4 files changed, 113 insertions, 1 deletions

diff --git a/issues/rdf/automate-rdf-generation-and-ingress.gmi b/issues/rdf/automate-rdf-generation-and-ingress.gmi
index ef4ba9f..dedf5d8 100644
--- a/issues/rdf/automate-rdf-generation-and-ingress.gmi
+++ b/issues/rdf/automate-rdf-generation-and-ingress.gmi
@@ -4,7 +4,7 @@
 
 * assigned: bonfacem
 * priority: high
-* tags: in-progress
+* tags: done
 * deadline: 2024-10-23 Wed
 
 We need to update Virtuoso in production.  At the moment this is done manually.  For the current set-up, we need to update the recent modified RIF+WIKI models:
@@ -35,3 +35,5 @@ CHECKPOINT;
 Above steps should be automated and tested in CD before roll-out in production.  Key considerations:
 
 - Pick latest important changes from git, so that we can pick what files to run instead of generating all the ttl files all the time.
+
+* closed
diff --git a/issues/rdf/expose-rdf-to-web.gmi b/issues/rdf/expose-rdf-to-web.gmi
new file mode 100644
index 0000000..e5da94a
--- /dev/null
+++ b/issues/rdf/expose-rdf-to-web.gmi
@@ -0,0 +1,85 @@
+# Expose Versioned "rdf.genenetwork.org" Namespaces
+
+* assigned: bonfacem
+* status: in-progress
+
+## Description
+
+We have switched all RDF namespaces from "genenetwork.org" to the versioned base "rdf.genenetwork.org/v1."   These endpoints don't resolve yet.
+
+## What changed
+
+Replaced
+
+* "http://genenetwork.org/id/" -> "http://rdf.genenetwork.org/v1/id/"
+* "http://genenetwork.org/category/" -> "http://rdf.genenetwork.org/v1/category/"
+* "http://genenetwork.org/term/" -> "http://rdf.genenetwork.org/v1/term/"
+
+## Current Problem
+
+New "rdf.genenetwork.org/v1/*" URIs return a 5XX/4XX which blocks validation, dereferencing and external re-use
+
+## Expected Behaviour
+
+All rdf.genenetwork.org/v1/* namespaces resolve over HTTP.  At minimum:
+
+* Human-readable HTML in a browser.
+* RDF (Turtle or RDF/XML) via content negotiation.
+
+## Notes
+
+(Example) Queries for all terms/categories/ids:
+
+```
+PREFIX gn: <http://rdf.genenetwork.org/v1/id/>
+PREFIX gnc: <http://rdf.genenetwork.org/v1/category/>
+PREFIX gnt: <http://rdf.genenetwork.org/v1/term/>
+
+CONSTRUCT {
+  gn:Arabidopsis_thaliana ?p ?o .
+} FROM <http://rdf.genenetwork.org/v1>
+WHERE {
+  gn:Arabidopsis_thaliana ?p ?o .
+  ?s ?p ?o .
+}
+
+CONSTRUCT {
+  gnc:phenotype ?p ?o .
+} FROM <http://rdf.genenetwork.org/v1>
+WHERE {
+  gnc:phenotype ?p ?o .
+  ?s ?p ?o .
+}
+
+CONSTRUCT {
+  gnt:shortName ?p ?o .
+} FROM <http://rdf.genenetwork.org/v1>
+WHERE {
+  gnt:shortName ?p ?o .
+  ?s ?p ?o .
+}
+
+```
+
+Some terms/categories/ids descriptions will have to be manually updated since querying them as a subject return nothing.
+
+When serving, all supported formats based off Virtuoso's content negotiation:
+
+=> https://docs.openlinksw.com/virtuoso/rdfsparqlprotocolendpoint/
+
+Location of all files (tux02): /export/data/genenetwork-virtuoso/
+
+For current gn3, old data is maintained in this named graph: "http://genenetwork.org" while new data is being uploaded to this named graph: "http://rdf.genenetwork.org/v1"
+
+## Tasks
+
+* [X] Set up new named graph for the rdf endpoint.   Maintain old named graph for gn3 stability.
+* [X] Serve: "/v1/id/<id>"; "/v1/category/<category>"; and "/v1/term/<term>" under "rdf.genenetwork.org" as "text/microdata+html"
+* [X] Verify: `curl -H "Accept: text/html" http://rdf.genenetwork.org/v1/term/...`
+* [X] Configure DNS (rdf.genenetwork.org) to point to gn-guile server.
+
+## Resolution
+
+=> https://git.genenetwork.org/gn-guile/commit/?id=45662839565f6482e7f034a07ae373bbeaeb9713
+
+* closed
diff --git a/issues/rdf/search-indexing-general-issues.gmi b/issues/rdf/search-indexing-general-issues.gmi
index 3bcc36a..bd49419 100644
--- a/issues/rdf/search-indexing-general-issues.gmi
+++ b/issues/rdf/search-indexing-general-issues.gmi
@@ -30,3 +30,5 @@ A fix for this would be to replace "add_boolean_prefix" with "add_prefix".
 ## CIS/TRANS Searches
 
 The challenge with this search is that we would have to compare valuse for each possible result against one another, necessitating the generation of position values separately for every possible result.  Also, for the devs (jnduli, bonfacem) we need to have a better understanding of how this work, which is currently vague.
+
+* closed
diff --git a/issues/rdf/virtuoso-container-log-permission-crash.gmi b/issues/rdf/virtuoso-container-log-permission-crash.gmi
new file mode 100644
index 0000000..14cbf4f
--- /dev/null
+++ b/issues/rdf/virtuoso-container-log-permission-crash.gmi
@@ -0,0 +1,23 @@
+# Virtuoso Fails to Start Due to Incorrect Log File Ownership
+
+* assigned: bonfacem
+* status: closed
+
+## Description
+
+In CD, the virtuoso container keeps exiting and being re-spawned with the following error:
+
+```
+Thu Jan 15 2026 11:20:44 Can't open log : Permission denied
+```
+
+## Resolution
+
+Fixed it by running (from inside the container):
+
+```
+chown virtuoso:virtuoso /var/lib/virtuoso
+chmod 755 /var/lib/virtuoso
+```
+
+* closed