CellMap

Protein Localization and Protein-Protein Interaction (PPI) visualization tool.

Live example:

cell.dallago.us

Prerequisites:

1. Mongo
2. Fantom data, turned into .json files inside the ./data folder. [1]
3. Küster data, turned into .json files inside the ./data folder.

Fill up database

• Once all prerequisites have been met, you can run npm run import to fill the database with the data contained in the .json files in the /data folder.
• The script that fills the database will only fill the collections for which a corresponsing file exists.
• The insertion happens through a mongo upsert, thus existing entries will be updated if existent, while new ones will be inserted anew.
• The list of file names accepted is:
  • proteinMapping.json [UniProt] --> Collection: mappings
  • ExpressionLigRec.json [Riken] --> Collection: expressions
  • PairsLigRec.json [Riken] --> Collection: pairs
  • SubcelLoc.Ages.Proteins.json [Riken] --> Collection: localization, Depends on: mappings
  • AllTissues.json [Küster] --> Collection: tissues
  • hippie.json [mschaefer] --> Collection: interactions, Depends on: mappings

[1]: You can use parsjs to convert the tab-separated files from the Riken group to json files.