Species information - Githubissues

cytoscape / enrichment-table-app

Creates a new table for performing, storing and viewing functional enrichment analysis

GNU Lesser General Public License v2.1

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Species information #53

Closed AlexanderPico closed 2 years ago

AlexanderPico commented 3 years ago

Some apps will have a species, organism or taxonomy id entry in the Network Table. Our app should check for this before setting our Enrichment Table::organism entry.

If the network has an entry, we should use this over the global default. If the user has made a setting change using our settings panel, then we would use this regardless, letting users override the other table information if they choose to.

AlexanderPico commented 3 years ago

Examples:

stringApp has species with latin names
NDEX has organism with common names
WikiPathways app doesn't have anything currently, but it could provide latin names in a future release.
IntAct provides IntAct::species with latin names in the Node Table (maybe query first entry or most frequent?)
PSIQCUIC provides Taxonomy ID with numeric IDs in the Node Table (maybe query first entry or most frequent?)

yihangx commented 2 years ago

I tested this on stringApp and NDEx. It works. @AkMo3 I will give Alex a demo tomorrow to double check this. After that, I can close this issue and merge the PR.