Shorten w3id prefix, stage redirect, dogfood #30 on SPRUCE

docs/cross_repo_linking.md

@@ -187,7 +187,7 @@ related_media:
 ### SPARQL: Find Media for Peatland Communities
 
 ```sparql
-PREFIX cm: <https://w3id.org/culturebot-ai/communitymech/>
+PREFIX cm: <https://w3id.org/communitymech/>
 
 SELECT ?community_name ?media_name ?culturemech_id ?relationship
 WHERE {
@@ -203,7 +203,7 @@ WHERE {
 ### SPARQL: Find Ingredients for an Environment
 
 ```sparql
-PREFIX cm: <https://w3id.org/culturebot-ai/communitymech/>
+PREFIX cm: <https://w3id.org/communitymech/>
 
 SELECT ?community_name ?ingredient ?mim_id ?relevance
 WHERE {
@@ -219,7 +219,7 @@ WHERE {
 ### SPARQL: Full Cross-Repo Join via Shared ENVO Terms
 
 ```sparql
-PREFIX cm: <https://w3id.org/culturebot-ai/communitymech/>
+PREFIX cm: <https://w3id.org/communitymech/>
 PREFIX cult: <https://w3id.org/culturebot-ai/culturemech/>
 PREFIX mim: <https://w3id.org/culturebot-ai/mediaingredientmech/>
 
@@ -240,7 +240,7 @@ WHERE {
 ### SPARQL: Reverse Lookup -- Communities for a CultureMech Medium
 
 ```sparql
-PREFIX cm: <https://w3id.org/culturebot-ai/communitymech/>
+PREFIX cm: <https://w3id.org/communitymech/>
 
 SELECT ?community_name ?environment ?relationship
 WHERE {

kb/communities/SPRUCE_Peatland_Methane_Cycling_Community.yaml

@@ -168,6 +168,40 @@ environmental_factors:
       to the peatland's CH4/CO2 carbon-chemistry gradient and depth/water structure -
       reinforcing peat chemistry (alongside the existing pH/TOC quantification) as a
       principal driver of community composition.
+related_ingredients:
+- preferred_term: humic substances
+  chebi_term:
+    id: CHEBI:34818
+    label: humic acid
+  relevance: Peat soil organic matter serves as an electron-acceptor pool that
+    sustains anaerobic respiration alongside methanogenesis at SPRUCE; humic
+    substances are the dominant electron-accepting fraction of that pool.
+  evidence:
+  - reference: PMID:40715043
+    supports: SUPPORT
+    evidence_source: COMPUTATIONAL
+    snippet: acquire electron acceptors from soil organic matter
+    explanation: The paper's headline claim links the SPRUCE peat microbial
+      community to soil-organic-matter electron acceptors, the humic-substance
+      fraction of which would anchor any environment-analog medium for this
+      community.
+- preferred_term: acetate
+  chebi_term:
+    id: CHEBI:30089
+    label: acetate
+  relevance: Acetate accumulates in deep peat from acetogenic Wood-Ljungdahl
+    activity and is the dominant substrate for acetoclastic methanogenesis at
+    the bog surface, so any cultivation medium designed around SPRUCE
+    methanogens would need acetate as a primary carbon and energy source.
+  evidence:
+  - reference: PMID:40715043
+    supports: SUPPORT
+    evidence_source: COMPUTATIONAL
+    snippet: the genomic potential for acetogenesis via the Wood-Ljungdahl pathway
+      continues to increase, resulting in the highest concentrations of acetate
+      in the deep peat
+    explanation: Anchors acetate as the dominant environmentally relevant
+      organic acid in SPRUCE peat porewater.
 associated_datasets:
 - name: SPRUCE peat metagenomes
   dataset_type: METAGENOME

src/communitymech/datamodel/communitymech.py

@@ -1,8 +1,8 @@
 # Auto generated from communitymech.yaml by pythongen.py version: 0.0.1
-# Generation date: 2026-05-16T01:52:45
+# Generation date: 2026-05-23T01:23:35
 # Schema: communitymech
 #
-# id: https://w3id.org/culturebot-ai/communitymech
+# id: https://w3id.org/communitymech
 # description: Schema for modeling microbial community structure, function, and ecological interactions
 # license: BSD-3-Clause
 
@@ -36,7 +36,7 @@
 NCBITAXON = CurieNamespace("NCBITaxon", "http://purl.obolibrary.org/obo/NCBITaxon_")
 PMID = CurieNamespace("PMID", "http://www.ncbi.nlm.nih.gov/pubmed/")
 UBERON = CurieNamespace("UBERON", "http://purl.obolibrary.org/obo/UBERON_")
-COMMUNITYMECH = CurieNamespace("communitymech", "https://w3id.org/culturebot-ai/communitymech/")
+COMMUNITYMECH = CurieNamespace("communitymech", "https://w3id.org/communitymech/")
 DOI = CurieNamespace("doi", "https://doi.org/")
 LINKML = CurieNamespace("linkml", "https://w3id.org/linkml/")
 XSD = CurieNamespace("xsd", "http://www.w3.org/2001/XMLSchema#")

src/communitymech/schema/communitymech.yaml

@@ -1,4 +1,4 @@
-id: https://w3id.org/culturebot-ai/communitymech
+id: https://w3id.org/communitymech
 name: communitymech
 title: Microbial Community Mechanisms Knowledge Base Schema
 description: Schema for modeling microbial community structure, function, and ecological interactions
@@ -11,7 +11,7 @@ imports:
 
 prefixes:
   linkml: https://w3id.org/linkml/
-  communitymech: https://w3id.org/culturebot-ai/communitymech/
+  communitymech: https://w3id.org/communitymech/
   NCBITaxon: http://purl.obolibrary.org/obo/NCBITaxon_
   ENVO: http://purl.obolibrary.org/obo/ENVO_
   CHEBI: http://purl.obolibrary.org/obo/CHEBI_

w3id/README.md

@@ -0,0 +1,42 @@
+# w3id.org redirect for CommunityMech
+
+This directory stages the upstream pull request to
+[perma-id/w3id.org](https://github.com/perma-id/w3id.org) that registers
+`https://w3id.org/communitymech/` as a permanent identifier prefix for
+CommunityMech CURIEs.
+
+## Files
+
+- `communitymech/.htaccess` — redirect rules. Copy verbatim to
+  `communitymech/.htaccess` in a fork of `perma-id/w3id.org` and open a PR.
+
+## Resolution targets
+
+| URL                                                          | Target                                                                                    |
+|--------------------------------------------------------------|-------------------------------------------------------------------------------------------|
+| `https://w3id.org/communitymech/`                            | `https://culturebotai.github.io/CommunityMech/`                                           |
+| `https://w3id.org/communitymech/<Name>`                      | `https://culturebotai.github.io/CommunityMech/communities/<Name>.html`                    |
+| `https://w3id.org/communitymech/<Name>.html`                 | same as above                                                                             |
+| `https://w3id.org/communitymech/<Name>.yaml`                 | `https://raw.githubusercontent.com/CultureBotAI/CommunityMech/main/kb/communities/<Name>.yaml` |
+| `https://w3id.org/communitymech/schema/communitymech.yaml`   | `https://raw.githubusercontent.com/CultureBotAI/CommunityMech/main/src/communitymech/schema/communitymech.yaml` |
+
+`<Name>` is the community filename slug (e.g., `EcoFAB_Ring_Trial_SynCom17`)
+that matches `kb/communities/<Name>.yaml`. CommunityMech also assigns each
+record a numeric identifier (`CommunityMech:NNNNNN`) which is recorded in
+the YAML body but not used as the URL path component.
+
+## Schema prefix update
+
+The LinkML schema's `communitymech` prefix was shortened from
+`https://w3id.org/culturebot-ai/communitymech/` to
+`https://w3id.org/communitymech/` in the same change that added this
+directory, so that the registered redirect matches the schema.
+
+## Submission
+
+1. Fork `perma-id/w3id.org`.
+2. Copy `communitymech/` from this directory into the fork root.
+3. Open a PR following the contribution guidelines in that repo
+   (`CONTRIBUTING.md`). Use this directory's README as PR context.
+
+Issue: [CultureBotAI/CommunityMech#12](https://github.com/CultureBotAI/CommunityMech/issues/12)

w3id/communitymech/.htaccess

@@ -0,0 +1,35 @@
+# Redirect rules for https://w3id.org/communitymech/
+#
+# Owner: CultureBotAI (https://github.com/CultureBotAI)
+# Contact: marcinjoachimiak@gmail.com
+# Source repo: https://github.com/CultureBotAI/CommunityMech
+#
+# Pattern summary:
+#   /                              -> CommunityMech docs landing page
+#   /<Name>                        -> Per-community HTML page on github.io
+#   /<Name>.html                   -> Same as /<Name>, idempotent
+#   /<Name>.yaml                   -> Source YAML on GitHub raw
+#   /schema/communitymech.yaml     -> LinkML schema source
+#
+# CommunityMech identifiers in the LinkML schema use the CURIE form
+# `CommunityMech:NNNNNN` (e.g., CommunityMech:000024). The community
+# slug (filename without .yaml) is what resolves here; the numeric ID
+# is recorded in the YAML body. See the project's docs for the mapping.
+
+Options +FollowSymLinks
+RewriteEngine On
+
+# Schema source
+RewriteRule ^schema/communitymech\.yaml$ https://raw.githubusercontent.com/CultureBotAI/CommunityMech/main/src/communitymech/schema/communitymech.yaml [R=302,L]
+
+# Per-community source YAML
+RewriteRule ^([A-Za-z0-9_]+)\.yaml$ https://raw.githubusercontent.com/CultureBotAI/CommunityMech/main/kb/communities/$1.yaml [R=302,L]
+
+# Per-community HTML page (canonical)
+RewriteRule ^([A-Za-z0-9_]+)\.html$ https://culturebotai.github.io/CommunityMech/communities/$1.html [R=302,L]
+
+# Per-community HTML page (extensionless CURIE local part)
+RewriteRule ^([A-Za-z0-9_]+)$ https://culturebotai.github.io/CommunityMech/communities/$1.html [R=302,L]
+
+# Landing page
+RewriteRule ^$ https://culturebotai.github.io/CommunityMech/ [R=302,L]