Thread:Whitespace in gene/metabolite identifiers (1)
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| 09:26, 30 November 2010 | Thomas (Talk | contribs) | New thread created |
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This pathway contained a lot of invalid gene/metabolite annotations (as noticed by the xref bot). I looked into this and it turned out that many were valid but contained trailing whitespace, causing them not to be recognized by the database. I fixed these identifiers, but please mind this in future edits (this white space is typically a result of bad copy/pasting).
There are still a lot of datanodes that have an invalid or unrecognized annotation (see below for report). There is an easy fix for many of the invalid Entrez Gene identifiers: use the corresponding Ensembl instead. The easiest way is to search by the gene name in the editor applet and then pick one of the annotations, this way you can be sure it's recognized by the database.
234 xrefs map to database 78 xref are not in database
- (:) --> These are datanodes without text label or annotation!
- (:)
- F2-Isoprostane (Cp:53788444)
- (:)
- (:)
- (:)
- (:)
- F2-Isoprostane (Cp:53788444)
- PGH3 (O:)
- (:)
- TRXR1 (L:7296)
- R-Triiodothyronine (rT3) (Ce:28774)
- Thyroxine (T4) (Ce:30660)
- R-Triiodothyronine (rT3) (Ce:28774)
- Thyroxine (T4) (Ce:30660)
- 5,6-Epoxytetraene (Ck:C14815)
- GPX 4 (L:2879)
- TRXR2 (L:10587)
- SelR (L:51734)
- GPX 3 (L:2878)
- Selenium (Cp:HMDB01349)
- Selenium (Cp:HMDB01349)
- Sep15 (L:9403)
- SelK (L:58515)
- GPX 6 (L:257202)
- Nicotinamidase (O:EC 3.5.1.19)
- Selenide (Ce:15076)
- GPX 3 (L:2878)
- GPX 2 (L:2877)
- SelP (L:6414)
- GPX 1 (L:2876)
- ROS (Ce:26523)
- RNS (Wi:)
- SelI (L:85465)
- SelT (L:51714)
- SelH (L:280636)
- SelV (L:348303)
- SPS2 (L:22928)
- DIO3 (L:1735)
- DIO2 (L:1734)
- SelM (L:140606)
- SelS (L:55829)
- SelP (L:6414)
- SelN (L:57190)
- SelO (L:83642)
- TAG (Ce:17855)
- LDL (Ce:39026)
- LDL (Ce:39026)
- HDL/APOA1 (Ce:39025)
- HDL/SAA (Ce:39025)
- HDL (Ce:39025)
- VLDL/APOB (Ce:39027)
- VLDL (Ce:39027)
- VLDL-TAG (Ce:47776)
- HDL (Ce:39025)
- TAG (Ce:17855)
- HDL-C (Ce:47775)
- SAA3 (L:6290)
- VLDL (Ce:39027)
- oxLDL (Ce:39026)
- HDL-C (Ce:47775)
- oxLDL (Ce:39026)
- VLDL-TAG (Ce:47776)
- O3 (Ce:25812)
- NO2 (Ce:33101)
- HNO2 (Ce:25567)
- D-dimer (Wi:)
- Fibrinogen (O:GO:0005577)
- HbA1c (O:)
- Fibrin (Cp:439199)
- Fibrinogen (O:GO:0005577)
- D-dimer (Wi:)
- HbA1c (O:)
- Fibrin (Cp:439199)
- SelW (L:6415)
- TRXR1 (L:7296)
- Ascorbate (Ce:38290)
- TRXR3 (L:114112)
