gn-transform-databases, branch masterData transformers for GeneNetwork (particularly to RDF)
http://git.genenetwork.org/gn-transform-databases/atom?h=master2026-04-20T07:12:30+00:00Add trait page link for probesets and phenotypes.2026-04-20T07:12:30+00:00Munyoki Kilyungi2026-04-20T07:12:30+00:00urn:sha1:b0ef58eaff0e5966dc1dafc6abba8e42e3db1fe2
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Add new term for traits page.2026-04-20T06:45:51+00:00Munyoki Kilyungi2026-04-20T06:42:18+00:00urn:sha1:7f7272be9e0c43a2b80ccecb4055cec58b888514
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Add wd: to global virtuoso namespace.2026-03-16T07:15:06+00:00Munyoki Kilyungi2026-03-16T07:15:06+00:00urn:sha1:399d12d79d82d2c35b65f83e4ec4880b1e31ca81
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Trigger CI.2026-03-10T04:56:06+00:00Munyoki Kilyungi2026-03-10T04:56:06+00:00urn:sha1:d8515ca22800acc88c13dc24bc0b865e2fa7e336
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Comment out node that points to lmdb data for probesets.2026-03-06T07:11:06+00:00Munyoki Kilyungi2026-03-06T07:10:34+00:00urn:sha1:02d5b8b4e478fd7f4eb9d53754fb846b5165b9d0
Right now, we have:
"dcat:distribution gnd:GTEx_Lung _0414_ENSG00000262400.1.json ;"
Note the space after the "Lung". Comment this out for now, so that we
agree with Alex how that should look like.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Revert "transform: add keyset pagination and streaming emit path"2026-03-04T15:16:59+00:00Munyoki Kilyungi2026-03-04T15:16:59+00:00urn:sha1:a5c1958d5b1abfaaa4ae2a2749ce7f8b0ed3055c
This reverts commit ba347362d64f9e634fad7f1aa8ab0a7753ff7a81. Causes
and endless loop. See:
https://ci.genenetwork.org/jobs/transform-genenetwork-database/99
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
transform: add keyset pagination and streaming emit path2026-03-02T15:30:01+00:00Munyoki Kilyungi2026-03-02T15:19:27+00:00urn:sha1:ba347362d64f9e634fad7f1aa8ab0a7753ff7a81
* transform/special-forms.scm (define-transformer): Add keyset
arguments and cursor return path; add SQL helpers for keyset
ordering/filtering; avoid po-alist allocation by streaming short
turtle emission.
(with-documentation): Add keyset pagination loop using per-input
cursor state and configurable chunk key field.
(emit-short-turtle): Emit triples in a single linear pass.
* examples/probesets-experiment-metadata.scm: Enable keyset pagination
and set composite chunk key fields for ProbeSetFreeze/ProbeSet join.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
examples: Align ontology with BFO and normalize snake_case terms2026-03-02T14:18:29+00:00Munyoki Kilyungi2026-03-02T14:18:09+00:00urn:sha1:083a1fc995e906b8323e3b58d61f5a226e408cb9
* examples/ontology.scm: Add BFO bridge classes and align GN classes
under material/information entities. Define missing `gnt:'/`gnc:'
terms used across transformers. Correct property kinds and
domains/ranges for dataset, phenotype, genotype, probeset, and gene
metadata.
* examples/genelist.scm: Replace gnc:ResourceLink and gnc:PantherLink
with snake_case terms.
* examples/probesets-experiment-metadata.scm: Rename gnt:SE -> gnt:se.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Sanitize experiment data.2026-02-19T13:11:15+00:00Munyoki Kilyungi2026-02-19T13:11:15+00:00urn:sha1:6fb74e2e1c59ed4934a1177816a717382c91e0cb
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Transform all wiki entries.2026-02-18T13:34:41+00:00Munyoki Kilyungi2026-02-18T13:34:41+00:00urn:sha1:6751c74040a72032f0f7db863cb68693a4e45167
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>