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UniProt-Or-Mapping

An object relational mapping of UniProtKB to a database and/or Java objects using Hibernate.

Auto-generate Java code and (optionally) to a relational database to manage UniProt data.

This projects uses the UniProt XML schema to auto-generate Java code as well as a relational database mapping.

How to parse a UniProt XML file into a Java data structure:

            URL u = UniProtTools.getURLforXML(accession);
            InputStream inStream = u.openStream();
            Uniprot up = UniProtTools.readUniProtFromInputStream(inStream);

Get Started

  1. Check out the code
  2. After running mvn install you can immediately parse UniProt XML files.

Load into a database

Once the initial code/database have been created any UniProt-XML file can get parsed and loaded into a database (however the code also works without a database by just reading UniProt XML files).

See here for how to load into a database.

Isoform mapping to alternative transcripts

This project can map UniProt isoforms to alternative transcripts using BioJava. For an example see isoforms.md

Use Case

A database that is maintained using this code base is used for the UniProt section of the RCSB PDB Protein Feature View that is available from e.g. here.

Still TODO

Release on Maven Central