file annotation template
Base annotations for files in synapse [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 | |
| analysisType | Type of analysis | False | STRING_LIST | 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 | |
| consortium | The name of the consortium | True | STRING_LIST | Sage Bionetworks | ManifestColumn | ELITE, ELITE CDCP, Not assigned | |
| 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_LIST | Sage Bionetworks | ManifestColumn | raw,processed,results,normalized,metadata, Not assigned | |
| dataType | True | STRING | 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 | ||
| 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_LIST | 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 | |
| projectShortName | True | STRING | Sage Bionetworks | ManifestColumn | LC,ILO,LLFS,LG, Not assigned | ||
| resourceType | The type of resource being stored and annotated | True | STRING_LIST | Sage Bionetworks | ManifestColumn | experimentalData,metadata,tool,analysis,computationalNotebook, Not assigned | |
| 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 | ||
| studyKey | The short acronym for a study name in a URL-friendly format (ex. LLFS_Metabolomics OR ELPSCRNA) | True | STRING | Sage Bionetworks | ManifestColumn | ||
| Component | False | ||||||
| Filename | False | STRING | |||||
| metadataType | For files of dataSubtype: metadata, a description of the type of metadata in the file | False | STRING_LIST | Sage Bionetworks | ManifestColumn | individual,biospecimen,assay,supplementary files,Not Assigned | |
| 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 | ||
| 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 | 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 | |
| individualID | Identifying string linked to the individual or animal being studied, provided by the data contributor | True | STRING | sage.annotations-experimentalData.individualID-0.0.2 | ManifestColumn | ||
| isMultiSpecimen | Boolean flag indicating whether or not a file has data for multiple specimens | True | STRING_LIST | Sage Bionetworks | ManifestColumn | true,fasle,Not assigned |