Fix/release workflow import refresh

.github/workflows/release.yml

@@ -132,19 +132,18 @@ jobs:
       # expanding $(ONTBASE) and $(VERSION) — make expands them itself using
       # values already defined in the ODK-generated Makefile.
       #
-      # IMP=false / PAT=false skips import refresh for speed — imports were
-      # already refreshed by the last regular build. Remove IMP=false to
-      # force a full import refresh as part of the release.
+      # refresh-imports is run before all_assets (same as qc.yml ontology-build)
+      # to ensure SLME modules are extracted from current mirrors.
       # ──────────────────────────────────────────────────────────────────────
       - name: Build release artifacts
         env:
           ROBOT_ENV: ROBOT_JAVA_ARGS=-Xmx6G
         run: |
           cd src/ontology
-          make IMP=false PAT=false \
+          make PAT=false \
             VERSION=${{ steps.version.outputs.version }} \
             'ANNOTATE_ONTOLOGY_VERSION=annotate -V $(ONTBASE)/$(VERSION) --annotation owl:versionInfo $(VERSION)' \
-            all_assets
+            refresh-imports all_assets
 
       # ── Commit release artifacts to main ─────────────────────────────────
       # Versioned artifacts must be in main so that docs.yml can find them

.github/workflows/seed.yml

@@ -0,0 +1,144 @@
+# SEEDING ODK workflow
+
+name: seed odk
+
+# Controls when the action will run.
+on:
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+    inputs:
+      ontology_id:
+        description: 'Ontology ID (replaces id in seed.yaml)'
+        required: true
+      uribase_suffix:
+        description: 'URI base suffix (replaces uribase_suffix in seed.yaml)'
+        required: true
+      odk_tag:
+        description: 'ODK Docker tag to use'
+        required: false
+        default: 'latest'
+      config_file:
+        description: 'Configuration file name'
+        required: false
+        default: 'seed-template.yaml'
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "seed_ontology"
+  seed_ontology:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+    container: obolibrary/odkfull:${{ github.event.inputs.odk_tag || 'latest' }}
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v4
+
+      - name: Set up Git config
+        run: |
+          git config --global user.name "${{ github.actor }}"
+          git config --global user.email "${{ github.actor }}@users.noreply.github.com"
+
+      - name: Generate unique branch name
+        run: |
+          BRANCH_NAME="fresh-seed-$(date +%Y%m%d-%H%M%S)"
+          echo "BRANCH_NAME=$BRANCH_NAME" >> $GITHUB_ENV
+
+      - name: Extract GitHub org and repo
+        run: |
+          GITHUB_ORG=$(echo "${{ github.repository }}" | cut -d'/' -f1)
+          GITHUB_REPO=$(echo "${{ github.repository }}" | cut -d'/' -f2)
+          echo "GITHUB_ORG=$GITHUB_ORG" >> $GITHUB_ENV
+          echo "GITHUB_REPO=$GITHUB_REPO" >> $GITHUB_ENV
+          echo "GitHub Organization: $GITHUB_ORG"
+          echo "GitHub Repository: $GITHUB_REPO"
+
+      - name: Verify seed config file exists
+        run: |
+          if [ ! -f "${{ github.event.inputs.config_file || 'seed-template.yaml' }}" ]; then
+            echo "Error: Configuration file ${{ github.event.inputs.config_file || 'seed-template.yaml' }} not found!"
+            exit 1
+          fi
+          echo "Using configuration file: ${{ github.event.inputs.config_file || 'seed-template.yaml' }}"
+
+      - name: Update seed-template.yaml with input values
+        run: |
+          CONFIG_FILE="${{ github.event.inputs.config_file || 'seed-template.yaml' }}"
+
+          echo "Original seed-template.yaml content:"
+          cat "$CONFIG_FILE"
+
+          # Replace id value
+          sed -i "s/^id:.*/id: ${{ github.event.inputs.ontology_id }}/" "$CONFIG_FILE"
+
+          # Replace uribase_suffix value
+          sed -i "s/^uribase_suffix:.*/uribase_suffix: ${{ github.event.inputs.uribase_suffix }}/" "$CONFIG_FILE"
+
+          # Replace uribase value
+          sed -i "s/^uribase_suffix:.*/uribase_suffix: https://w3id.org/pmd/${{ github.event.inputs.uribase_suffix }}/" "$CONFIG_FILE"
+
+          # Replace github_org value
+          sed -i "s/^github_org:.*/github_org: $GITHUB_ORG/" "$CONFIG_FILE"
+
+          # Replace repo value
+          sed -i "s/^repo:.*/repo: $GITHUB_REPO/" "$CONFIG_FILE"
+
+          echo "Updated seed-template.yaml content:"
+          cat "$CONFIG_FILE"
+
+      - name: Run ODK seed
+        env:
+          ODK_IMAGE: odkfull
+          ODK_TAG: ${{ github.event.inputs.odk_tag || 'latest' }}
+          ODK_GITNAME: ${{ github.actor }}
+          ODK_GITEMAIL: ${{ github.actor }}@users.noreply.github.com
+        run: |
+          echo "This script only works with ODK 1.3.2 and later. For ODK 1.3.1 or earlier, use https://raw.githubusercontent.com/INCATools/ontology-development-kit/v1.3.1/seed-via-docker.sh"
+          /tools/odk.py seed \
+            --gitname "$ODK_GITNAME" \
+            --gitemail "$ODK_GITEMAIL" \
+            -c \
+            -C ${{ github.event.inputs.config_file || 'seed-template.yaml' }}
+
+      - name: Copy generated files to root
+        run: |
+          TARGET_DIR="target/${{ github.event.inputs.ontology_id }}"
+          if [ ! -d "$TARGET_DIR" ]; then
+            echo "Error: Target directory $TARGET_DIR not found!"
+            exit 1
+          fi
+
+          echo "Copying files from $TARGET_DIR to root, excluding .git and .github directories..."
+
+          # Copy all files and directories except .git and .github
+          find "$TARGET_DIR" -mindepth 1 -maxdepth 1 ! -name '.git' ! -name '.github' -exec cp -r {} . \;
+
+          # List what was copied
+          echo "Files copied to root:"
+          ls -la
+
+      - name: Clean up target directory
+        run: |
+          echo "Removing target directory to avoid git conflicts..."
+          rm -rf target/
+          git status
+
+      - name: Create Pull Request
+        uses: peter-evans/create-pull-request@v5
+        with:
+          branch: ${{ env.BRANCH_NAME }}
+          base: main
+          title: "ODK Seed: ${{ github.event.inputs.ontology_id }}"
+          commit-message: "ODK seed generated files for ${{ github.event.inputs.ontology_id }} using ${{ github.event.inputs.config_file || 'seed.yaml' }}"
+          body: |
+            ## ODK Seed Generated Files
+
+            - **Ontology ID**: `${{ github.event.inputs.ontology_id }}`
+            - **URI Base Suffix**: `${{ github.event.inputs.uribase_suffix }}`
+            - **GitHub Organization**: `${{ env.GITHUB_ORG }}`
+            - **Repository**: `${{ env.GITHUB_REPO }}`
+            - **Config File**: `${{ github.event.inputs.config_file || 'seed-template.yaml' }}`
+            - **ODK Tag**: `${{ github.event.inputs.odk_tag || 'latest' }}`
+
+            This PR contains the generated ontology files from ODK seed.

.github/workflows/update_repo.yml

@@ -0,0 +1,34 @@
+# Basic ODK workflow
+
+name: update_repo
+
+# Controls when the action will run.
+on:
+  # Triggers the workflow on push or pull request events but only for the main branch
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "ontology_qc"
+  odk_update_repo:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+    container: obolibrary/odkfull:v1.6
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v4
+
+      - name: Build ontology
+        env:
+          DEFAULT_BRANCH: main
+        run: cd src/ontology && make update_repo ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G'
+      - name: Commit files # commit the src folder
+        uses: EndBug/add-and-commit@v9
+        with:
+          message: "updated ontology"
+          add: "*.* --force"
+          cwd: "./src/"
+          default_author: github_actions

.gitignore

@@ -4,12 +4,71 @@
 .DS_Store
 semantic.cache
 bin/
-.trunk/
+
 *.tmp
 *.tmp.obo
 *.tmp.owl
 *.tmp.json
 *-relation-graph.tsv.gz
 .template.db
 
-.github/token.txt
+.github/token.txt
+
+/log.owl
+/log.obo
+/log.json
+/log.db
+/log-base.*
+/log-basic.*
+/log-full.*
+/log-simple.*
+/log-simple-non-classified.*
+/mappings/
+/patterns/
+/reports/
+/subsets/
+
+src/ontology/mirror
+src/ontology/mirror/*
+src/ontology/reports/*
+!src/ontology/reports/release-diff.md
+src/ontology/log.owl
+src/ontology/log.obo
+src/ontology/log.json
+src/ontology/log.db
+src/ontology/log-base.*
+src/ontology/log-basic.*
+src/ontology/log-full.*
+src/ontology/log-simple.*
+src/ontology/log-simple-non-classified.*
+
+src/ontology/seed.txt
+src/ontology/dosdp-tools.log
+src/ontology/ed_definitions_merged.owl
+src/ontology/ontologyterms.txt
+src/ontology/simple_seed.txt
+src/ontology/patterns
+src/ontology/merged-log-edit.owl
+src/ontology/log-edit.properties
+
+src/ontology/target/
+src/ontology/tmp/*
+!src/ontology/tmp/.gitkeep
+!src/ontology/tmp/README.md
+
+src/ontology/run.sh.conf
+src/ontology/run.sh.env
+
+src/ontology/imports/*_terms_combined.txt
+
+src/patterns/data/**/*.ofn
+src/patterns/data/**/*.txt
+src/patterns/pattern_owl_seed.txt
+src/patterns/all_pattern_terms.txt
+
+
+# patterns: track hand-written files, ignore generated autoshapes
+!/patterns/
+/patterns/autoshape/auto-shapes-*.ttl
+
+# End of ODK-managed rules

ACKNOWLEDGEMENTS.md

@@ -0,0 +1,43 @@
+# Acknowledgements
+
+## IOF Supply Chain Module
+
+The majority of classes and properties in LOG are adopted from the
+[IOF Supply Chain Module](https://spec.industrialontologies.org/ontology/supplychain/Metadatasupplychain/supplychainModule),
+developed by the [Industrial Ontologies Foundry (IOF)](https://www.industrialontologies.org/).
+Term provenance is recorded per-entity via `IAO:0000412` ("imported from") annotations.
+The IOF Supply Chain Module is licensed under the MIT License.
+
+## PMD Core Ontology (PMDCo)
+
+LOG extends the [PMD Core Ontology (PMDCo) 3.0.0](https://w3id.org/pmd/co),
+developed by the [Platform MaterialDigital (PMD)](https://www.materialdigital.de/).
+PMDCo is licensed under [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/).
+
+## W3C Organization Ontology
+
+Organization, membership, post, and site modeling uses the
+[W3C Organization Ontology](https://www.w3.org/TR/vocab-org/) (W3C, CC BY 4.0).
+
+## FOAF Vocabulary
+
+Person modeling uses the [FOAF Vocabulary](http://xmlns.com/foaf/0.1/).
+
+## Basic Formal Ontology (BFO)
+
+All classes are aligned to [BFO 2020](https://basic-formal-ontology.org/),
+the top-level ontology underpinning both IOF and PMDCo.
+
+## Funding
+
+This work was carried out at the [Fraunhofer Institute for Mechanics of Materials IWM](https://www.iwm.fraunhofer.de/)
+and is funded by the [German Federal Ministry for Research, Technology and Space (BMFTR)](https://www.bmftr.bund.de)
+under the [Plattform MaterialDigital (PMD)](https://www.materialdigital.de/) framework.
+
+Development was supported by the PMD-X project
+[EDCar](https://www.iwm.fraunhofer.de/de/forschungsprojekte-des-fraunhofer-iwm/EDCar.html)
+(Förderkennzeichen: 13XPM504B) —
+*Automotive End-of-Life Datenaustausch für Circular Economy*
+(07/2025–06/2026), coordinated by Fraunhofer IWM in collaboration with
+Fraunhofer IPK, BASF SE, BMW Group, Robert Bosch GmbH, Schaeffler Technologies,
+LRP-Autorecycling Leipzig GmbH, tec4U Solutions GmbH, and light ds GmbH.

CHANGELOG.md

@@ -0,0 +1,59 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+Format follows [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
+
+## [1.0.0] - 2026-04-17
+
+### First release
+
+The PMD Logistics Application Ontology (LOG) is a BFO- and IOF-conformant ontology
+for logistics and supply chain management in the materials science and engineering domain.
+
+#### Origin
+
+LOG originates from a need to model logistics and supply chain processes within the
+[Platform MaterialDigital (PMD)](https://www.materialdigital.de/) ecosystem in a way
+that is interoperable with existing PMD ontologies and compatible with industrial standards.
+The ontology was developed at Fraunhofer IWM and adopts the
+[IOF Supply Chain Module](https://spec.industrialontologies.org/ontology/supplychain/Metadatasupplychain/supplychainModule)
+as its primary source, extending and aligning it to the
+[PMD Core Ontology (PMDCo)](https://w3id.org/pmd/co) 3.0.0.
+Development was supported by the PMD-X project EDCar (Förderkennzeichen: 13XPM504B).
+
+#### What it covers
+
+- **Organizations and roles** — business organizations, suppliers, manufacturers, carriers,
+  freight forwarders and their BFO-aligned roles; integrated with W3C ORG vocabulary
+- **Persons** — modeled via FOAF, linked to organizations through `org:Membership` and `org:Post`
+- **Locations and premises** — physical premises, geospatial sites with WGS84 coordinates,
+  ship-from/ship-to locations, supply chain nodes
+- **Shipments and cargo** — shipment, load, cargo, lot, traceable resource unit,
+  bill of lading, purchase order
+- **Transport** — transport process, seaway, airway, shipping route, multimodal chains
+- **Facilities** — facility, storage facility, distribution center, warehouse
+- **Agreements** — commercial service agreement, bill of lading, framework contracts
+- **Processes** — transport, receiving, warehousing, packaging, procurement, selling,
+  manufacturing, supply chain processes
+- **Plan specifications** — shipment plan, warehousing plan, supply chain plan
+
+#### Usage patterns (SHACL-validated)
+
+Four real-world usage patterns with annotated example data are included,
+each validated with [pyshacl](https://github.com/RDFLib/pySHACL):
+
+| Pattern | Scenario |
+|---------|----------|
+| [Shipment by Sea](patterns/shipment-by-sea/) | Steel coil shipment Baosteel → Volkswagen via COSCO |
+| [Contract Negotiation](patterns/contract-negotiation/) | Annual steel supply framework agreement |
+| [Warehouse Receiving](patterns/warehouse-receiving/) | Steel coils received at DB Schenker Hamburg |
+| [Multimodal Transport](patterns/multimodal-transport/) | Multi-leg transport chain |
+
+#### Ontology artifacts
+
+| File | Description |
+|------|-------------|
+| `log.owl` / `log.ttl` | Full ontology with all imports merged |
+| `log-base.owl` / `log-base.ttl` | Base ontology without imports |
+| `log-simple.owl` / `log-simple.ttl` | Simplified profile |
+| `log-full.owl` / `log-full.ttl` | Full reasoned version |