assay metabolomics annotation template
Template for file-based Metabolomics annotations [Download]
| Attribute | Description | Required | columnType | DependsOn | Source | Parent | Valid Values |
|---|---|---|---|---|---|---|---|
| ModelSystemType | Type of model system | False | BOOLEAN | Sage Bionetworks | ManifestColumn | animal, cerebral organoid, immortalized cell line, iPSC, organoid, primary cell culture, Not assigned | |
| isModelSystem | Boolean flag indicating whether or not a file has data from a model system | True | BOOLEAN | Sage Bionetworks | ManifestColumn | True, False, Not assigned | |
| 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 | |||
| analysisType | Type of analysis | False | STRING | Sage Bionetworks | ManifestColumn | ANOVA,batch effect correction,clustering,data normalization,de-novo assembly,dose response study,enrichment analysis,genome-wide association,mendelian randomization analysis,network analysis,polygenic risk scores, Not assigned | |
| 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 | |||
| consortium | The name of the consortium | True | STRING | Sage Bionetworks | ManifestColumn | ELITE, ELITE CDCP, Not assigned | |
| 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 | |||
| dataSubtype | Further qualification of dataType, which may be used to indicate the state of processing of the data, aggregation of the data, or presence of metadata | True | STRING | Sage Bionetworks | ManifestColumn | raw,processed,results,normalized,metadata, Not assigned | |
| dataType | The category or format of data generated or collected in an experiment, describing the kind of information the dataset contains (for example, genomics, imaging, proteomics, or behavioral data). | True | STRING_LIST | Sage Bionetworks | ManifestColumn | clinical,drugScreen,electrophysiology,epigenetics,geneExpression,genomeAssembly,genomicVariants,imaging,lipidomics,metabolomics,metagenomics,Not applicable,Not collected,Not specified,Other,phenotype,proteomics,Unknown,wearableData | |
| 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 | |||
| fileFormat | Defined format of the data file, typically corresponding to extension, but sometimes indicating more general group of files produced by the same tool or software | True | STRING | Sage Bionetworks | ManifestColumn | FASTQ, FASTA, SAM, BAM, CRAM, VCF, BCF, GTF, GFF, GFF3, BED, BigBed, WIG, BigWig, CSV, TSV, MTX, H5AD, LOOM, RDS,PED, MAP, BED_PLINK, TPED, TFAM, BEDGRAPH, NARROWPEAK, BROADPEAK, TAGALIGN, OME-TIFF, ND2, CZI, LSM, H5, HDF5, PARQUET, PDB, MMCIF, JSON, YAML, XML, TXT, XLSX, CSV, Not assigned | |
| 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 | Bisulfite sequencing,Clinical data,Genome-wide association study,High-performance liquid chromatography tandem mass spectrometry,Liquid chromatography mass spectrometry,Liquid chromatography tandem mass spectrometry,Mass spectrometry,Metabolomics,MetaX-processed metabolomics data,Proximity extension assay,RNA sequencing,Single-cell RNA sequencing,Shotgun metagenomic sequencing,Single nucleotide polymorphism array,Tandem Mass Tag proteomics,Whole-genome sequencing,Unknown,Other,Not collected,Not applicable,Not specified | ||
| 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 | |||
| resourceType | The type of resource being stored and annotated | True | STRING | Sage Bionetworks | ManifestColumn | experimentalData,metadata,tool,analysis,computationalNotebook,softwareTool,Not assigned | |
| 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 | |||
| speciesGroup | The taxonomic ranking including both species and subspecies the individual belongs to. | True | STRING | ManifestColumn | Amphibian,Bird,Fish,Invertebrate,Mammal,Not applicable,Not collected,Not specified,Reptile,Unknown | ||
| speciesName | The scientific name of the species (typically a taxonomic group, ex. "Eremophila alpestris) the individual belongs to.""" | True | STRING | ManifestColumn | Acomys cahirinus, Acomys russatus, Accipiter cooperii, Actitis macularius, Aix sponsa, Anas acuta, Anas carolinensis, Anas platyrhynchos, Antigone canadensis, Archilochus colubris, Artibeus jamaicensis, Baeolophus bicolor, Balaena mysticetus, Blarina brevicauda, Bombycilla cedrorum, Bonasa umbellus, Bos taurus, Branta canadensis, Bubo virginianus, Buteo jamaicensis, Buteo lineatus, Canis latrans, Cardinalis cardinalis, Castor canadensis, Cavia porcellus, Charadrius vociferus, Chinchilla lanigera, Columba livia, Condylura cristata, Corvus brachyrhynchos, Cricetomys ansorgei, Cricetulus barabensis, Cricetulus griseus, Cryptomys damarensis, Cuniculus paca, Cyanocitta cristata, Cygnus olor, Dryobates pubescens, Dumetella carolinensis, Ellobius lutescens, Ellobius talpinus, Eonycteris spelaea, Eptesicus fuscus, Equus caballus, Eremophila alpestris, Fukomys damarensis, Haemorhous mexicanus, Heterocephalus glaber, Hirundo rustica, Homo sapiens, Hydrochoerus hydrochaeris, Hydroprogne caspia, Hylocichla mustelina, Icteria virens, Larus argentatus, Larus delawarensis, Macaca fascicularis, Macaca mulatta, Mareca strepera, Marmota monax, Melanerpes carolinus, Meleagris gallopavo, Melospiza melodia, Meriones unguiculatus, Mesocricetus auratus, Microtus pennsylvanicus, Mimus polyglottos, Molothrus ater, Multi-species, Mus musculus, Myocastor coypus, Myotis lucifugus, Nannospalax galili, Neosciurus carolinensis, Neotoma cinerea, Neotoma floridana, Not applicable, Not collected, Not provided, Not specified, Octodon degus, Odocoileus virginianus, Ondatra zibethicus, Other, Pan troglodytes, Papio anubis, Passer domesticus, Passerina caerulea, Passerina cyanea, Peromyscus gossypinus, Peromyscus leucopus, Peromyscus maniculatus, Phalacrocorax auritus, Phasianus colchicus, Picoides villosus, Pipilo erythrophthalmus, Poecile carolinensis, Quiscalus quiscula, Rattus norvegicus, Rattus rattus, Regulus calendula, Saimiri boliviensis, Sayornis phoebe, Scalopus aquaticus, Sciurus carolinensis, Sciurus niger, Sciurus vulgaris, Scolopax minor, Setophaga citrina, Setophaga coronata, Setophaga dominica, Setophaga petechia, Setophaga pinus, Sialia sialis, Sigmodon hispidus, Sitta carolinensis, Spatula clypeata, Spinus tristis, Spizella passerina, Spizella pusilla, Spizelloides arborea, Struthio camelus, Sturnus vulgaris, Sus scrofa, Sylvilagus floridanus, Tachycineta bicolor, Tamias striatus, Tamiasciurus hudsonicus, Thryothorus ludovicianus, Toxostoma rufum, Troglodytes aedon, Turdus migratorius, Tursiops truncatus, Vicugna pacos, Vireo griseus, Vireo olivaceus, Zalophus californianus, Zenaida macroura, Zonotrichia albicollis, Unknown | ||
| specimenType | Type of biological material sample taken from a biological entity for research purposes | True | STRING_LIST | ManifestColumn | blood, brain, buffy coat, cell line, cells, nervous system, organoid, plasma, saliva, serum, skin, stool, tissue, urine, Not applicable, Not collected, Not specified, Other, Unknown | ||
| studyKey | The short acronym for a study name in a URL-friendly format (ex. LLFS_Metabolomics OR ELPSCRNA) | True | STRING | Sage Bionetworks | 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 | ||
| Filename | False | STRING | |||||
| acquistionSoftwareVersion | False | STRING | |||||
| batchSizeUnit | False | STRING | |||||
| experimentalBatchSize | False | INTEGER | |||||
| metadataType | For files of dataSubtype: metadata, a description of the type of metadata in the file | False | STRING | Sage Bionetworks | ManifestColumn | individual,biospecimen,assay,supplementary files,Not Assigned | |
| processingBatchSize | False | INTEGER | |||||
| processingBatchSizeUnit | False | STRING | |||||
| project | The ELITE project short name associated with the tool | True | STRING | Sage Bionetworks | ILO BU, ILO TGEN, LC, LG, LLFS, NECS APOE, Not assigned | ||
| sampleBatchSize | False | INTEGER | |||||
| sampleBatchSizeUnit | False | STRING | |||||
| batchSize | The number of samples | False | NUMBER | sage.annotations-experimentalData.batchSize-0.0.2 | ManifestColumn | ||
| organ | Indicate the organ the specimen is from. An organ is a unique macroscopic (gross) anatomic structure that performs specific functions. It is composed of various tissues. | True | STRING | sage.annotations-experimentalData.organ-0.0.4 | ManifestColumn | blood, bone marrow, brain, breast, Bursa Of Fabricius, cerebrospinal fluid, colon, kidney, large intestine, liver, lung, lymph node, mammary gland, nerves, nose, ovary, pancreas, prostate, skin, spleen, Not collected, Not specified, Not applicable, Other, Unknown, plasma, gonadal fat, inguinal fat, gastrocnemius muscle | |
| tissue | Indicate the tissue the specimen is from. A tissue is a multicellular anatomical structure that consists of many cells of one or a few types arranged in an extracellular matrix. | True | STRING_LIST | sage.annotations-experimentalData.tissue-0.0.11 | ManifestColumn | amygdala, amygdaloid complex, anterior cingulate cortex, angular gyrus, blood, bone marrow, Buccal Mucosa, Buffy Coat, caudate nucleus, cecum derived fecal material, cerebellar cortex, cerebellum, cerebral cortex, cortical plate, dorsal anterior cingulate cortex, dorsal pallium, Dorsal Root Ganglion, dorsolateral prefrontal cortex, dorsomedial prefrontal cortex, embryonic tissue, entorhinal cortex, fecal material, forebrain, frontal cortex, frontal lobe, frontal pole, fusiform gyrus, hippocampus, head of caudate nucleus, inferior frontal gyrus, inferior temporal cortex, inferior temporal gyrus, inferolateral temporal cortex, insula, insular cortex, lateral entorhinal cortex, left cerebral hemisphere, liver, mammillary body, medial dorsal nucleus of thalamus, medial entorhinal cortex, medial frontal cortex, medial ganglionic eminence, medial orbital frontal cortex, medial prefrontal cortex, meninges, midbrain, middle frontal gyrus, middle temporal gyrus, nerve tissue, Not Applicable, nucleus accumbens, occipital lobe, occipital visual cortex, olfactory neuroepithelium, orbitofrontal cortex, parahippocampal gyrus, parietal cortex, parietal lobe, plasma, posterior cingulate cortex, posteroinferior parietal cortex, posterior inferior parietal cortex, posterior superior temporal cortex, precentral gyrus, prefrontal cortex, primary auditory cortex, primary motor cortex, primary somatosensory cortex, primary tumor, primary visual cortex, putamen, right cerebral hemisphere, serum, splenocyte, striatum, subgenual anterior cingulate cortex, subgenual cingulate cortex, superior parietal lobe, superior temporal gyrus, temporal cortex, temporal lobe, temporal pole, thalamus, unspecified, ventricular zone, ventrolateral prefrontal cortex, VZ/SVZ, whole brain, gonadal fat, inguinal fat, kidney, plasma, liver, gastrocnemius muscle | |
| familyStudyParticipant | Indicates whether or not a file has data from a human participant involved in a family study (ex. LLFS) | False | STRING | sage.annotations-demographics.ethnicityfamilyStudyParticipant-0.0.2 | ManifestColumn | Yes, No, Not Assigned | |
| assay | The analysis or technology used to generate the data in this file | True | STRING_LIST | sage.annotations-experimentalData.assay-0.0.26 | ManifestColumn | 10x multiome, 16SrRNAseq, active avoidance learning behavior, anxiety-related behavior, ATACSeq, atomicForceMicroscopy, autoradiography, Baker Lipidomics, Biocrates Bile Acids, Biocrates p180, Biocrates Q500, bisulfiteSeq, Blood Chemistry Measurement, brightfieldMicroscopy, cellViabilityAssay, ChIPSeq, CITESeq, contextual conditioning behavior, CUT&Tag, DIA, DNA optical mapping, electrochemiluminescence, elevated plus maze test, elevated T maze apparatus method, ELISA, errBisulfiteSeq, exomeSeq, FIA-MSMS, FitBark, frailty assessment, Genotyping, HI-C, HiChIPseq, high content screen, HPLC, HPLC-MSMS, Immunocytochemistry, immunofluorescence, immunohistochemistry, in vivo bioluminescence, ISOSeq, jumpingLibrary, kinesthetic behavior, label free mass spectrometry, Laser Speckle Imaging, LC-MS, LC-MSMS, LC-SRM, Leiden Oxylipins, lentiMPRA, LFP, liquid chromatography-electrochemical detection, lncrnaSeq, locomotor activation behavior, long-read rnaSeq, LTP, MDMS-SL, memory behavior, Metabolon, methylationArray, MIB/MS, microRNAcounts, mirnaArray, mirnaSeq, MRI, mRNAcounts, MudPIT, m6A-rnaSeq, nextGenerationTargetedSequencing, Nightingale NMR, NOMe-Seq, novelty response behavior, open field test, oxBS-Seq, pharmacodynamics, pharmacokinetics, photograph, polymeraseChainReaction, Positron Emission Tomography, proximity extension assay, questionnaire, Rader Lipidomics, Real Time PCR, Ribo-Seq, rotarod performance test, rnaArray, rnaSeq, RPPA, sandwich ELISA, Sanger sequencing, scale, scATACSeq, scCGIseq, scirnaSeq, scrnaSeq, scwholeGenomeSeq, SiMoA, snpArray, snATACSeq, snrnaSeq, spontaneous alternation, STARRSeq, TMT quantitation, tractionForceMicroscopy, UPLC-MSMS, UPLC-ESI-QTOF-MS, UC Davis GCTOF, UCSD Untargeted Metabolomics, Vernier Caliper, von Frey test, westernBlot, wheel running, whole-cell patch clamp, wholeGenomeSeq, Wishart Catecholamines, Wishart High Value Metabolites, Zeno Electronic Walkway, Not collected, Not specified, Not applicable, Other, Unknown | |
| 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 | ||
| isMultiSpecimen | Boolean flag indicating whether or not a file has data for multiple specimens | True | STRING | Sage Bionetworks | ManifestColumn | true,false,Not assigned | |
| spectrometerFrequency | The frequency at which a spectrometer causes hydrogen atoms to resonate (in MHz) | False | NUMBER | sage.annotations-experimentalData.spectrometerFrequency-0.0.2 | ManifestColumn |