Add 'Archive' or 'Software archive' as new link type

[hansioan]

@matuskalas @hmenager @bio-tools/core-dev

We got a message from Dr. Pierre Poulain requesting to add a new link type of Archive or Software archive
What do you think?

I would like to know if you would agree to add a new link type, regarding the "Links" tab in the bio.tool registry.

As for now, link type could be:

• Discussion forum
• Galaxy service
• Helpdesk
• Issue tracker
• Mailing list
• Mirror
• Repository
• Service
• Social media
• Software catalogue
• Technical monitoring
• Other

Given the ability to archive software source code in general repositories such as Zenodo or figshare or specialized one such as Software Heritage, it might be interesting to add a link type reflecting the archiving of software source code, for instance "Archive" or "Software archive".

(Long-term) source code archiving looks important to insure reproducibility but also permanent availability of the source code of research software.

My opinion is that there is a use case for this, but we have to be careful since we also have Download type of Software package and Source code.
The other question is should it be a link type or a download type?

[jvanheld]

Hi Hans Thanks for putting me in the loop. I have no specific preference as to the archives should be documented as a Software package, Source code or a new type of link named "Archive". Pierre Poulain is a very active and efficient colleague, I am really glad to see him involved in EDAM ! Cheers Jacques Aix-Marseille Université (AMU). Lab. Theory and Approaches of Genomic Complexity (TAGC) INSERM Unit UMR_S 1090, 163, Avenue de Luminy, 13288 MARSEILLE cedex 09. France Office: INSERM building, block 6 Fax: +33 4 91 82 87 01 ***@***.*** https://orcid.org/0000-0002-8799-8584

…

On 16 Jun 2021, at 10:53, Hans Ienasescu ***@***.***> wrote: @matuskalas <https://github.com/matuskalas> @hmenager <https://github.com/hmenager> @bio-tools/core-dev <https://github.com/orgs/bio-tools/teams/core-dev> We got a message from Dr. Pierre Poulain <https://orcid.org/0000-0003-4177-3619> requesting to add a new link type of Archive or Software archive What do you think? I would like to know if you would agree to add a new link type, regarding the "Links" tab in the bio.tool registry. As for now, link type could be: Discussion forum Galaxy service Helpdesk Issue tracker Mailing list Mirror Repository Service Social media Software catalogue Technical monitoring Other Given the ability to archive software source code in general repositories such as Zenodo or figshare or specialized one such as Software Heritage, it might be interesting to add a link type reflecting the archiving of software source code, for instance "Archive" or "Software archive". (Long-term) source code archiving looks important to insure reproducibility but also permanent availability of the source code of research software. My opinion is that there is a use case for this, but we have to be careful since we also have Download type of Software package and Source code. The other question is should it be a link type or a download type? — You are receiving this because you are on a team that was mentioned. Reply to this email directly, view it on GitHub <#203>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACT3M2XMYFIMYU6WP5DTAEDTTBRA7ANCNFSM46Y6XTJQ>.

[pierrepo]

Dear all,

@hansioan, thank you very much for putting my request into this issue.
@jvanheld, thank you for your kind introduction 😉

For full transparency, I would like to say I'm a Software Heritage archive ambassador.

I'm also an associate professor in bioinformatics. As a researcher, I develop software and tools for computational biology. I really appreciate the bio.tools registry. I have a lot of concerns however regarding reproducibility and long-term archiving of the source code of software in bioinformatics. This is the reason why I contacted bio.tools support / @hansioan

Regarding the Link vs Download type, AFAIK, all archive repositories allow to download a zip file containing the source code. In the Download section, I see the Software package type useful to point toward package repositories such as PyPI, CRAN or anaconda/bioconda. I personally use the Source code type to indicate the source code repository (GitHub, GitLab). In conclusion, maybe a Source code archive type within the Download section would be more appropriate in this case.

[matuskalas]

I think Software archive or Source code archive would make a lot of sense. And yes, it could be a Link or Download.

And I'd strongly suggest renaming Repository (Link) to Source code repository for disambiguation.

However, for storing DOIs such as the Zenodo ones, I think Publication is a much better property than just a Link or Download.

It can also be scripted in CI so that whenever a DOI is recorded as a Link, it will be moved to Publication. And if a repo is recorded as Source code (Download), it should be moved to Source code repository (Link).

What other highly useful links to archives do you have in mind @pierrepo?

[pierrepo]

Hello @matuskalas

However, for storing DOIs such as the Zenodo ones, I think Publication is a much better property than just a Link or Download.

I think that could be confusing for users. The DOI provided by Zenodo is an identifier commonly used for papers but that, in this case, does not point to a paper. Instead, Zenodo DOI, when used for software archiving, usually points to a software type record that contains a zip file that itself contains the source code.

Software Heritage, however, does not provide a DOI. It provides instead a permanent intrinsic identifier called SWHID.