peptide, protein, metabolite, lipid)Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | ManifestColumn | |||
| msAssayTechnique | Specified the mass spectrometer technique used or the name of the proteomics assay used (ex. DDA)Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | ManifestColumn | |||
| msTarget | Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay | True | STRING | ManifestColumn | Not applicable,Not available,Not collected,Not specified,Targeted,Unknown,Untargeted | ||
| processingBatchID | Processing batch identifier, provided by the data contributor to Sage Bionetworks. The batch identifier(s) must be stored in a data dictionary .csv file uploaded to Synapse | False | STRING | ManifestColumn | |||
| sampleBatchID | Sample batch lot identifier, provided by the data contributor to Sage Bionetworks. The batch identifier(s) must be stored in a data dictionary .csv file uploaded to Synapse | False | STRING | ManifestColumn | |||
| sampleIntroduction | The sample introduction and delivery. From GC, from LC, direct infusion without chromatography, direct infusion using dedicated autosampler flow rate. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | ManifestColumn | |||
| samplePrepProtocol | An internet address that may provide more details of the protocol information (web link). Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | ManifestColumn | |||
| sampleType | The type of sample collected or the term used to describe the source of a biospecimen used for a laboratory test. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | ManifestColumn | |||
| technologyPlatformVersion | The specific version (application, manufacturer, model, lab, etc.) of a technology that is used to carry out a laboratory or computational experiment. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | ManifestColumn | |||
| vacuumPressure | The recorded vacuum pressure value | False | NUMBER | ManifestColumn | |||
| vacuumPressureUnit | Unit of vacuum pressure value | False | STRING | ManifestColumn | AFU,AI,AU/ml,bp g/dl,DK units/ml,g/l,gm,HAU,IU,iu/l,IU/ml,Kallikrein Inactivator Unit per Milliliter,kg,l,M,mg,mg/dl,mg/l,mg/ml,miu/ml,ml,mM,MOI,ng,ng/dl,ng/ml,ng/nl,ng/ul,nl,nM,Not specified,NPX,optical density,PFU,PFUe,pg,pg/mg creatinine,pg/ml,pg/nl,pg/ul,pl,pM,Pound,TCID50,ug,ug/dl,ug/l,ug/ml,ug/ul,uiu/ml,ul,uM,umol/l,units/ml | ||
| Component | False | ||||||
| Filename | False | ||||||
| acquistionSoftwareVersion | False | ||||||
| batchSizeUnit | False | ||||||
| experimentalBatchSize | False | ||||||
| processingBatchSize | False | ||||||
| processingBatchSizeUnit | False | ||||||
| sampleBatchSize | False | ||||||
| sampleBatchSizeUnit | False | ||||||
| batchSize | The number of samples | False | NUMBER | sage.annotations-experimentalData.batchSize-0.0.2 | ManifestColumn | ||
| specimenID | Identifying string linked to a particular sample or specimen, provide by the data contributor | True | STRING | sage.annotations-experimentalData.specimenID-0.0.2 | ManifestColumn | ||
| controlType | Control samples suitable for normalization and batch correction.Possible example values - GIS, GoldenWest, NIST SRM 1950, AIBL pool,Baker pool,water plus Baker ISTD, study pool, internal standards, Other, Unknown, Not collected, Not applicable, Not specified | False | STRING | sage.annotations-experimentalData.controlType-0.0.5 | ManifestColumn | AIBL pool, Baker pool, blank injection, GIS, GoldenWest, NIST SRM 1950, qc mix, Replicate, study pool, water plus Baker ISTD | |
| platformLocation | The name of the laboratory, facility, vendor, company, or location where the data generation platform was located, provided by the data contributor. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | sage.annotations-experimentalData.platformLocation-0.0.2 | ManifestColumn | ||
| spectrometerFrequency | The frequency at which a spectrometer causes hydrogen atoms to resonate (in MHz) | False | NUMBER | sage.annotations-experimentalData.spectrometerFrequency-0.0.2 | ManifestColumn |