From abdc5eba7a8967a396fe15f5b2e9d3d2d3108c26 Mon Sep 17 00:00:00 2001 From: YvonneKallberg Date: Mon, 16 Dec 2024 12:16:25 +0100 Subject: [PATCH] Add draft genomics readme Add background and ENA experiment metadata fields --- genomics/README.md | 35 ++++++++++++++++++++++++++++++++++- 1 file changed, 34 insertions(+), 1 deletion(-) diff --git a/genomics/README.md b/genomics/README.md index 2751013..3fb94b0 100644 --- a/genomics/README.md +++ b/genomics/README.md @@ -1 +1,34 @@ -# TODO: put info about genomics template here. +# SciLifeLab Genomics Technical Metadata Template +The main recipient repositories for genomic data are [European Nucleotide Archive](https://www.ebi.ac.uk/ena/) (ENA) and [ArrayExpress](https://www.ebi.ac.uk/biostudies/arrayexpress). Note that the nucleotide sequencing data submitted to ArrayExpress is forwarded (by them via brokering) to ENA. + +For this purpose data type specific templates will be created, aiming to capture technical metadata for genomics data produced at the Genomics platform, compatible with submission requirements from ENA and ArrayExpress. + +Within a template each template field needs to have: +- Field name +- Level of requirement/cardinality (mandatory vs optional) +- Description +- List of controlled vocabulary terms if applicable + +## ENA experiment metadata + +| Field name | Cardinality | Description | Controlled vocabulary | +|:------------------------------|:--------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| (study_alias) | mandatory | (from study metadata, provided by submitter) Identifies the parent study. | | +| (sample_alias) | mandatory | (from sample metadata, provided by submitter) Identifies the sample the experiment is linked to. | | +| name | mandatory | Name or title of the experiment, short text that can be used to call out experiment records in searches or in displays. | | +| design_description | optional | Goal and setup of the individual library including how library was constructed. (either this or the field library_construction_protocol should be populated) | | +| library_construction_protocol | optional | Free form text describing the protocol by which the sequencing library was constructed. (either this or the field design_description should be populated) | | +| library_name | optional | The submitter's name for this library. | | +| library_strategy | mandatory | Sequencing technique intended for this library. | WGS, WGA, WXS, RNA-Seq, ssRNA-seq, snRNA-seq, miRNA-Seq, ncRNA-Seq, FL-cDNA, EST, Hi-C, ATAC-seq, WCS, RAD-Seq, CLONE, POOLCLONE, AMPLICON, CLONEEND, FINISHING, ChIP-Seq, MNase-Seq, DNase-Hypersensitivity, Bisulfite-Seq, CTS, MRE-Seq, MeDIP-Seq, MBD-Seq, Tn-Seq, VALIDATION, FAIRE-seq, SELEX, RIP-Seq, ChIA-PET, Synthetic-Long-Read, Targeted-Capture, Tethered Chromatin Conformation Capture, NOMe-Seq, ChM-Seq, GBS, Ribo-Seq, OTHER | +| library_source | mandatory | The library_source specifies the type of source material that is being sequenced. | GENOMIC, GENOMIC SINGLE CELL, TRANSCRIPTOMIC, TRANSCRIPTOMIC SINGLE CELL, METAGENOMIC, METATRANSCRIPTOMIC, SYNTHETIC, VIRAL RNA, OTHER | +| library_selection | mandatory | Method used to enrich the target in the sequence library preparation. | RANDOM, PCR, RANDOM PCR, RT-PCR, HMPR, MF, repeat fractionation, size fractionation, MSLL, cDNA, cDNA_randomPriming, cDNA_oligo_dT, PolyA, Oligo-dT, Inverse rRNA, Inverse rRNA selection, ChIP, ChIP-Seq, MNase, DNase, Hybrid Selection, Reduced Representation, Restriction Digest, 5-methylcytidine antibody, MBD2 protein methyl-CpG binding domain, CAGE, RACE, MDA, padlock probes capture method, other, unspecified | +| library_layout | optional | Library_layout specifies whether to expect single, paired, or other configuration of reads. | SINGLE, PAIRED, Other | +| insert_size | optional | Insert size for paired reads. | | +| instrument_model | mandatory | Model of the sequencing instrument. | 454 GS, 454 GS 20, 454 GS FLX, 454 GS FLX Titanium, 454 GS FLX+, 454 GS Junior, AB 310 Genetic Analyzer, AB 3130 Genetic Analyzer, AB 3130xL Genetic Analyzer, AB 3500 Genetic Analyzer, AB 3500xL Genetic Analyzer, AB 3730 Genetic Analyzer, AB 3730xL Genetic Analyzer, AB 5500 Genetic Analyzer, AB 5500xl Genetic Analyzer, AB 5500xl-W Genetic Analysis System, AB SOLiD 3 Plus System, AB SOLiD 4 System, AB SOLiD 4hq System, AB SOLiD PI System, AB SOLiD System, AB SOLiD System 2.0, AB SOLiD System 3.0, BGISEQ-50, BGISEQ-500, Complete Genomics, DNBSEQ-G400, DNBSEQ-G400 FAST, DNBSEQ-G50, DNBSEQ-T7, Element AVITI, FASTASeq 300, GENIUS, GS111, Genapsys Sequencer, GenoCare 1600, GenoLab M, GridION, Helicos HeliScope, HiSeq X Five, HiSeq X Ten, Illumina Genome Analyzer, Illumina Genome Analyzer II, Illumina Genome Analyzer IIx, Illumina HiScanSQ, Illumina HiSeq 1000, Illumina HiSeq 1500, Illumina HiSeq 2000, Illumina HiSeq 2500, Illumina HiSeq 3000, Illumina HiSeq 4000, Illumina HiSeq X, Illumina MiSeq, Illumina MiniSeq, Illumina NovaSeq 6000, Illumina NovaSeq X, Illumina iSeq 100, Ion GeneStudio S5, Ion GeneStudio S5 Plus, Ion GeneStudio S5 Prime, Ion Torrent Genexus, Ion Torrent PGM, Ion Torrent Proton, Ion Torrent S5, Ion Torrent S5 XL, MGISEQ-2000RS, MinION, NextSeq 1000, NextSeq 2000, NextSeq 500, NextSeq 550, Onso, PacBio RS, PacBio RS II, PromethION, Revio, Sentosa SQ301, Sequel, Sequel II, Sequel IIe, Tapestri, UG 100, unspecified | +| file_name | mandatory | The name or relative pathname of a run data file. The field is used for all file types except paired fastq files. | | +| file_md5 | mandatory | The MD5 checksum of the file. This field is mandatory if submitter do not use the Webin File Uploader or upload the checksum using a .md5 file. The field is used for all file types except paired fastq files. | | +| forward_file_name | mandatory | The name or relative pathname of forward run data file. The field is only used for paired fastq files. | | +| forward_file_md5 | mandatory | The MD5 checksum of the file. This field is mandatory if submitter do not use the Webin File Uploader or upload the checksum using a .md5 file. The field is only used for paired fastq files. | | +| reverse_file_name | mandatory | The name or relative pathname of reverse run data file. The field is only used for paired fastq files. | | +| reverse_file_md5 | mandatory | The MD5 checksum of the reverse file. This field is mandatory if submitter do not use the Webin File Uploader or upload the checksum using a .md5 file. The field is only used for paired fastq files. | | +| file_format | mandatory | Format of the sequence file(s). | bam, cram, fastq, PacBio_HDF5, OxfordNanopore_native | \ No newline at end of file