Best Practice Handbook

Best Practice Handbook

Introduction

• About reBiND
• How to use this manual

System Installation and Administration (Technical information for administrators and IT specialists)

• Installation

Before you use the reBiND archiving system the data must be transformed into a suitable XML format. We use ABCD format and to create ABCD XML files we recommend using the Biocase Provider Software (BPS). To install this software please follow the installation instructions in the BPS wiki:

• • Installing BioCASe Provider Software
  • Installing eXist
  • Installing reBiND Framework
  • Configuring eXist/reBiND Framework
• Administration
  • Management of reBiND data in the eXist database
  • Rights management
  • Documentation of Correction Modules
  • Writing Custom Correction Modules (How to modify the correction configuration file)
  • Using a different XML format
  • Using a different metadata format (Discussion of different Metadata standards)

Data Archiving (Information for content administrators and contributing scientists)

• Workflow (An overview of the pipeline)
  • Data Preparation
    • Prepare the content for ABCD mapping: resolve abbreviations, add units, concatenate atomised scientific name, additional information from data documentation, add metadata, denormalise
    • ABCD Mapping (see BioCASE documentation) plus additional examples
  • XML Export from BioCASE provider software (mention other like Pentaho Kettle?)
  • Creating a new project and uploading data to the reBiND data portal
    • Logon
    • Create project
    • Import from XML file system
    • Connect to BioCASE and upload XML
  • Validation and Corrections (An overview of the reBiND interface showing correction and validation)
    • Validation
    • Running the automated correction
      • Default correction (selecting existing correction module)
      • Modifiy correction
      • Add additional modules
  • Reviewing the XML file (Some notes on manual review)
  • Entering metadata (An overview of the different forms in the Metadata Editor tool)
  • Publishing the dataset

Data Access and Search

• Search via reBiND web interface
• Search via Biodiversity networks (GBIF)

Case Studies

• Case studies with single data sets from different providers ( reBiND stories)
• General observations

Data Rescue (outdated software and hardware)

• Software
  • Identifying Unknown File Formats
  • Conversion for selected file formats
    • DataPerfect
    • Paradox
    • dBase
    • Harvard Graphics
    • Word 3 for DOS
    • Excel to Access database
  • Document new data formats for others
• Hardware
  • 3.5" Floppies
  • 5.25 " Floppies

Supporting data preparation

• Software Products
  • Data Splitter
  • Character Encoding Correcter
  • Stand-alone Correction Manager
• Supporting procedures
  • Retrieving Geocoordinates From Points In Images

Technical Background

• eXist (The role of eXist in the reBiND project)
• XQuery
• ABCD in reBiND
• Ecologial Metadata Language

Glossary

• A description of some of the terms used in this manual