From 3b96bf11f1e8c672c236dbaaf77d9dff2c5f995d Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Fri, 31 Mar 2023 15:53:48 +0300 Subject: List down issues encountered with GeneRIF dump Signed-off-by: Munyoki Kilyungi --- issues/dump-genewiki-metadata.gmi | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'issues') diff --git a/issues/dump-genewiki-metadata.gmi b/issues/dump-genewiki-metadata.gmi index 056d8ed..420d7f0 100644 --- a/issues/dump-genewiki-metadata.gmi +++ b/issues/dump-genewiki-metadata.gmi @@ -10,3 +10,29 @@ Dump the tables: * GeneRIF * GeneRIF_BASIC + +## Issues + +* Some entries in the GeneRIF table don't have any entries in the GeneRIF_BASIC table: + +``` +SELECT * FROM GeneRIF LEFT JOIN GeneRIF_BASIC USING (symbol) LEFT JOIN GeneRIFXRef ON GeneRIFXRef.GeneRIFId = GeneRIF.Id LEFT JOIN GeneCategory ON GeneRIFXRef.GeneCategoryId = GeneCategory.Id WHERE GeneRIF.display > 0 AND GeneRIF.VersionId = 0 AND GeneRIF_BASIC.GeneId IS NULL\G +``` + +* Missing data: some GeneIds stored in GN are not in GeneInfo. These can be conceptualised as anonymous genewiki entries. One example is the symbol "Mul1" with the GeneId 68350. This example exists in GN with different GeneId's. Example query: + +=> + +``` +SELECT * FROM GeneInfo WHERE GeneId = 68350\G +``` + +* NEWENTRY: We have many genes with the "NEWENTRY". In GN1, these are represented in one very big page: + +=> https://gn1.genenetwork.org/webqtl/main.py?FormID=geneWiki&symbol=NEWENTRY + +To query these entries: + +``` +SELECT * FROM GeneRIF_BASIC WHERE symbol = 'NEWENTRY'\G +``` -- cgit v1.2.3