Thread:Comments on the annotation of the pathway (1)
From WikiPathways
(New page: Hi, Thank you for the continued development of these pathway. Some comments, especially on the annotation of the datanodes would help the readability of the pathway on PathVisio. 1. Som...) |
Current revision (11:51, 11 April 2023) (view source) |
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5. Some of the nodes which have a pathway name like 'Apoptosis pathway' if in a node would have to be a pathway node to be linked to other pathways in WikiPathways database. | 5. Some of the nodes which have a pathway name like 'Apoptosis pathway' if in a node would have to be a pathway node to be linked to other pathways in WikiPathways database. | ||
6. It might be better to remove the a different color labelling for increased and decreased expression of gene as that is data-dependent. | 6. It might be better to remove the a different color labelling for increased and decreased expression of gene as that is data-dependent. | ||
| - | 7. Also, the pathway itself is quite intense with a lot of different interactions and experimental conditions. Maybe , breaking this pathway down to sub-pathways might be better for pathway readabililty. But then this is jusy a suggesstion as it depends on the purpose of this pathway. | + | 7. Also, the pathway itself is quite intense with a lot of different interactions and experimental conditions. Maybe , breaking this pathway down to sub-pathways might be better for pathway readabililty. But then this is jusy a suggesstion as it depends on the purpose of this pathway. |
| + | 8. The descritpion of the pathway can also be made a bit more elaborate to understand the relevance of the pathway. | ||
| + | |||
If you have any questions or require any further clarifications please do not hesitate to get back to me. | If you have any questions or require any further clarifications please do not hesitate to get back to me. | ||
Thank you. | Thank you. | ||
Current revision
Hi,
Thank you for the continued development of these pathway.
Some comments, especially on the annotation of the datanodes would help the readability of the pathway on PathVisio. 1. Some nodes in the pathways are not annotated with a unique persistent identifier. 2. There are issues with selection of the identifier and the database for some nodes ex. CAMKK2 which had a Entrez gene ID but had the NCBI protein as the database selected. This prevents Wikipathways and PathVisio to link this idenitifer to other databases. 3. When annotating with NCBI protein id in this pathway : the NP_ is for the RefSeq database. Also, the decimal point of the Refseq identifier has to be omitted for the identifier to be recongnised in WikiPathways. ex. PRKAA1 : 'NP_996790.3' would be 'NP_996790'. 4. Some datanodes should just be a text label : ex Receptor internalisation and recycling 5. Some of the nodes which have a pathway name like 'Apoptosis pathway' if in a node would have to be a pathway node to be linked to other pathways in WikiPathways database. 6. It might be better to remove the a different color labelling for increased and decreased expression of gene as that is data-dependent. 7. Also, the pathway itself is quite intense with a lot of different interactions and experimental conditions. Maybe , breaking this pathway down to sub-pathways might be better for pathway readabililty. But then this is jusy a suggesstion as it depends on the purpose of this pathway. 8. The descritpion of the pathway can also be made a bit more elaborate to understand the relevance of the pathway.
If you have any questions or require any further clarifications please do not hesitate to get back to me.
Thank you.
