Difference between revisions of "Best Practice Handbook"
From reBiND Documentation
LornaMorris (talk | contribs) (→Data Archiving (Information for content administrators and contributing scientists)) |
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*** Import from XML file system | *** Import from XML file system | ||
*** Connect to BioCASE and upload XML | *** Connect to BioCASE and upload XML | ||
− | ** [[Validation_and_Corrections |Validation and Corrections]]([http://rebind.bgbm.org/first_screenshots An overview of the reBiND interface showing correction and validation]) | + | ** [[Validation_and_Corrections |Validation and Corrections]] ([http://rebind.bgbm.org/first_screenshots An overview of the reBiND interface showing correction and validation]) |
*** Validation | *** Validation | ||
*** Running the automated correction | *** Running the automated correction |
Revision as of 13:19, 13 October 2014
Contents
- 1 Introduction
- 2 The reBiND workflow
- 3 System Installation and Administration (Technical information for administrators and IT specialists)
- 4 Data Archiving (Information for content administrators and contributing scientists)
- 5 Data Access and Search
- 6 Case Studies
- 7 Supporting data preparation
- 8 Technical Background
- 9 FAQ
- 10 Glossary
- 11 References
Introduction
- About reBiND
- How to use this manual
The reBiND workflow
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- Data Rescue (outdated software and hardware)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a core part of the workflow, however during the project we gained experience with tranforming data stored in old and outdated software and hardware formats.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 Preparation
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