Difference between revisions of "Best Practice Handbook"

Revision as of 18:18, 10 October 2014

Introduction

• About reBiND
• How to use this manual

The reBiND workflow

• An overview of the reBiND pipeline

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 (ABCD_in_reBiND) 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• Data Rescue (outdated software and hardware)

This is not a core part of the workflow, however during the project we gained experience with tranforming data stored in old and outdated software and hardware formats.

• • 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

Data Archiving (Information for content administrators and contributing scientists)

• Workflow
  • 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

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

FAQ

Glossary

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

References