From 564e5a29a92308eb2f40ecc7e01720789067fb73 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Thu, 5 Feb 2026 22:42:33 +0300 Subject: Update issue. Signed-off-by: Munyoki Kilyungi --- issues/rdf/rdf-refinement.gmi | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/issues/rdf/rdf-refinement.gmi b/issues/rdf/rdf-refinement.gmi index 50be9d64..c37fa0d2 100644 --- a/issues/rdf/rdf-refinement.gmi +++ b/issues/rdf/rdf-refinement.gmi @@ -272,8 +272,9 @@ Genotypes and markers are different but related. Different Species can have dif * [X] Publications. * [X] gn:set->gn:dataset. * [X] gn:dataset->gn:trait -* [-] probesets -* [ ] genotypes +* [-] DNA markers and snps +* [ ] Link geno-files to the correct data (ref gn2 code on how this is done) +* [ ] probesets ## Link experiment data from LMDB / Compute Data / RIF / Case Attributes -- cgit 1.4.1 From ebd253c551ef2f2336d292957504b740be883bfb Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Fri, 6 Feb 2026 06:41:08 +0300 Subject: Update issue. Signed-off-by: Munyoki Kilyungi --- issues/rdf/rdf-refinement.gmi | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/issues/rdf/rdf-refinement.gmi b/issues/rdf/rdf-refinement.gmi index c37fa0d2..9359f2e3 100644 --- a/issues/rdf/rdf-refinement.gmi +++ b/issues/rdf/rdf-refinement.gmi @@ -250,7 +250,7 @@ We only have 532,248 markers: ``` Instead, present the number of markers. Link the snps/dna-markers to species. Show how to access them. -* [ ] gn-dataset -> marker_count/example-query +* [X] gn-dataset -> marker_count/example-query * [ ] markers -> metadata ### Phenotype Dataset @@ -272,8 +272,9 @@ Genotypes and markers are different but related. Different Species can have dif * [X] Publications. * [X] gn:set->gn:dataset. * [X] gn:dataset->gn:trait -* [-] DNA markers and snps -* [ ] Link geno-files to the correct data (ref gn2 code on how this is done) +* [X] DNA markers and snps +* [-] Link geno-files to the correct data (ref gn2 code on how this is done) +=> https://files.genenetwork.org/current/ Genotype files. The dir reps the InfoPages.AccesionId. * [ ] probesets ## Link experiment data from LMDB / Compute Data / RIF / Case Attributes -- cgit 1.4.1 From ea1c7818355fad2783daba92f98568618fa5b171 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Fri, 6 Feb 2026 09:26:00 +0300 Subject: Update issue. Signed-off-by: Munyoki Kilyungi --- issues/rdf/expose-lmdb-view-in-rdf.gmi | 5 +++++ issues/rdf/rdf-refinement.gmi | 25 ++++++++----------------- 2 files changed, 13 insertions(+), 17 deletions(-) diff --git a/issues/rdf/expose-lmdb-view-in-rdf.gmi b/issues/rdf/expose-lmdb-view-in-rdf.gmi index 275cf289..07b258ac 100644 --- a/issues/rdf/expose-lmdb-view-in-rdf.gmi +++ b/issues/rdf/expose-lmdb-view-in-rdf.gmi @@ -58,6 +58,11 @@ Prototype: * [ ] (bonfacem, pjotrp, alexm) How to work with case-attributes metadata. * [ ] (bonfacem) Add above link to RDF. +## Case Attributes / Compute Data +* [ ] Case Attributes. +* [ ] Individual Strains. +* [ ] (GEMMA/ Rqtl) Compute data. + ## Probeset strains * [ ] Mount LMDB_DATA_PATH to another partition because of "size" constraints(?) diff --git a/issues/rdf/rdf-refinement.gmi b/issues/rdf/rdf-refinement.gmi index 9359f2e3..c3e0f24e 100644 --- a/issues/rdf/rdf-refinement.gmi +++ b/issues/rdf/rdf-refinement.gmi @@ -265,7 +265,7 @@ Data entry error in: => https://info.genenetwork.org/infofile/source.php?GN_AccesionId=626 -## Phenotypes / RIF / Case Attributes / Individual Strains / Publications +## Phenotypes / Publications / DNA Markers / Probesets / RIF Genotypes and markers are different but related. Different Species can have different markers * [X] Phenotypes. @@ -273,29 +273,20 @@ Genotypes and markers are different but related. Different Species can have dif * [X] gn:set->gn:dataset. * [X] gn:dataset->gn:trait * [X] DNA markers and snps -* [-] Link geno-files to the correct data (ref gn2 code on how this is done) +* [X] Link geno-files to the correct data (ref gn2 code on how this is done) => https://files.genenetwork.org/current/ Genotype files. The dir reps the InfoPages.AccesionId. +* [X] Create global namespace for geno-files. * [ ] probesets - -## Link experiment data from LMDB / Compute Data / RIF / Case Attributes - -* [ ] (GEMMA/ Rqtl) Compute data. -* [ ] RIF. -* [ ] Case Attributes. -* [ ] Individual Strains. +* [ ] RIF +* [ ] (?) Gene Symbols ## GN Ontology -* [ ] Create endpoints that lists all "gnt:" and "gnc:" terms -* [ ] Create aliases for ontology. - -## Private data / Extras - +* [X] Create endpoints that lists all "gnt:" and "gnc:" terms * [ ] Add sparql queries as an example. -* [ ] ! Generate a list of data older than 2020 and ping Rob/Pjotr. ## Post Mark-up - -* [ ] Re-visit how we store all HTML metadata. Clean this up. +* [ ] ! Generate a list of data older than 2020 and ping Rob/Pjotr. +* [-] (Cancelled) Re-visit how we store all HTML metadata. Clean this up. * [ ] Sync mariadb tux01 with tux02; have rdf.genenetwork.org be the latest. * [ ] Make sure that the rdf.genenetwork.org named graph is available on public end-point (mention to Fred about the nuance of moving to a new graph without breaking CD/Prod from old code that used the old genenetwork.org graph). -- cgit 1.4.1