3 | 1.3.1 & 1.3.2 | Support software metadata | 5

[sync-by-unito]

References:

• Planning Board

Problem Statement
Code and documentation to support software metadata

Proposed Solution
Implement an MVP solution

Acceptance Criteria

• Determine what parts of Codemeta and RO Crate that are not implemented,
• Design and implement codemeta and RO Crate,
• Test and document RO Crate.

List of issues includes...

• 7844 codemeta schema dataverse#7877
• Feature Request/Idea: Add Computational Workflow Metadata and Related Docs dataverse#8639
• Feature Request/Idea: File type recognition based on filename dataverse#8740
• Feature Request/Idea: File type recognition based on filename dataverse#8740
• File Recognition - Add support for files without extensions dataverse#8744
• Feature Request/Idea: File type recognition - Add computational workflow file types dataverse#8759
• Feature Request/Idea: Improve ignored files for BagIt handler dataverse#8754
• BagIt Support - Improve error messages for BagIt handler dataverse#8792
• Added Computational Workflow metadata and related documentation dataverse#8812
• Added new static facet to show metadata blocks with values dataverse#8793
• BagIt Support - Improved ignored files for BagIt handler dataverse#8755
• File Recognition - Added computational workflow file types dataverse#8761
• Feature Request/Idea: Improve error messages for BagIt handler dataverse#8787

See comments for monthly updates.

---

┆Issue is synchronized with this Smartsheet row by Unito

[mreekie]

This issue represents a deliverable funded by the NIH
This deliverable supports the NIH Initiative to Improve Access to NIH-funded Data

Aim 3: Support standards for sharing code, workflows, and containers

The Harvard Dataverse currently supports depositing any type of file, including code/software and documentation files that accompany data, or files within a research replication package. In this project, we plan to facilitate researchers’ efforts to share and publish their entire workflows or containers that describe the main transformations and analysis of the data, following the FAIR (Findable, Accessible, Interoperable, and Reusable) principles. As a result, the research findings will be portable and reproducible (ideally) with a single command. Though the services will be available to any researcher, special attention will be given to the NIH-funded work. The Dataverse project has already undertaken the development of Codemeta metadata (based on the standard schema.org) within the software. The project will assess the use of Codemeta for research software code and incorporate RO-Crate (for research objects metadata), which allows high flexibility in replication package content. Further, we will explore container metadata and the use of standardized container images for research. Containerization services, including software security scanning, exist for the Harvard Medical School (HMS) O2 high performance computing cluster, are in use by a number of laboratories, and are being developed by BioGrids, a HMS partner that specializes in creating replicable biomedical software packages and containers. As part of this project, we will explore the integration of these containerization services with the Harvard Dataverse repository to support sharing, discovery, and archival of replicable biomedical research.

1.3.1 | 3 | Support software metadata | 5
1.3.2 | 3 | Research and discovery phase for biomedical workflows support | 5
2.3.1 | 3 | Support biomedical workflows | 5
2.3.2 | 3 | Research and discovery phase for containers and research objects support | 5
3.3.1 | 3 | Support containers and research objects  | 10
4.3.1 | 3 | Apply container, RO, workflows support to a few NIH-funded projects | 10

[mreekie]

Who

• Jim
• Phil
• Stephen

[poikilotherm]

A part of this is provided by merging IQSS/dataverse#7877, offering a first iteration of the CodeMeta support

[mreekie]

Our next step here is to meet with Mohommad. I was not able to get this together in November.

[poikilotherm]

I'd appreciate if we'd come together on this topic, as the goal of making Dataverse a "research software ready repository" seem to be overlapping between HERMES, HDC and the NIH GREI grant.

[mreekie]

Last Updated: October 10

(1.3.1, 1.3.2) The changes for the MVP on this Aim have been released with Dataverse 5.12. Work on expanding the CodeMeta and workflow functionalities will continue with Mohammed Shad from FAS Research Computing joining the team and leveraging his experience with collaborating with biomedical researchers.

[mreekie]

Last Updated: Monday Dec 5 (No changes)

(1.3.1, 1.3.2) The changes for the MVP on this Aim have been released with Dataverse 5.12. Work on expanding the CodeMeta and workflow functionalities will continue with Mohammed Shad from FAS Research Computing joining the team and leveraging his experience with collaborating with biomedical researchers.

50%

[mreekie]

Next Steps:

• I'm behind on this. - Add the issues tht were associated with this deliverable to this Deliverables Planning project tab

[mreekie]

Pulled into Dataverse Deliverables Planning project the related issues/PRs that were released with 5.12. The list may not be totally accurate. It was before I was tracking in the way I am now so I cast a wide net.

Next steps:
Edit the issues/PRs that are in this project so that they represent the work that was done to support the MVP.
Understand what work is outstanding past the MVP.

• Reach out to Aday who i know was involved with the MVP work.
• Reach out to Mahmood and bring him into the prio meeting. He's running this effort.
  • This reachout is way overdue. Len and Stefano have been asking for this for awhile.
• Reach out to Oliver and understand how his work overlaps and contributes (Need phil and maybe Mahmood for this too)

[mreekie]

Last updated: Thu Dec 15 2022 before I left for the holiday. No Change.
Report: Dec 2022

(1.3.1, 1.3.2) The changes for the MVP on this Aim have been released with Dataverse 5.12. Work on expanding the CodeMeta and workflow functionalities will continue with Mohammed Shad from FAS Research Computing joining the team and leveraging his experience with collaborating with biomedical researchers.

50%

[mreekie]

priority discussion with Stefano;

• Let's get this moving ahead with this!
• This work is in Mahmood's bailiwick.
• I put a stake in the ground for meeting next Tuesday 17th 4PM, Stefano, Tanya, mahmood

[mreekie]

Discussion with Mahmood.

• Implementation will not be a challenge.
• When computational workflow was done, we added a new metadata block.
• The metadata terms need to be reviewed.
• In upload page, not every field for code-meta is exposed.
• In a meeting with Phillip, Oliver, Ana, Julian - finalize the metadata terms.
• Ensure that what is included is correct and theen this can be merged.

[mreekie]

monthly

• Realized that this deliverable can be closed.

Next steps:

• Summarize what was delivered.
• Get started on 3 | 2.3.2 | Research and discovery phase for containers and research objects support#9372 using the notes just prior to this

[mreekie]

Monthly January:

(1.3.1, 1.3.2) The MVP was delivered with Dataverse 5.12. Work on expanding the CodeMeta and workflow functionalities will continue with Mohammed Shad from FAS Research Computing as part of 2.3.1 and 2.3.2

[mreekie]

Monthly report
(1.3.1, 1.3.2) The MVP was delivered with Dataverse 5.12. Work on expanding the CodeMeta and workflow functionalities will continue with Mohammed Shad from FAS Research Computing as part of 2.3.1 and 2.3.2

[mreekie]

Closed out the 1.3.2 deliverable and folded it in here.

• See: #9034. 3 | 1.3.2 | Research and discovery phase for biomedical workflows support | 5 dataverse#9139

[mreekie]

march Update:

(1.3.2) This activity was completed.