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add template ARC
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README.md

MAdLand ARC Template

Thank you for creating an ARC for your MAdLand project! This document has some useful information to help you get started, including a checklist at the end.

Quickstart: Useful links

What are ARCs?

  • Annotated Research Context
  • Goal: share your research data with others (great to add to your paper!)
  • What goes in an ARC?
    • General information about the project (title, description, collaborators, papers)
    • Metadata
      • Sample sheet
      • Cultivation conditions, harvesting, …,
      • Metadata about the assays (e.g. sequencing)
      • Raw data of assays (sequencing, MassSpec, anything else you did)
      • Workflows (or code, scripts, commands used for analysis)
      • Analysis results
      • Basically, anything you mention that you did in your paper, should go in here :)

Publishing ARCs

There are 3 places that ARCs are currently published (all still under development by NFDI4Plants).

  1. ARChive
    • More formal publishing process
    • There is a review by DATAplant to check your ARC
    • You get a citable DOI for your ARC (e.g. to use in your publication)
    • Example published ARC here
  2. ARCSearch
    • Any public ARCs on GitLab that pass validation appear here
  3. ISASearch
    • Any public ARCs on GitLab that pass validation appear here

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How to define an ARC

  • Structure of an ARC
    • ISA structure
      • Investigation (project context) (e.g. your overarching research interest)
      • Study (unit of research) (e.g. one research question/paper)
      • Assay (measurement) (e.g. RNA-Seq, MS, metabolomics..)
    • Workflows (code, analysis)
    • Runs (outputs of code/analysis)
  • Each investigation can have multiple studies
  • Each study can have multiple assays (e.g. RNA-Seq, MS, ..
  • Metadata
    • Must follow a very specific structure and use specific ontologies
    • Templates exist (also MAdLand-specific templates)
    • SWATE Excel plugin to help you fill them in using correct ontology, saves a lot of time!

Creating your ARC

Warning: fill the spreadsheet using Excel. Editing them in e.g. OpenOffice on Linux corrupts them unfortunately :(

Checklist for your ARC

To fill your ARC, please perform the following tasks.

Example of a MAdLand ARC: Ppatens-light-signaling-2022 (Public GitLab Repo)

  1. Fill in the following metadata files using SWATE

    • MAdLand_sample_sheets.xlsx
    • MAdLand_bioanalyzer.xlsx
    • MAdLand_cultivation_conditions.xlsx
    • MAdLand_harvesting.xlsx
    • MAdLand_nanodrop.xlsx

  2. Investigation - isa.investigation.xlsx file

    • Add Title and Description, etc
    • Add all investigation contacts, one per column
      • Roles are optional, but must be one of the roles in the ScoRo ontology (e.g. technician, PI) if used
      • All must have an email address
      • Add ORCIDs for everyone who has one
    • Add any publications based on the data in this ARC.
      • Publication status must be from PSO ontology (e.g. “open access”)
    • Ignore the bottom half of this sheet for now (row 33+)

  3. Studies - studies/<study-id>/ information about your samples (do this for each study)

    • Make as many copies of the study folder as you need
      • change folder names to something informative (e.g. Ppatens)
    • Metadata: Fill in isa.study.xlsx in each study folder
      • Sheet 1 “Study”: Study Title, description, etc
      • Sheet 2 “study-id”: your sample sheet from step 1 (use SWATE to fill this!)
      • Sheet 3: Your Harvesting metadata file from step 1
      • Sheet 4: Your Culturing Conditions file from step 1
    • Protocols: in studies/<study-id>/protocols/ folder
      • Public MAdLand protocols are in there (remove any that are not relevant)
      • Add any other protocol documents relevant to your study
    • Resources: in studies/<study-id>/resources
      • Copy in any other documents related to your samples, lab notes, ..
      • Don’t have to follow a structure, just add anything that helps understand your samples and or lab work etc.

  4. Assays - assays/<assy-id>/ information about your measurements (do this for each assay)

    • Make as many copies of the assay folder as you need, give them informative names
    • Metadata: Fill in isa.assay.xlsx (do this for each assay)
      • Sheet 1 “Assay”: Fill in the main metadata sheet
      • Remaining sheets: depend on the assay (Saskia can prepare them for you), fill these in as best you can!
      • For RNASeq, Nanodrop and Bioanalyzer assays, see example ARC
    • Protocols: assays/<assay-id>/protocols/ folder,
      • Copy in anything related to how you performed the assay
      • E.g. Lab notes, documentation from the sequencing center, etc
      • Doesn’t have to follow any structure or ontology, just copy any files in
    • Datasets: assays/<assay-id>/protocols/ folder
      • Raw outputs of your assays (e.g. sequencing fastq files)
      • Make sure to use Git LFS for this (or just tell Saskia where to find the raw data)

  5. Workflows folder

    • Add any code, commands and/or workflows used in analysis in this folder
    • Preferably CWL workflows, but..
    • The code doesn't have to be pretty! if you used it, just add it! Even if it's just calling a bunch of standard tools

  6. Runs folder

    • Add any results from your analysis here
    • organize in folders as best you can)
    • Can be text files, tables, sequences, plots, …, anything generated from your raw data

  7. Misc: Do you have any other files or lab notes etc related to your work but not sure where to put them? Just put them in the root folder and Saskia will try to place them somewhere.