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  • What labs or how many are using GeneWays?

    - Rzhetsky lab, Califano lab, a few external users

  • Who is the main “database authority” for GeneWays?

    - Marc Hadfield

  • What kind of database is it? (flat-file, relational, XML, etc)

    - relational & indexed flat-files

  • Size of database?
    - Flat-file/Lucene indices: 500 GB

    - Oracle part: 5-10 GB

  • Anticipated yearly growth? (Megabytes/Gigabytes)

    - will probably make the Terabyte range in a year or so

  • Backup procedures? How often?
    • Database backups (Hot, Cold, Both) [and/or]
    • Operating system backup

      - ask Hans-Erik

  • What servers/operating systems are hosting them (IP addresses)
  • Approximately how many *active* users?
  • - approximately 200 users signed up, but difficult to find out the amount per user

  • How often is the database used? (Daily, Weekly, Monthly)

    - daily

  • What platforms are being used? (Oracle, MySQL, PostgreSQL, etc)

    - Oracle 9i Release 2

  • What applications are using these databases?
    • Web interface?
    • Application (GUI)?
    • Command line interface (CUI)?
    • Web interface
    • CUI - used infrequently
  • What is the primary purpose of the database & types of data stored?
    • Geneways is built to help integrate research results by providing automatic tools to gather knowledge from scientific literature
    • It scans thousands of research articles in order to automatically extract relevant molecular knowledge
    • It seeks to provide the collective knowledge of the whole research community in an integrated form
    • The core of the system is a knowledge base of molecular actions which can be queried, analyzed, critiqued, and visualized


  • Are there any issues or problems with the database?
    • Specific error messages popping up?
    • Problems connecting from the application or web interface?
    • Performance issues (queries are slow, freezes at times, etc)
  • it is slow due to an old server which they are looking to replace
  • Would they like help in administering the database?
  • not at the moment
  • What additional features or changes would users like to see?
    • new tables or queries
    • additional screens on application or web interface
    • migrate to different database platform (i.e. MySQL to Oracle)
      • the user interface needs improvement
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