MicroScope Platform Overview
- Overview of the annotation editor
- Annotation Rules
- BLAST results
- Compositional features
- E. coli K12
- B. subtilis
- MaGe/Curated annotations
- Syntonome / Syntonome RefSeq
- Similarities SwissProt / TrEMBL
- Predicted MetaCyc Pathways
MicroScope - Tutorial » Metabolism » Pathway Curation
How to access to the Pathway Curation Tool ?
Pathway Curation tool is accessible in the Metabolism section of the main navigation menu.
What is the usefulness of this tool ?
This tool presents a list of predicted MicroCyc pathways in a given organism, coming from pathway-tools software results, for which statuses can be curated by the annotator (3).
The current state of curation is resumed at the top of the page (1).
How to read the result table ?
1 : buttons to change the pathway status (validated, unknown, non-fonctionnal, deleted)
2 : current curation status of the pathway
3 : pathway identifier and name
4 : completion of the pathway in the organism
5 : number of reactions in the pathway (excluding spontaneous reactions)
What are the different curation statuses ?
Users are able to curate the prediction for a given organism by assigning different statuses.
The different statuses are:
A complete pathway cannot be deleted.
How to use this tool ?
The pathway status can be modified using the buttons "validate", "variant needed", "unknown", "non-fonctionnal" and "delete".
Moreover, it is possible to add a MetaCyc pathway which has not been predicted by using a keyword search tool.
1 ) Enter a keyword relative to the pathway of interest (ex: glucose).
2 ) Click on "search" button.
3 ) Select the correct pathway
4 ) Click on "Add" button in order to set the pathway as present in the organism.