CommunityCurationProtocol
From WikiPathways
(Difference between revisions)
(New page: In the coming weeks, we are going to review all pathways on WikiPathways to make them more usable for computational analysis. The main improvements we want to make are: * Provide a proper ...) |
|||
| Line 7: | Line 7: | ||
The following steps could help in reviewing and improving a pathway. | The following steps could help in reviewing and improving a pathway. | ||
| + | * Identify stacked datanodes and group them (CTRL-G) | ||
| + | TODO: Example | ||
| + | * Find labels that span multiple lines. If multiple labels are used to represent a single block of text, convert them to a single multi-line label | ||
| + | TODO: Example | ||
* Check for labels that represent a gene-product or metabolite and convert them to a properly annotated DataNode | * Check for labels that represent a gene-product or metabolite and convert them to a properly annotated DataNode | ||
{|class="prettytable" | {|class="prettytable" | ||
| Line 16: | Line 20: | ||
|http://ftp2.bigcat.unimaas.nl/~thomas.kelder/images/wikipathways_curation/label2datanode_after.png | |http://ftp2.bigcat.unimaas.nl/~thomas.kelder/images/wikipathways_curation/label2datanode_after.png | ||
|} | |} | ||
| - | |||
| - | |||
* Replace multiple line segments with a single connector | * Replace multiple line segments with a single connector | ||
TODO: Example | TODO: Example | ||
* Replace arc/arrowhead combinations with curved connectors | * Replace arc/arrowhead combinations with curved connectors | ||
TODO: Example | TODO: Example | ||
| - | * Link lines between elements | + | * Link lines between elements. You can press CTRL-R to reveal all unlinked line ends. |
TODO: Example | TODO: Example | ||
* ... | * ... | ||
Revision as of 17:59, 14 May 2008
In the coming weeks, we are going to review all pathways on WikiPathways to make them more usable for computational analysis. The main improvements we want to make are:
- Provide a proper graph representation by connecting all lines and arrows that represent an interaction
- Group complexes and other elements that act together
- Check the annotation of gene-products and metabolites
Protocol
The following steps could help in reviewing and improving a pathway.
- Identify stacked datanodes and group them (CTRL-G)
TODO: Example
- Find labels that span multiple lines. If multiple labels are used to represent a single block of text, convert them to a single multi-line label
TODO: Example
- Check for labels that represent a gene-product or metabolite and convert them to a properly annotated DataNode
| Before | After |
|---|---|
| 
|
- Replace multiple line segments with a single connector
TODO: Example
- Replace arc/arrowhead combinations with curved connectors
TODO: Example
- Link lines between elements. You can press CTRL-R to reveal all unlinked line ends.
TODO: Example
- ...
Problems
Please use the talk page to discuss problematic pathways.
