Merge pull request #792 from bigbio/dev

VERSIONING and TEMPLATE specifications changed, additionally a file for LLM interations has been created

Author: ypriverol

.gitignore

@@ -78,6 +78,7 @@ site/sdrf-data.json
 # Claude Code #
 ###############
 .claude/
+CLAUDE.md
 .codacy/
 
 # Local files for developers are in folder in local-info

README.md

@@ -1,13 +1,13 @@
 # Proteomics Sample Metadata Format
 
 [![Version](https://flat.badgen.net/static/sdrf-proteomics/1.0.1/orange)](CHANGELOG.md)
-[![License](https://flat.badgen.net/github/license/bigbio/proteomics-metadata-standard)](https://github.com/bigbio/proteomics-metadata-standard/blob/master/LICENSE)
-[![Open Issues](https://flat.badgen.net/github/open-issues/bigbio/proteomics-metadata-standard)](https://github.com/bigbio/proteomics-metadata-standard/issues)
-[![Open PRs](https://flat.badgen.net/github/open-prs/bigbio/proteomics-metadata-standard)](https://github.com/bigbio/proteomics-metadata-standard/pulls)
-![Contributors](https://flat.badgen.net/github/contributors/bigbio/proteomics-metadata-standard)
-![Watchers](https://flat.badgen.net/github/watchers/bigbio/proteomics-metadata-standard)
-![Stars](https://flat.badgen.net/github/stars/bigbio/proteomics-metadata-standard)
-[![llms.txt](https://flat.badgen.net/static/llms.txt/available/blue)](https://github.com/bigbio/proteomics-metadata-standard/blob/master/llms.txt)
+[![License](https://flat.badgen.net/github/license/bigbio/proteomics-sample-metadata)](https://github.com/bigbio/proteomics-sample-metadata/blob/master/LICENSE)
+[![Open Issues](https://flat.badgen.net/github/open-issues/bigbio/proteomics-sample-metadata)](https://github.com/bigbio/proteomics-sample-metadata/issues)
+[![Open PRs](https://flat.badgen.net/github/open-prs/bigbio/proteomics-sample-metadata)](https://github.com/bigbio/proteomics-sample-metadata/pulls)
+![Contributors](https://flat.badgen.net/github/contributors/bigbio/proteomics-sample-metadata)
+![Watchers](https://flat.badgen.net/github/watchers/bigbio/proteomics-sample-metadata)
+![Stars](https://flat.badgen.net/github/stars/bigbio/proteomics-sample-metadata)
+[![llms.txt](https://flat.badgen.net/static/llms.txt/available/blue)](llms.txt)
 
 ## Improving metadata annotation of Proteomics datasets
 
@@ -45,7 +45,7 @@ In the [annotated projects](https://github.com/bigbio/proteomics-metadata-standa
 Annotate a dataset in 5 steps:
 
 - Read the [SDRF-Proteomics specification](https://github.com/bigbio/proteomics-metadata-standard/tree/master/sdrf-proteomics).
-- Depending on the type of dataset, choose the appropriate [sample template](https://github.com/bigbio/proteomics-metadata-standard/tree/master/sdrf-proteomics#sdrf-templates).
+- Depending on the type of dataset, choose the appropriate [sample template](https://github.com/bigbio/proteomics-sample-metadata/tree/master/sdrf-proteomics#sdrf-templates).
 - Annotate the corresponding ProteomeXchange PXD dataset following the guidelines.
 - Validate your SDRF file:
 

psi-document/sdrf-proteomics-specification-v1.1.0-dev.pdf

@@ -249,7 +249,7 @@ The validator (sdrf-pipelines) is how most users discover that a newer version e
 ----
 INFO: Template 'human v1.2.0' is available.
   Your file uses 'human v1.1.0' and is valid under that version.
-  See CHANGELOG for what changed: https://github.com/bigbio/.../CHANGELOG.md
+  See CHANGELOG for what changed: https://github.com/bigbio/proteomics-sample-metadata/blob/master/CHANGELOG.md
 ----
 
 The validator **never fails** a file that is valid under its declared version. It only emits INFO messages pointing to newer versions. The user decides when to upgrade.
@@ -496,14 +496,14 @@ When a breaking change is introduced, a migration guide MUST be provided. The gu
 | **Migration tooling**
 | Every breaking change includes a `parse_sdrf migrate` command to automate file updates.
 
-| **Machine-readable schedules**
-| The deprecation schedule and template compatibility information are machine-readable YAML, enabling automated monitoring by CI pipelines.
+| **Machine-readable metadata**
+| Template definitions and compatibility rules are provided in YAML formats that can be consumed by CI pipelines for automated monitoring.
 |===
 
 == See Also
 
 * link:README.adoc[SDRF-Proteomics Core Specification] — see <<versioning>> section
 * link:metadata-guidelines/template-definitions.adoc[Template Definitions Guide] — YAML schema structure
-* link:open-issues.adoc[Open Issues and Future Decisions] — active community discussions
+* https://github.com/bigbio/proteomics-sample-metadata/issues[Open Issues and Future Decisions] — active community discussions
 * https://semver.org/[Semantic Versioning 2.0.0]
 * https://github.com/bigbio/proteomics-sample-metadata/issues/771[Issue #771: Versioning strategy discussion]

sdrf-proteomics/VERSIONING.adoc

@@ -76,6 +76,14 @@ data file	comment	MS:1000577	minimum, default, human, cell-lines, single-cell, i
 modification parameters	comment	MS:1001055	dia-acquisition, dda-acquisition	Unimod, PSI-MOD	Post-translational modifications searched	true	false	false
 precursor mass tolerance	comment	PRIDE:0000575	dia-acquisition, dda-acquisition	pattern: number + ppm/Da	Precursor mass tolerance for database search	true	true	false
 fragment mass tolerance	comment	PRIDE:0000576	dia-acquisition, dda-acquisition	pattern: number + ppm/Da	Fragment mass tolerance for database search	true	true	false
+precursor min mz	comment	PRIDE:0000476	dia-acquisition, dda-acquisition	numeric (m/z)	MS method-defined minimum precursor m/z setting used to acquire the data	true	true	false
+precursor max mz	comment	PRIDE:0000477	dia-acquisition, dda-acquisition	numeric (m/z)	MS method-defined maximum precursor m/z setting used to acquire the data	true	true	false
+precursor min charge	comment	PRIDE:0000472	dia-acquisition, dda-acquisition	integer	MS method-defined minimum precursor charge state setting used to acquire the data	true	true	false
+precursor max charge	comment	PRIDE:0000473	dia-acquisition, dda-acquisition	integer	MS method-defined maximum precursor charge state setting used to acquire the data	true	true	false
+min retention time	comment	PRIDE:0000474	dia-acquisition, dda-acquisition	numeric (minutes)	LC method-defined minimum retention time setting used to acquire the data	true	true	false
+max retention time	comment	PRIDE:0000475	dia-acquisition, dda-acquisition	numeric (minutes)	LC method-defined maximum retention time setting used to acquire the data	true	true	false
+min ion mobility	comment	PRIDE:0000841	dia-acquisition, dda-acquisition	numeric (1/K0 or Vs/cm2)	MS method-defined minimum ion mobility setting used to acquire the data	true	true	false
+max ion mobility	comment	PRIDE:0000842	dia-acquisition, dda-acquisition	numeric (1/K0 or Vs/cm2)	MS method-defined maximum ion mobility setting used to acquire the data	true	true	false
 passage number	comment	to be filled	cell-lines	integer or range	Passage number of the cell line	true	true	false
 cell line source	comment	to be filled	cell-lines	free text	Repository or source from which the cell line was obtained	true	true	false
 authentication method	comment	to be filled	cell-lines	free text	Method used to authenticate the cell line identity	true	true	false

sdrf-proteomics/metadata-guidelines/sdrf-terms.tsv

@@ -579,9 +579,9 @@ NOTE: MS-specific validations (label, cleavage agent, etc.) do not apply to affi
 [[template-file]]
 == Template File
 
-The affinity proteomics SDRF template file is available in this directory:
+The affinity proteomics SDRF template file is available in the sdrf-templates repository:
 
-- link:affinity-proteomics-template.sdrf.tsv[affinity-proteomics-template.sdrf.tsv]
+- link:https://github.com/bigbio/sdrf-templates/blob/main/affinity-proteomics/1.1.0/affinity-proteomics.sdrf.tsv[affinity-proteomics.sdrf.tsv]
 
 [[related-templates]]
 == Related Templates

sdrf-proteomics/templates/affinity-proteomics/README.adoc

@@ -28,5 +28,5 @@ Use one of the following technology templates instead:
 [[files]]
 == Template Files
 
-* `base.yaml` - YAML template definition for validation
-* `base-template.sdrf.tsv` - Column header template
+- link:https://github.com/bigbio/sdrf-templates/blob/main/base/1.1.0/base.yaml[base.yaml] - YAML template definition for validation
+- link:https://github.com/bigbio/sdrf-templates/blob/main/base/1.1.0/base.sdrf.tsv[base.sdrf.tsv] - Column header template

sdrf-proteomics/templates/base/README.adoc

@@ -582,9 +582,9 @@ For cell lines where donor information is unknown:
 [[template-file]]
 == Template File
 
-The cell line SDRF template file is available in this directory:
+The cell line SDRF template file is available in the sdrf-templates repository:
 
-- link:cell-lines-template.sdrf.tsv[cell-lines-template.sdrf.tsv]
+- link:https://github.com/bigbio/sdrf-templates/blob/main/cell-lines/1.1.0/cell-lines.sdrf.tsv[cell-lines.sdrf.tsv]
 
 [[validation]]
 == Validation

sdrf-proteomics/templates/cell-lines/README.adoc

@@ -489,6 +489,13 @@ parse_sdrf validate-sdrf --sdrf_file your_file.sdrf.tsv \
   --template crosslinking
 ----
 
+[[template-file]]
+== Template File
+
+The crosslinking SDRF template file is available in the sdrf-templates repository:
+
+- link:https://github.com/bigbio/sdrf-templates/blob/main/crosslinking/1.1.0/crosslinking.sdrf.tsv[crosslinking.sdrf.tsv]
+
 [[references]]
 == References
 

sdrf-proteomics/templates/crosslinking/README.adoc

@@ -125,6 +125,62 @@ ifdef::backend-html5[]
 <td><a href="https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000443">PSI-MS (MS:1000443)</a></td>
 <td>NT=orbitrap;AC=MS:1000484</td>
 </tr>
+<tr>
+<td><code>comment[precursor min mz]</code></td>
+<td><span class="optional-badge">OPTIONAL</span></td>
+<td>MS method-defined minimum precursor m/z setting used to acquire the data</td>
+<td><a href="https://www.ebi.ac.uk/ols4/ontologies/pride/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPRIDE_0000476">PRIDE (PRIDE:0000476)</a></td>
+<td>350, 400</td>
+</tr>
+<tr>
+<td><code>comment[precursor max mz]</code></td>
+<td><span class="optional-badge">OPTIONAL</span></td>
+<td>MS method-defined maximum precursor m/z setting used to acquire the data</td>
+<td><a href="https://www.ebi.ac.uk/ols4/ontologies/pride/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPRIDE_0000477">PRIDE (PRIDE:0000477)</a></td>
+<td>1600, 2000</td>
+</tr>
+<tr>
+<td><code>comment[precursor min charge]</code></td>
+<td><span class="optional-badge">OPTIONAL</span></td>
+<td>MS method-defined minimum precursor charge state setting used to acquire the data</td>
+<td><a href="https://www.ebi.ac.uk/ols4/ontologies/pride/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPRIDE_0000472">PRIDE (PRIDE:0000472)</a></td>
+<td>1, 2</td>
+</tr>
+<tr>
+<td><code>comment[precursor max charge]</code></td>
+<td><span class="optional-badge">OPTIONAL</span></td>
+<td>MS method-defined maximum precursor charge state setting used to acquire the data</td>
+<td><a href="https://www.ebi.ac.uk/ols4/ontologies/pride/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPRIDE_0000473">PRIDE (PRIDE:0000473)</a></td>
+<td>4, 6</td>
+</tr>
+<tr>
+<td><code>comment[min retention time]</code></td>
+<td><span class="optional-badge">OPTIONAL</span></td>
+<td>LC method-defined minimum retention time setting used to acquire the data</td>
+<td><a href="https://www.ebi.ac.uk/ols4/ontologies/pride/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPRIDE_0000474">PRIDE (PRIDE:0000474)</a></td>
+<td>0, 5</td>
+</tr>
+<tr>
+<td><code>comment[max retention time]</code></td>
+<td><span class="optional-badge">OPTIONAL</span></td>
+<td>LC method-defined maximum retention time setting used to acquire the data</td>
+<td><a href="https://www.ebi.ac.uk/ols4/ontologies/pride/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPRIDE_0000475">PRIDE (PRIDE:0000475)</a></td>
+<td>120, 90</td>
+</tr>
+<tr>
+<td><code>comment[min ion mobility]</code></td>
+<td><span class="optional-badge">OPTIONAL</span></td>
+<td>MS method-defined minimum ion mobility setting used to acquire the data</td>
+<td><a href="https://www.ebi.ac.uk/ols4/ontologies/pride/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPRIDE_0000841">PRIDE (PRIDE:0000841)</a></td>
+<td>0.6, 0.7</td>
+</tr>
+<tr>
+<td><code>comment[max ion mobility]</code></td>
+<td><span class="optional-badge">OPTIONAL</span></td>
+<td>MS method-defined maximum ion mobility setting used to acquire the data</td>
+<td><a href="https://www.ebi.ac.uk/ols4/ontologies/pride/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPRIDE_0000842">PRIDE (PRIDE:0000842)</a></td>
+<td>1.4, 1.6</td>
+</tr>
 </tbody>
 </table>
 ++++
@@ -140,6 +196,14 @@ ifndef::backend-html5[]
 |comment[precursor mass tolerance] |OPTIONAL |Mass tolerance for precursor ions in database search |Numeric value with unit |10 ppm, 20 ppm
 |comment[fragment mass tolerance] |OPTIONAL |Mass tolerance for fragment ions in database search |Numeric value with unit |0.02 Da, 20 ppm
 |comment[MS2 mass analyzer] |OPTIONAL |Mass analyzer used for MS2 acquisition |PSI-MS (MS:1000443) |NT=orbitrap;AC=MS:1000484
+|comment[precursor min mz] |OPTIONAL |MS method-defined minimum precursor m/z setting used to acquire the data |PRIDE (PRIDE:0000476) |350, 400
+|comment[precursor max mz] |OPTIONAL |MS method-defined maximum precursor m/z setting used to acquire the data |PRIDE (PRIDE:0000477) |1600, 2000
+|comment[precursor min charge] |OPTIONAL |MS method-defined minimum precursor charge state setting used to acquire the data |PRIDE (PRIDE:0000472) |1, 2
+|comment[precursor max charge] |OPTIONAL |MS method-defined maximum precursor charge state setting used to acquire the data |PRIDE (PRIDE:0000473) |4, 6
+|comment[min retention time] |OPTIONAL |LC method-defined minimum retention time setting used to acquire the data |PRIDE (PRIDE:0000474) |0, 5
+|comment[max retention time] |OPTIONAL |LC method-defined maximum retention time setting used to acquire the data |PRIDE (PRIDE:0000475) |120, 90
+|comment[min ion mobility] |OPTIONAL |MS method-defined minimum ion mobility setting used to acquire the data |PRIDE (PRIDE:0000841) |0.6, 0.7
+|comment[max ion mobility] |OPTIONAL |MS method-defined maximum ion mobility setting used to acquire the data |PRIDE (PRIDE:0000842) |1.4, 1.6
 |===
 endif::[]
 
@@ -354,9 +418,9 @@ NOTE: For TMT experiments, multiple samples share the same raw file. Use `commen
 [[template-file]]
 == Template File
 
-The DDA SDRF template file is available in this directory:
+The DDA SDRF template file is available in the sdrf-templates repository:
 
-- link:dda-acquisition-template.sdrf.tsv[dda-acquisition-template.sdrf.tsv]
+- link:https://github.com/bigbio/sdrf-templates/blob/main/dda-acquisition/1.1.0/dda-acquisition.sdrf.tsv[dda-acquisition.sdrf.tsv]
 
 [[validation]]
 == Validation