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| author | Munyoki Kilyungi | 2023-06-06 14:41:50 +0300 |
|---|---|---|
| committer | BonfaceKilz | 2023-06-12 19:06:36 +0300 |
| commit | 7121155871b500bf49e4f1ffa13ed66601acff8b (patch) | |
| tree | ad6d1ddf52ec731fa7e3b2b66fbb8adb8c84492c | |
| parent | d7c1100ebbb79839b84e7641e8a50a44841515eb (diff) | |
| download | gn-transform-databases-7121155871b500bf49e4f1ffa13ed66601acff8b.tar.gz | |
Make geoSeries a link during dataset dump
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| -rwxr-xr-x | examples/dump-dataset-metadata.scm | 10 | ||||
| -rwxr-xr-x | examples/dump-probesetfreeze.scm | 1 |
2 files changed, 8 insertions, 3 deletions
diff --git a/examples/dump-dataset-metadata.scm b/examples/dump-dataset-metadata.scm index 92e858c..5b57890 100755 --- a/examples/dump-dataset-metadata.scm +++ b/examples/dump-dataset-metadata.scm @@ -163,9 +163,12 @@ (set gn:aboutTissue (sanitize-rdf-string (field Datasets AboutTissue))) (set gn:geoSeries - (and (not (string-prefix-ci? "no geo series" - (field Datasets GeoSeries))) - (field Datasets GeoSeries))) + (let ((s + (string-match "GSE[0-9]*" + (field ("IFNULL(Datasets.GeoSeries, '')" GeoSeries))))) + (if s (ontology + 'geoSeries: (match:substring s)) + ""))) (set gn:title (regexp-substitute/global #f "^[Nn]one$" @@ -226,6 +229,7 @@ (prefix "dct:" "<http://purl.org/dc/terms/>") (prefix "foaf:" "<http://xmlns.com/foaf/0.1/>") (prefix "generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>") + (prefix "geoSeries:" "<http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=>") (prefix "gn:" "<http://genenetwork.org/>") (prefix "owl:" "<http://www.w3.org/2002/07/owl#>") (prefix "phenotype:" "<http://genenetwork.org/phenotype/>") diff --git a/examples/dump-probesetfreeze.scm b/examples/dump-probesetfreeze.scm index 605e415..3e0c930 100755 --- a/examples/dump-probesetfreeze.scm +++ b/examples/dump-probesetfreeze.scm @@ -68,6 +68,7 @@ (prefix "dct:" "<http://purl.org/dc/terms/>") (prefix "foaf:" "<http://xmlns.com/foaf/0.1/>") (prefix "generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>") + (prefix "geoSeries:" "<http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=>") (prefix "gn:" "<http://genenetwork.org/>") (prefix "owl:" "<http://www.w3.org/2002/07/owl#>") (prefix "phenotype:" "<http://genenetwork.org/phenotype/>") |