Pathway Talk:WP15
From WikiPathways
- This looks like the start of an interesting pathway. I have a few questions and suggestions:
- What is the difference between the blue and magenta metabolites?
- I'm assuming 'B' is for binding events. What is 'T'? While the line semantics aren't yet complete, you can represent binding events (and other specific relationships) with a special kind a line, 'mim-binding' using the Properties pull-down menu when the line is selected.
- You may was to make a simple legend in the corner to identify your color and label scheme
- I converted a couple of your segmented 90-degree lines into single lines with elbows (see connections from thioredoxin to ascorbic acid and lipoic acid). You can see it looks the same in the end, but it's now modeled correctly (a direct connection between the entities) and it was actually easier to draw. You can add elbows and curves to any line by right-clicking on the line and changing the line type.
- Check out other drawing tips here: http://www.wikipathways.org/index.php/Help:Guidelines
- AlexanderPico 17:57, 8 June 2008 (UTC)
- This pathway looks great! An additional suggestion:
- You may want to annotate the metabolites and enzymes with identifiers from databases such as Entrez Gene or HMDB. This allows you (and other users) to view detailed information on the enzymes and to use the pathway for computational data analyses (such as microarray data in GenMAPP). As an example, I added identifiers to the PNPO enzyme and the Methionine sulfoxide metabolite (see the table at the bottom of the pathway page). See the tutorial on how to add identifiers: Annotating DataNodes. You can use the search function for both enzymes as metabolites.
- Thomas 14:57, 9 June 2008 (UTC)
- Wow! Great improvements. Here's another tip:
- While in edit mode, you can press ctrl-L to highlight all the line ends that are not connected to an object. You may want to go through and connect these to the target spots to form a more complete model of your pathway network. These connections, for example, will be preserved when imported into Cytoscape.
- AlexanderPico 23:27, 9 June 2008 (UTC)
Whitespace in gene/metabolite identifiers (1)
There have been no changes to this discussion for at least 30 days. If it is concluded, you may want to write a summary.
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)
Is this pathway complete? (8)
There have been no changes to this discussion for at least 30 days. If it is concluded, you may want to write a summary.
Hello,
This pathway looks mostly complete. If you confirm that it is indeed complete, it will be included in the distributed GenMAPP pathway archives.
Also, the pathway still includes "B" and "T" for lines, in the form of DataNodes. This is unfortunate since these appear in the DataNode list, although they are actually labels. If you want to keep the B and T labels for lines, please change them into the Label type instead.
Thanks,
Kristina
