import for enzyme/protein data from uniprot

[cleberecht]

Evaluate the UniProtJAPI or use REST and an xml parser to get entries from the uniprot.

[cleberecht]

I cannot get the UniProtJAPI to work correctly and it has a huge dependency overhead (bummer :disappointed:). Probably xml is the better alternative.

Next steps:

• create a classical parser service and
• xml contenthandler.

[cleberecht]

Bare Bones parser is ready .

Attributes to cast: required:

• accession number
• recommended full name
• comment on subunit (see below)
• mass

nice to have

• alternative names as annotation
• organism as annotation
  • scientific name
  • taxonomy identifier
  • common name
  • linage
• sequence as annotation
• comments on
  • function as annotation
  • catalytic activity as annotation
  • cofactor
  • subcellular location (might come in handy later)

Subunit should be needed to calculate diffusion speed. Lots of proteins are naturally occurring as dimers or similar. This should be parsed and used to calculate something as effective weight.

Edit 1: Commit d84688c adds basic parser and features. Edit 2: Commit 9418a33 adds functionality.

[cleberecht]

Parsing currently works as expected. The remainder of the attributes to cast have been moved to separate issues, so they can be handled later.