analysis results metadata template
Template for analysis and results [Download]
| Attribute | Description | Required | columnType | DependsOn | Source | Parent | Valid Values |
|---|---|---|---|---|---|---|---|
| algorithm | A resolvable URL or Synapse ID for the algorithm or set of rules used by the analysis. | False | STRING | https://w3id.org/reproduceme#Algorithm | ManifestColumn | ||
| dataFormat | The semantic format category of the represented data. | False | STRING | http://edamontology.org/ | ManifestColumn | Alignment format, Annotated text format, Article format, Bibliographic reference format, Biodiversity data format, Biological pathway or network format, Biological pathway or network report format, Chemical data format, Data index format, Database hits (sequence) format, Dirichlet distribution format, Document format, Enzyme kinetics report format, Experiment annotation format, FF parameter format, Gene annotation format, Gene expression report format, Graph format, HMM emission and transition counts format, Image format, Individual genetic data format, Linked data format, Map format, Mass spectrometry data format, Matrix format, NLP format, NMR data format, Nucleic acid features (primers) format, Nucleic acid features (restriction sites) format, Ontology format, Phylogenetic character data format, Phylogenetic tree format, Phylogenetic tree report (tree distances) format, Protein domain classification format, Protein family report format, Protein interaction format, Protein report format, Protein secondary structure format, Protein structure report (quality evaluation) format, Query language, Raw microarray data format, Raw sequence data format, RNA annotation format, RNA secondary structure format, Sequence assembly format, Sequence cluster format, Sequence distance matrix format, Sequence feature annotation format, Sequence features (repeats) format, Sequence motif format, Sequence profile format, Sequence quality report format (text), Sequence range format, Sequence record format, Sequence variation annotation format, Sequence-profile alignment format, Tertiary structure format, Text mining report format, Topology format, Trajectory format, Workflow format, Other | |
| entityType | The type of entity that is the subject of the analysis or result. | False | STRING | https://www.w3.org/TR/prov-o/ | ManifestColumn | experimental material, file, image, result, analysis, collection, instrument, plan, setting, Other, Not applicable | |
| environment | A resolvable URL or Synapse ID for instructions or a definition used to create the computational environment. | False | STRING | https://w3id.org/reproduceme#EnvironmentSetup | ManifestColumn | ||
| experimentalDesign | The design of an experiment intended to test a hypothesis or describe empirical data obtained under defined conditions. | False | STRING | http://edamontology.org/ | ManifestColumn | Animal study, GWAS study, Preclinical study, Clinical study, Other, Not applicable | |
| library | A resolvable URL, Synapse ID, or name and version of a software library used by the analysis. | False | STRING | https://w3id.org/reproduceme#Library | ManifestColumn | ||
| notebook | A resolvable URL or Synapse ID for a computational notebook used by the analysis. | False | STRING | https://w3id.org/reproduceme#Notebook | ManifestColumn | ||
| operatingSystem | The name and version of the operating system used to run the analysis. | False | STRING | https://w3id.org/reproduceme#OperatingSystem | ManifestColumn | ||
| parameters | A resolvable URL or Synapse ID for the parameters used to configure the analysis. | False | STRING | https://w3id.org/reproduceme#Parameter | ManifestColumn | ||
| programmingLanguage | The name and version of the programming language used to implement or run the analysis. | False | STRING | https://w3id.org/reproduceme#ProgrammingLanguage | ManifestColumn | ||
| protocol | A resolvable URL or Synapse ID for the instructions or protocol used to perform the analysis. | False | STRING | https://w3id.org/reproduceme#Protocol | ManifestColumn | ||
| resultType | The category or presentation type of the reported result. | False | STRING | http://edamontology.org/ | ManifestColumn | Final Result, Intermediate Result, Negative Result, Positive Result, Available, Not available, Tabular, Graphical, Descriptive/summary statistics, Other, Not applicable | |
| script | A resolvable URL or Synapse ID for a script used to perform the analysis. | False | STRING | https://w3id.org/reproduceme#Script | ManifestColumn | ||
| settings | A resolvable URL or Synapse ID for the settings under which the analysis was performed. | False | STRING | https://w3id.org/reproduceme#Setting | ManifestColumn | ||
| software | The name and version of software used to perform the analysis. | False | STRING | https://w3id.org/reproduceme#Software | ManifestColumn | ||
| workflowFormat | The format or workflow language used to represent the computational workflow. | False | STRING | http://edamontology.org/format_2032 | ManifestColumn | CWL, gxformat2, KNIME datatable format, MATLAB script, Perl script, Python script, R Markdown, R script, Taverna workflow format, Quarto, Snakemake, Nextflow, Bash script, Other, Not applicable | |
| 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, expression analysis, genetic variation analysis, image analysis, pathway analysis, phylogenetic analysis, protein function analysis, sequence analysis, spectral analysis, structure analysis, text mining, transmembrane protein analysis, Other, Not applicable | |
| dataTypeAll | 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 | 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 | |
| entityID | Synapse ID of the entity | False | STRING | Sage Bionetworks | |||
| hasAlgorithm | Whether an algorithm resource is supplied for the analysis. | False | BOOLEAN | Sage Bionetworks | ManifestColumn | FALSE, TRUE | |
| hasEnvironment | Whether computational-environment information is supplied. | False | BOOLEAN | Sage Bionetworks | ManifestColumn | FALSE, TRUE | |
| hasLibrary | Whether a software-library or package resource is supplied for the analysis. | False | BOOLEAN | Sage Bionetworks | ManifestColumn | FALSE, TRUE | |
| hasNotebook | Whether a computational notebook is supplied for the analysis. | False | BOOLEAN | Sage Bionetworks | ManifestColumn | FALSE, TRUE | |
| hasOperatingSystem | Whether operating-system information is supplied. | False | BOOLEAN | Sage Bionetworks | ManifestColumn | FALSE, TRUE | |
| hasParameters | Whether analysis parameters are supplied. | False | BOOLEAN | Sage Bionetworks | ManifestColumn | FALSE, TRUE | |
| hasProgrammingLanguage | Whether programming-language information is supplied. | False | BOOLEAN | Sage Bionetworks | ManifestColumn | FALSE, TRUE | |
| hasProtocol | Whether a protocol resource is supplied for the analysis. | False | BOOLEAN | Sage Bionetworks | ManifestColumn | FALSE, TRUE | |
| hasScript | Whether a script resource is supplied for the analysis. | False | BOOLEAN | Sage Bionetworks | ManifestColumn | FALSE, TRUE | |
| hasSettings | Whether settings information is supplied for the analysis. | False | BOOLEAN | Sage Bionetworks | ManifestColumn | FALSE, TRUE | |
| hasSoftware | Whether software information is supplied for the analysis. | False | BOOLEAN | Sage Bionetworks | ManifestColumn | FALSE, TRUE | |
| 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 |