v3.0.0-draft.2

Annotated Research Context Specification version 3.0.0-draft.2

This draft release mainly bundles changes which further align the experimental provencance (ISA) with the computational provencance (CWL). For this, isa.run.xlsx and isa.workflow.xlsx files were specified which follow the structural conventions of the ISA-XLSX specification, but describe computational entities stemming from the CWL context.

It includes the specification of the ISA-XLSX format at the same version and is marked as draft to allow bundling subsequent breaking changes into a single major release (3.x)

ARC Specification changes

• Add isa.run.xlsx to run folder by @HLWeil in #157
• Add isa.workflow.xlsx to workflow folder by @HLWeil in #159
• Allow datamap only as own file by @HLWeil in #142

ISA-XLSX Specification changes

NEW RUN Section

• Define RUN section and RUN file by @HLWeil in #157

NEW WORKFLOW Section

• Define WORKFLOW section and WORKFLOW file by @HLWeil in #159

STUDY Section

• Datamap may no longer be a worksheet in the isa.study.xlsx file by @HLWeil in #142

ASSAY Section

• Datamap may no longer be a worksheet in the isa.assay.xlsx file by @HLWeil in #142
• Assay section now has new properties Identifier, Title and Description by @HLWeil in #154

DATAMAP Section

• Added Label column by @HLWeil in #155

Other

• Fixed dead link to specification file from readme by @floWetzels in #148

• Changes for v3.0-draft.2 - Workflow and Run ISA integration by @HLWeil in #162

Full Changelog: 3.0.0-draft.1...3.0.0-draft.2

v3.0.0-draft.1

Annotated Research Context Specification version 3.0.0-draft.1

This draft release mainly bundles changes necessary to generate ARCs with metadata that can be converted into valid ISA RO-crates. It includes the specification of the ISA-XLSX format at the same version and is marked as draft to allow bundling subsequent breaking changes into a single major release (3.x)

ARC Specification changes

• Added clarification on how the specification is versioned.
• Added a section about optionally licensing ARCs, specifying default licensing and where and how to add customized licenses.
• Fixed some typos.

ISA-XLSX Specification changes

INVESTIGATION Section > INVESTIGATION

• Investigation Identifier, Investigation Title, and Investigation Description are now mandatory fields.

STUDY Section > STUDY

• Study Identifier and Study Title are now mandatory fields.

ASSAY Section > ASSAY

• Added a new mandatory Assay Identifier field.
• Added new optional Assay Title and Assay Description fields.

Annotation Table sheets > Inputs/Outputs

• Rewrote the whole section to use less confusing wording.
• Added clarification that Input and Output columns are optional.
• Added clarification that when present, Input and Output columns are not allowed to contain empty cells.

Full Changelog: 2.1...3.0.0-draft.1

Annotated Research Context Specification, v2.1

What's Changed

• CWL and ISA harmonization @caroott

  • #111
  • Specified how to include ISA-Metadata in .cwl and .yml files, allowing a more harmonized datamodel
  • More explicit wording and typo fixes

• Allow Datamap sheets to be used in Assay and Study files @Freymaurer

  • #113

• Allow annotating web ressources @HLWeil

  • #117
  • Specified rules for annotating data files located on the WWW instead of in the ARC

• Improving wording for explicity

  • #124
  • #120
  • #118

New Contributors

• @caroott made their first contribution in #111

Full Changelog: 2.0...2.1

Annotated Research Context Specification, v2.0

What's Changed

• Big Overhaul of data representation by @HLWeil

  • Two core concepts now extend the base data model:
    • Data can now not only refer to a file, but also a specific part of the file. This is done by making use of Data fragment selectors defined here: https://www.w3.org/TR/annotation-model/#selectors
    • Additionaly, data objects can now be further contextualized in a Datamap file.
  • #104
  • #93
  • #78

• Mechanisms for ARC Quality Control section by @kMutagene

  • #98
  • #96
  • #95

• Various changes to xlsx table representation

  • #78
  • #84
  • #85

• Make study section in investigaiton file optional

  • #101

• Various clarifications and fixes

  • #83
  • #100
  • #91
  • #90
  • #88

New Contributors

• @kMutagene made their first contribution in #88

Full Changelog: 1.2...2.0

Annotated Research Context Specification, v1.2

Now, including further explanations and specifications about ISA-XLSX. These are linked in the main ARC-specification text and can be found here. This was necessary, as the ISA-XLSX strayed so far from originall ISA-Tab, referencing the latter only caused confusion. Instead, now we have a new specification incorporating the capabalities of multi-sheet xlsx files. This specification still implements the ISA abstract model, allowing for the conversion to ISA-Json still being a first-class operation. For additional motivation, discussion and documentation, see the following:

• For initial list of changes in ISA-XLSX vs ISA-Tab see here: #71
• For discussion and incorporation of changes in ISA-XLSX vs ISA-Tab see here: #72
• For discussion and incorpation of ISA-XLSX specification in ARC-specification see here: #76

What's Changed

• Update link to ARC specification by @Brilator in #69
• Merge ISA-Tab specification with ISA-XLSX changes by @HLWeil in #72
• Remove note on planned release from README.md by @Brilator in #75
• Include isa-xlsx for ARC-specification 1.2 by @HLWeil in #76

New Contributors

• @HLWeil made their first contribution in #72

Full Changelog: 1.1-rfc...1.2

Annotated Research Context Specification, v1.1-rfc

Release for DOI creation of v1.1-rfc

What's Changed

• Update ARC specification.md by @dvs-frbg in #1
• Update ARC specification.md by @dvs-frbg in #2
• First draft for RO-Crate conversion by @chgarth in #3
• Minor edits and comments below by @Brilator in #6
• Update README.md by @dvs-frbg in #7
• Update capitalized subtitles and open a pull request example by @xiaoranzhou in #8
• Corrected some typos by @Martin-Kuhl in #12
• Update ARC specification.md by @dvs-frbg in #11
• Update ARC specification.md by @kruegerjens in #14
• Minor corrections by @HGauza in #21
• Removed some "-"s (preprocessing, reuse ...) by @HGauza in #22
• Dominik v1.1 by @Brilator in #55
• Updated description RO-Crate Conversion by @floWetzels in #68

New Contributors

• @dvs-frbg made their first contribution in #1
• @chgarth made their first contribution in #3
• @Brilator made their first contribution in #6
• @xiaoranzhou made their first contribution in #8
• @Martin-Kuhl made their first contribution in #12
• @kruegerjens made their first contribution in #14
• @HGauza made their first contribution in #21
• @floWetzels made their first contribution in #68

Full Changelog: https://github.com/nfdi4plants/ARC-specification/commits/1.1-rfc