bhg2023-omero-arc

https://github.com/nfdi4bioimage/bhg2023-omero-arc

Science Score: 67.0%

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Links to: zenodo.org
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Last synced: 6 months ago · JSON representation ·

Repository

Basic Info

Host: GitHub
Owner: NFDI4BIOIMAGE
License: cc-by-4.0
Language: Python
Default Branch: main
Size: 5.26 MB

Statistics

Stars: 0
Watchers: 6
Forks: 4
Open Issues: 0
Releases: 0

Created about 2 years ago · Last pushed about 2 years ago

Metadata Files

Readme Contributing License Citation Zenodo

👋 BHG2023-OMERO-ARC

🚧 Under construction. 🚧

This repository is still growing.
For some preparatory work for this topic from another hackathon, please see this repository or the respective publication at Zenodo.

Repository for documentation during the 2nd de.NBI BioHackathon Germany - 11.-15.12.2023 - OMERO-ARC project (in short: BHG2023-OMERO-ARC)

Code of Conduct

Please also adhere here to the ELIXIR Germany Code of Conduct.

Task_Groups

Initially prepared and suggested based on defined task of participants.

Branch protection

The main branch is protected. For merging a branch into main you need a PR with at least one approving review.
@andreaschrader only initially bypasses this in order to set up the repository for the participants for the Hackathon.

.gitignore

currently selected: Visual Studio
Prep_stage/
- You can create this directroy inside your cloned BHG2023-OMERO-ARC repo and use it when you want to prepare files or place data in this repo locally but do not want to push these to this repo.

Overview of the content in this repository

. ├── .zenodo.json ├── CITATION.cff ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── Reporting │ ├── BioHack_2023_Final_OMERO_ARC.pdf │ └── BioHack_2023_Intro_OMERO_ARC.pdf ├── Task_Groups │ ├── 01_Roadmap │ │ ├── README.md │ │ └── arc-omero-roundtrip-proposal.md │ ├── 02_Use_Cases │ │ └── README.md │ ├── 03_RDMcompliant_Metadata │ │ ├── IDRtemplates-2-ARC │ │ ├── IDRtemplates-2-ARC.md │ │ ├── README.md │ │ ├── REMBI-2-ARC │ │ ├── REMBI-2-ARC.md │ │ ├── REMBI_Templates │ │ │ └── RGC_Ca2+_imaging.csv │ │ └── REMBI_Templates.md │ ├── 04_Metadata_Transfer │ │ └── README.md │ ├── 05_OMERO-2-ARC │ │ └── README.md │ ├── 06_ARC-2-OMERO │ │ ├── README.md │ │ ├── metadata_filler.py │ │ ├── requirements.txt │ │ ├── transfer.xml │ │ └── workflow.sh │ ├── 07_Test_Tools │ │ ├── README.md │ │ ├── omero-cli-transfer-arc-installation.md │ │ └── omero-cli-transfer-arc-report.md │ ├── 08_Teaching_Material │ │ └── README.md │ ├── 09_Documentation │ │ └── README.md │ └── README.md └── images └── rat-brain-ls.png 21-01-2024 (created using tree v2.1.1 © 1996 - 2023 by Steve Baker, Thomas Moore, Francesc Rocher, Florian Sesser, Kyosuke Tokoro)

Contributions

Notes on contributions during the Hackathon are here.

🙌 Thank you for any contribution to the BHG2023-OMERO-ARC repository!!!

When contributing, please consider that (parts of) this repository might be used by people with various background and intentions including teaching in the future. Therefore, it is appreciated if you can provide a brief non-specialist targeted introduction / summary preceding your content and work on Hackathon tasks.

Contributors

🤝 Participants contributing to the BHG2023-OMERO-ARC project can provide their name, GitHub handle, ORCID iD and ROR here - if you like.

Suggestion: alphabetical order (surname):

|name|GitHub|ORCID|ROR|
|---|---|---|---|
|Mohamed Abdrabbou|@MM-abdrabbou | https://orcid.org/0000-0003-2778-7483| |Michele Bortolomeazzi|@MicheleBortol|https://orcid.org/0000-0001-5805-5774|| |Jean-Marie Burel|@jburel|https://orcid.org/0000-0002-1789-1861|https://ror.org/03h2bxq36| |Niraj Kandpal|@Nirkan|https://orcid.org/0009-0007-5101-4786|https://ror.org/00rcxh774
https://ror.org/04c4bwh63| |Josh Moore|@joshmoore|https://orcid.org/0000-0003-4028-811X|https://ror.org/05tpnw772| |Andrea Schrader|@andreaschrader|https://orcid.org/0000-0002-3879-7057|https://ror.org/034waa237
https://ror.org/00rcxh774| |Peter Zentis|@pzentis|https://orcid.org/0000-0002-6999-132X|https://ror.org/00rcxh774
https://ror.org/04c4bwh63 |

Acknowledgement

🚧 Under construction. 🚧

To be filled after the Hackathon.

Funding enabling project leads organization and Hackathon participation

DataPLANT and NFDI4BIOIMAGE

We acknowledge the support of DataPLANT and NFDI4BIOIMAGE, both funded by the German Research Foundation (DFG) within the framework of the NFDI – project numbers: 442077441 and 501864659.

Other Organisations

CEPLAS

Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) within Germany’s Excellence Strategy – EXC-2048/1 – project number 390686111.

CECAD

Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy - EXC 2030 - 390661388.

CRC TRR341

Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – Project-ID 456082119.

Owner

Name: NFDI4BioImage
Login: NFDI4BIOIMAGE
Kind: organization

Website: https://nfdi4bioimage.de/
Twitter: nfdi4bioimage
Repositories: 1
Profile: https://github.com/NFDI4BIOIMAGE

Research Data Management for Microscopy and BioImage Analysis

Citation (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

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Dependencies

Task_Groups/06_ARC-2-OMERO/requirements.txt pypi

argparse ==1.4.0
ome-types ==0.4.2
omero-cli-transfer ==0.8.0
omero-py ==5.13.1
pandas ==2.1.4

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