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osmose-model / osmose-web-api

Web service that generates Osmose configuration files from data sources like Fishbase and SeaLifeBase. Used by https://www.config.osmose-model.org .
MIT License
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prepare and publish fishbase/sealifebase archives so that they can be cited #186

Closed jhpoelen closed 5 years ago

jhpoelen commented 5 years ago

Currently, the osmose-web-api uses fishbase/sealifebase archives made available at https://github.com/jhpoelen/fishbase_archiver . In order to make these archives citable in our upcoming paper, I would suggest to take the following steps.

Suggested steps:

  1. create a new repository called "fishbase-archive" or "fishbase-sealifebase-archive". If there's no organization associated with fishbase/sealifebase on github, I'd suggest to create one.
  2. add a short description for the repository.
  3. add a README.md with a description of what the archives contain and how they are produced (e.g., using fishbase_archiver)
  4. add a LICENSE file . Many organization now use CC0 while others use CC-BY or CC-BY-NC .
  5. enable the Zenodo-GitHub integration for the repository
  6. for each existing releases on https://github.com/jhpoelen/fishbase_archiver, download the files and README, commit the files to the new repository and create a release. So, this would be
  7. (optional) After creating each (patch) release, add the DOIs to the pre-existing releases on fishbase_archiver to indicate that a permanent record of the archives exist elsewhere.
  8. after all the releases have been published to Zenodo, share the DOI with Arnaud so that the archives can be cited.
FIN-casey commented 5 years ago

Hello @jhpoelen, CC: @FIN-JBarile

I would like to clarify step 6. Based on our understanding, we need integrate the fishbase_archiver to Zenodo then add somewhere on the Readme file the DOI for it together with the DOI of the current repository of the archiver. If that is what you expect, I cannot integrate it to Zenodo because I don't have enough access credentials. If not, kindly clarify it. Also, kindly check if what I did will suffice the need for the new repository. Thanks!

Hello @agruss2,

Sharing with you the DOI for the new fishbase-sealifebase-archiver DOI. DOI

jhpoelen commented 5 years ago

Hi @FIN-casey - I've seen that you've copied over the artifacts from the github releases on https://github.com/osmose-model/fishbase-sealifebase-archiver. As you probably noticed, Zenodo does not archive binaries attached to a release. Zenodo does archive files committed to the repository itself. This is why https://zenodo.org/record/1418646#.W5vESmCZ2is only contains a readme, license and the table_names.tsv .

Suggested is to:

  1. commit the binaries the repository, not as binaries to the release pages.
  2. once the binaries for a specific release on fishbase_archiver have been commited, create a release with a description detailing how and when the files were generated and what changed.
  3. after creating the release, confirm that zenodo contains the readme, license, table_names.tsv and all associated table .

Please note that the LICENSE file is currently an MIT license, while I understand that you'd like to use some creative commons license. Creative commons licenses are often used with data.

Without completing the steps outline above, the valuable fishbase / sealifebase archives are not archived to Zenodo.

Please let me know if you have any questions.

jhpoelen commented 5 years ago

Also, I would strongly suggest to claim the fishbase github organization and create the archives in there. The archives are not specific to osmose and making them part of the fishbase organization would emphasize this.

QQ-Sortiz commented 5 years ago

Hello @jhpoelen, CC:@Dengaloo @FIN-JBarile

I added a new folder tables on the github repository so that the data files can now be included when cited to Zenodo. Thanks!

FIN-JBarile commented 5 years ago

Hi,

Please see https://github.com/FiN-FBSLB/fishbase-sealifebase-archive

@agruss2

jhpoelen commented 5 years ago

This looks great!

Minor comment is to to add a LICENSE file with the CC-BY-NC terms (see https://github.com/FiN-FBSLB/fishbase-sealifebase-archive/issues/1) . This way, github and others can easily be made a aware of the license terms.

agruss2 commented 5 years ago

@QQ-Sortiz (CC: @FIN-JBarile @jhpoelen ) I am closing this issue, since the only comment that remains to be addressed can also be found here: FiN-FBSLB/fishbase-sealifebase-archive#1 Many thanks for everything!