CITATION.cff

cff-version: 1.2.0
message: "If you use content of this repository, please cite it using these metadata. Authors are in alphabetical order!"
repository: "https://github.com/NFDI4BIOIMAGE/BHG2023-OMERO-ARC"
authors:
  - affiliation: Department of Biology/Chemistry and Center for Cellular Nanoanalytics, University Osnabrück, Germany
    alias: MM-abdrabbou
    city: Osnabrück
    country: DE
    family-names: Abdrabbou
    given-names: Mohamed M.
    orcid: "https://orcid.org/0000-0003-2778-7483"
  - affiliation: Center for Advanced Imaging, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany 
    alias: Tom-TBT
    city: Düsseldorf
    country: DE
    family-names: Boissonnet
    given-names: Tom
    orcid: "https://orcid.org/0000-0002-3328-9467"
  - affiliation: Single-cell Open Lab, German Cancer Research Center (DKFZ), Heidelberg, Germany
    alias: MicheleBortol 
    city: Heidelberg
    country: DE
    family-names: Bortolomeazzi
    given-names: Michele
    orcid: "https://orcid.org/0000-0001-5805-5774"
  - affiliation: Divisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK
    alias: jburel 
    city: Dundee
    country: UK
    family-names: Burel
    given-names: Jean-Marie
    orcid: "https://orcid.org/0000-0002-1789-1861"
  - affiliation: Regional Computer Center (RRZK), University of Cologne, Cologne, Germany
    alias: eik-dahms
    city: Cologne
    country: DE
    family-names: Dahms
    given-names: Eik
    orcid: "https://orcid.org/0000-0002-7452-1146"
  - affiliation: Imaging Platform & Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
    city: Cologne
    country: DE
    family-names: Kakanj
    given-names: Parisa
  - affiliation: Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
    alias: Nirkan
    city: Cologne
    country: DE
    family-names: Kandpal
    given-names: Niraj
    orcid: "https://orcid.org/0009-0007-5101-4786"
  - affiliation: The Jackson Laboratory, Farmington, CT, USA
    alias: erickmartins
    city: Farmington
    country: USA
    family-names: Martins Ratamero
    given-names: Erick
    orcid: "https://orcid.org/0000-0002-7545-3675"
  - affiliation: Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
    alias: cmohl2013
    city: Bonn
    country: DE
    family-names: Möhl
    given-names: Christoph
    orcid: "https://orcid.org/0000-0002-0829-5101"
  - affiliation: German BioImaging—Society for Microscopy and Image Analysis e.V., Constance, Germany
    alias: joshmoore
    city: Constance 
    country: DE
    family-names: Moore
    given-names: Joshua A.
    orcid: "https://orcid.org/0000-0003-4028-811X"
  - affiliation: Computational Systems Biology, University of Kaiserslautern-Landau, Kaiserslautern, Germany
    alias: muehlhaus
    city: Kaiserslautern
    country: DE
    family-names: Mühlhaus
    given-names: Timo
    orcid: "https://orcid.org/0000-0003-3925-6778"
  - affiliation: Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
    alias: AstridSchauss
    city: Cologne
    country: DE
    family-names: Schauss
    given-names: Astrid
    orcid: "https://orcid.org/0000-0002-6658-2192"
  - affiliation: Computational Systems Biology, University of Kaiserslautern-Landau, Kaiserslautern, Germany
    alias: kMutagene 
    city: Kaiserslautern 
    country: DE
    family-names: Schneider
    given-names: Kevin
    orcid: "https://orcid.org/0000-0002-2198-5262" 
  - affiliation: Data Science and Management & Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
    alias: andreaschrader
    city: Cologne
    country: DE
    family-names: Schrader
    given-names: Andrea
    orcid: "https://orcid.org/0000-0002-3879-7057"
  - affiliation: Leibniz Institute for Neurobiology (LIN), Magdeburg, Germany
    alias: tstoeter
    city: Magdeburg
    country: DE
    family-names: Stöter 
    given-names: Torsten
  - affiliation: Regional Computer Center (RRZK), University of Cologne, Cologne, Germany
    alias: mvals
    city: Cologne
    country: DE
    family-names: Valencia-Schneider 
    given-names:  Monica E.
    orcid: "https://orcid.org/0000-0003-3430-2683"
  - affiliation: Computational Systems Biology, University of Kaiserslautern-Landau, Kaiserslautern, Germany
    alias: HLWeil
    city: Kaiserslautern 
    country: DE
    family-names: Weil
    given-names: H. Lukas
    orcid: "https://orcid.org/0000-0003-1945-6342"
  - affiliation: Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
    alias: pzentis
    city: Cologne
    country: DE
    family-names: Zentis
    given-names: Peter
    orcid: "https://orcid.org/0000-0002-6999-132X"
date-released: "2023-12-07"
keywords:
  - OMERO
  - ARC
  - REMBI
  - metadata
  - use cases
  - multimodal data
  - hackathon
  - NFDI4Bioimage
  - DataPLANT
  - CECAD
  - CEPLAS
  - CRC-TRR341
license: CC-BY-4.0
title: BHG2023-OMERO-ARC (2nd e.NBI BioHackathon Germany project, repository)
version: 0.9.0
references:
  - authors:
      - family-names: Allen
        given-names: Chris
      - family-names: Burel
        given-names: Jean-Marie
      - family-names: Moore
        given-names: Joshua A.
      - family-names: Blackburn
        given-names: Colin
      - family-names: Linkert
        given-names: Melissa
      - family-names: Loynton
        given-names: Scott
      - family-names: MacDonald
        given-names: Donald
      - family-names: Moore
        given-names: William J.
      - family-names: Neves
        given-names: Carlos
      - family-names: Patterson
        given-names: Andrew
      - family-names: Porter
        given-names: Michael
      - family-names: Tarkowska
        given-names: Aleksandra
      - family-names: Loranger
        given-names: Brian
      - family-names: Avondo
        given-names: Jerome
      - family-names: Lagerstedt
        given-names: Ingvar
      - family-names: Lianas
        given-names: Luca
      - family-names: Leo
        given-names: Simone
      - family-names: Hands
        given-names: Katherine
      - family-names: Hay
        given-names: Ron T.
      - family-names: Patwardhan
        given-names: Ardan
      - family-names: Best
        given-names: Christoph
      - family-names: Kleywegt
        given-names: Gerard J.
      - family-names: Zanetti
        given-names: Gianluigi
      - family-names: Swedlow
        given-names: Jason R.
    date-published: "2012-02-28"
    doi: 10.1038/nmeth.1896
    end: 253
    issue: 3
    journal: Nature Methods
    scope: "A reference for OMERO - model-driven data management for experimental biology."
    start: 245
    title: "OMERO: flexible, model-driven data management for experimental biology"
    type: article
    url: "https://doi.org/10.1038/nmeth.1896"
    volume: 9  
  - authors:
      - family-names: Baker
        given-names: Steve
      - name: "tree contributors"
    date-accessed: "2023-12-07"
    license: GPL-2.0
    repository: "https://github.com/Old-Man-Programmer/tree"
    scope: "Used to create the file tree in the README provided as an overview of the repository."
    title: tree
    type: software
    url: "https://oldmanprogrammer.net/source.php?dir=projects/tree"
    version: v2.1.1
    year: 2023
  - authors:
      - name: "DataPLANT community"
    date-accessed: "2023-11-38"
    license: CC-BY-4.0
    repository: "https://github.com/nfdi4plants/ARC-specification"
    scope: "The ARC specification underlying the conceptual discussions and setup towards OMERO-ARC interoperability."
    title: "nfdi4plants/ARC-specification: 1.2"
    type: software
    url: "https://doi.org/10.5281/zenodo.10091038"
    version: v1.2
    year: 2023
  - authors:
      - family-names: Frey
        given-names: Kevin
      - name: "Swate contributors"
    license: MIT
    repository: "https://github.com/nfdi4plants/Swate"
    scope: "Used for annotating an imaging experiment with respective ontologies."
    title: "Swate v0.6.2 (GitHub repository)"
    type: software
    version: v0.6.2
    year: 2022
  - authors:
      - family-names: Martins Ratamero
        given-names: Erick
      - family-names: Burel
        given-names: Jean-Marie
      - family-names: Sobolewski
        given-names: Peter
      - family-names: Moore
        given-names: William J.
    doi: 10.5281/zenodo.8383499
    license: GPL-2.0
    repository: "https://github.com/ome/omero-cli-transfer"
    scope: "omero-cli-transfer is used in OMERO_ARC interoperability which was mainly covered here in a conceptual way in the interoperability topic and also by the OMERO-ARC plugin of C. Möhl for the omero-cli-transfer."
    title: "ome/omero-cli-transfer: 0.8.0 - new `--simple` option in `pack` (0.8.0)"
    type: software
    url: https://doi.org/10.5281/zenodo.8383499
    version: v0.8.0
    year: 2023
  - authors:
      - family-names: Möhl
        given-names: Christoph
    license: GPL-3.0
    repository: "https://github.com/cmohl2013/omero-arc"
    scope: "Plugin for omero-cli-transfer for OMERO-ARC export."
    title: "OMERO-ARC Plugin (GitHub repository)"
    type: software
    version: v0.0.1
    year: 2023
  - authors:
      - affiliation: Oxford e-Research Centre, University of Oxford, UK
        family-names: Sansone
        given-names: Susanna-Assunta
      - affiliation: Oxford e-Research Centre, University of Oxford, UK
        family-names: Rocca-Serra
        given-names: Philippe
      - affiliation: Oxford e-Research Centre, University of Oxford, UK
        family-names: Gonzalez-Beltran
        given-names: Alejandra
      - affiliation: Oxford e-Research Centre, University of Oxford, UK
        family-names: Johnson
        given-names: David
      - name: ISA Community
    date-released: "2016-10-28"
    doi: 10.5281/zenodo.163640
    license: CC-BY-4.0
    publisher: Zenodo
    repository: "https://github.com/ISA-tools/isa-specs"
    scope: "ARC metadata is based on the isa model which also needs to be considered in OMERO-ARC interoperability."
    title: ISA Model and Serialization Specifications 1.0 
    type: technical note
    version: 1.0
    year: 2016
  - authors:
      - family-names: Sarkans
        given-names: Ugis
      - family-names: Chiu
        given-names: Wah
      - family-names: Collinson
        given-names: Lucy
      - family-names: Darrow
        given-names: Michele C.
      - family-names: Ellenberg
        given-names: Jan
      - family-names: Grunwald
        given-names: David
      - family-names: Hériché
        given-names: Jean-Karim
      - family-names: Iudin
        given-names: Andrii
      - family-names: Martins
        given-names: Gabriel G.
      - family-names: Meehan
        given-names: Terry
      - family-names: Narayan
        given-names: Kedar
      - family-names: Patwardhan
        given-names: Ardan
      - family-names: Russell
        given-names: Matthew Robert Geoffrey
      - family-names: Saibil
        given-names: Helen R.
      - family-names: Strambio-De-Castillia
        given-names: Caterina
      - family-names: Swedlow
        given-names: Jason R.
      - family-names: Tischer
        given-names: Christian
      - family-names: Uhlmann
        given-names: Virginie
      - family-names: Verkade
        given-names: Paul
      - family-names: Barlow
        given-names: Mary
      - family-names: Bayraktar
        given-names: Omer
      - family-names: Birney
        given-names: Ewan
      - family-names: Catavitello
        given-names: Cesare
      - family-names: Cawthorne
        given-names: Christopher
      - family-names: Wagner-Conrad
        given-names: Stephan
      - family-names: Duke
        given-names: Elizabeth
      - family-names: Paul-Gilloteaux
        given-names: Perrine
      - family-names: Gustin
        given-names: Emmanuel
      - family-names: Harkiolaki
        given-names: Maria
      - family-names: Kankaanpää
        given-names: Pasi
      - family-names: Lemberger
        given-names: Thomas
      - family-names: McEntyre
        given-names: Jo
      - family-names: Moore
        given-names: Josh
      - family-names: Nicholls
        given-names: Andrew W.
      - family-names: Onami
        given-names: Shuichi
      - family-names: Parkinson
        given-names: Helen
      - family-names: Parsons
        given-names: Maddy
      - family-names: Romanchikova
        given-names: Marina
      - family-names: Sofroniew
        given-names: Nicholas
      - family-names: Swoger
        given-names: Jim
      - family-names: Utz
        given-names: Nadine
      - family-names: Voortman
        given-names: Lenard M.
      - family-names: Wong
        given-names: Frances
      - family-names: Zhang
        given-names: Peijun
      - family-names: Kleywegt
        given-names: Gerard J.
      - family-names: Brazma
        given-names: Alvis
    date-published: "2021-05-21"
    doi: 10.1038/s41592
    end: 1422
    issue: 12
    journal: Nature Methods
    scope: "Used for the 'REMBI - Mapping' part. Templates from CAi were based on this publication as well as filling one of these templates on site and conceptual discussions on mapping touched the publication's content."
    start: 1418
    title: "REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology"
    type: article
    url: "https://doi.org/10.1038/s41592-021-01166-8"
    volume: 18
    year: 2021
  - authors:
      - affiliation: Computational Systems Biology, University of Kaiserslautern-Landau, Kaiserslautern, Germany
        alias: HLWeil
        city: Kaiserslautern 
        country: DE
        family-names: Weil
        given-names: H. Lukas
        orcid: "https://orcid.org/0000-0003-1945-6342"
      - name: "ARC Commander contributors"
    license: MIT
    repository: "https://github.com/nfdi4plants/arcCommander"
    scope: "Used for creating ARCs by the OMERO-ARC export plugin and exemplary ARCs created prior to this and subsequent OMERO-ARC interoperability work."
    title: ARC Commander (GitHub repository)
    type: software
    version: v0.5.0
    year: 2023