Thread:Initial review (1)
From WikiPathways
(New page: After quickly reviewing your pathway, it looks well annotated and most of the lines are connected! Well done! I have a couple of small questions: 1. It seems your pathway contains four i...) |
Current revision (11:51, 31 August 2023) (view source) |
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After quickly reviewing your pathway, it looks well annotated and most of the lines are connected! Well done! | After quickly reviewing your pathway, it looks well annotated and most of the lines are connected! Well done! | ||
I have a couple of small questions: | I have a couple of small questions: | ||
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1. It seems your pathway contains four independent pathways. Wouldn't it make sense to split them into four pathway models on WikiPathways? This might increase their usability in downstream analyses. | 1. It seems your pathway contains four independent pathways. Wouldn't it make sense to split them into four pathway models on WikiPathways? This might increase their usability in downstream analyses. | ||
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2. I saw that you used fill color to indicate expression changes. We usually advise against adding actual expression data in the pathway models. That is usually done downstream in the data overlay in PathVisio or Cytoscape. By purely describing the biological processes, the data from any experimental dataset can then be visualized on the pathways in downstream analyses, thereby increasing the reusability of the pathway. | 2. I saw that you used fill color to indicate expression changes. We usually advise against adding actual expression data in the pathway models. That is usually done downstream in the data overlay in PathVisio or Cytoscape. By purely describing the biological processes, the data from any experimental dataset can then be visualized on the pathways in downstream analyses, thereby increasing the reusability of the pathway. | ||
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3. I saw an issue with the encoding of three references (25, 30, 106). Which operating systems are you using? Are you using the new installers for PathVisio? | 3. I saw an issue with the encoding of three references (25, 30, 106). Which operating systems are you using? Are you using the new installers for PathVisio? | ||
Current revision
After quickly reviewing your pathway, it looks well annotated and most of the lines are connected! Well done!
I have a couple of small questions:
1. It seems your pathway contains four independent pathways. Wouldn't it make sense to split them into four pathway models on WikiPathways? This might increase their usability in downstream analyses.
2. I saw that you used fill color to indicate expression changes. We usually advise against adding actual expression data in the pathway models. That is usually done downstream in the data overlay in PathVisio or Cytoscape. By purely describing the biological processes, the data from any experimental dataset can then be visualized on the pathways in downstream analyses, thereby increasing the reusability of the pathway.
3. I saw an issue with the encoding of three references (25, 30, 106). Which operating systems are you using? Are you using the new installers for PathVisio?
