Difference between revisions of "Best Practice Handbook"
From reBiND Documentation
(→The reBiND workflow) |
|||
| Line 21: | Line 21: | ||
** Using a different XML format | ** Using a different XML format | ||
** Using a different metadata format ([[Metadata|Discussion of different Metadata standards]]) | ** Using a different metadata format ([[Metadata|Discussion of different Metadata standards]]) | ||
| + | |||
| + | *Data Rescue (outdated software and hardware) | ||
| + | This is not a code part of the workflow, however during the project we gained experience with the following software and hardware formats. | ||
| + | ** [[Identifying Unknown File Formats]] | ||
| + | ** Conversion for [[File Type Overview|selected file formats]] | ||
| + | *** [[Export DataPerfect|DataPerfect]] | ||
| + | *** [[Export Paradox Data|Paradox]] | ||
| + | *** [[Export dBase Data|dBase]] | ||
| + | *** Harvard Graphics | ||
| + | *** Word 3 for DOS | ||
| + | *** Excel to Access database | ||
| + | ** Document new data formats for others | ||
| + | * Hardware | ||
| + | ** 3.5" Floppies | ||
| + | ** [[Reading 5.25" Floppy Disks|5.25 " Floppies]] | ||
==Data Archiving (Information for content administrators and contributing scientists) == | ==Data Archiving (Information for content administrators and contributing scientists) == | ||
| Line 51: | Line 66: | ||
* General observations | * General observations | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
== Supporting data preparation == | == Supporting data preparation == | ||
Revision as of 18:57, 10 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 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 code part of the workflow, however during the project we gained experience with the following 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
