[REVISION] Chapter: 6 - Data in Other Repositories

[gremau]

What guide are you proposing revisions for?

• EML Best Practices guide
• Dataset Design For Special Cases
• Domain Specific Guides

Chapter and Revision Information

Chapter Number: 6
Chapter Title: Data in other repositories
Current Version/Commit:
File Path:
Reviewer(s):
Review Date:

Revision overview

Give a brief overview of the changes you are proposing for this chapter. This might include summarizing new content needed, sections to remove, reorganization of existing content/sections, wording changes, conceptual changes, etc.

Detailed Content Feedback

Major Issues

Identify and describe any major content revisions needed for the chapter. Please identify by section header or line numbers, and itemize multiple proposed changes by adding to the numbered list below.

The reviewers didn't have any major concerns or revisions for this chapter. In general it made sense and seemed well justified, but there were areas where clarity could be increased.

1. Issue: Improve 4th bullet point under "Considerations for creating linked data"

   • Location: Considerations for creating linked data (4th bullet point)
   • Current text: When a derived data product is archived in a different repository than the source (raw) data, this section gives advice for how to point to the source. However, it does not refer to the provenance elements of EML, which may do a more-than adequate job of indicating the relationship to data in another repository.
   • Suggested change: Add text about data provenance, and when to use it vs. when to use a manifest/inventory table.
   • Rationale: There should be a clear distinction between use cases for data inventory/manifests and data provenance information, whether pulled in from EDI or elsewhere.

2. Issue: Improve recommendations for keywording of datasets that reference other repositories

   • Location: "General metadata for linked data packages in EDI" subheading, "Keywords" bullet point
   • Current text: Current text does not include anything with the external repository name.
   • Suggested change: Need to include a keyword for repository name where the other data are published
   • Rationale: This would make it easier to search for data in other repositories.

3. Issue: Example datasets are out of date or don't follow advice.

   • Location: Examples in Table 6.3
   • Current text: All the datasets are out of date and don't necessarily conform to the advice given in the best practices guide.
   • Suggested change: Update all the examples! This may mean updating the data packages themselves and the metadata they contain. Some just need to reference the current dataset.
   • Rationale: We should be providing clear examples and following our own best practices.

4. Issue: Something should be done to improve or reorganize the Genomic and sequencing section

   • General thoughts: The "Genomic and Sequencing Data" sections (main text and appendix) are sort of a special case within a special case. Maybe these recommendations belong in their own chapter, or in a section of this chapter devoted to working with "sparse metadata" repositories. There should be clear recommendations (probably from NMDC, MixS creators, etc.) on how to provide complete, usable metadata for these data types.

Minor Issues

Identify and describe minor content issues that should be revised. Please identify by section header or line numbers.

• Case 2: The table references are off - should be 6.n
• Case 3: Add ezEML method here

Missing Content

Describe new content that should be added to the chapter. Include a suggested location for the addition, and if suggesting text include it in quotes.

• Nothing identified as missing.

Structure and Formatting

Describe any necessary restructuring or formatting changes for the chapter. This may include comments about organization, section/heading hierarchies, formatting consistency, use of figures/tables, citations and references, etc.

• No specific structural changes, though see the referencing section.

Style

Describe any style or writing issues that should be addressed. This may include comments about language, grammar, technical level, consistent terminology, flow, etc.

• No style revisions suggested so far

Technical Revisions

Fact checks

Briefly describe any specific claims, data, or other technical details that need verification or validation.

• No fact checks identified so far

Code/Figures Review

List any issues with code examples and figures. Identify code examples that are incorrect or non-functional, or that don't follow established style guidelines. Are the figures clear, relevant, and helpful?

• Table 1 should be 6.1
• Table 2 should be 6.2
• Example 1 should be 6.1

Cross-referencing and Hyperlinks

List any issues with internal document references, or with links to outside resources.

• There are some issues with Table and Example numbering. Ensure that references to these are correct and consistent within the chapter.

Bibliography

List any sources that are improperly cited, missing, out-of-date, or poorly formatted. To suggest new references include the full citation.

• [Describe bibliography issue]
• [add more items as needed....]

Additional Recommendations and Comments

Do you have any other recommendations or comments?