Difference between revisions of "Best Practice Handbook"

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=reBiND Best Practice Handbook=
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==Introduction==
 
==Introduction==
* About reBiND
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* [[About reBiND]]
 
* [[Introduction|How to use this manual]]
 
* [[Introduction|How to use this manual]]
  
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==System Installation and Administration (Technical information for administrators and IT specialists)==
 
==System Installation and Administration (Technical information for administrators and IT specialists)==
 
* [[Installation]]
 
* [[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:
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* [[Administration]]
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* [[Data Rescue - outdated software and hardware]]
  
** [http://wiki.bgbm.org/bps/index.php/Installation Installing BioCASe Provider Software]
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==Data Archiving (Information for content administrators and contributing scientists) ==
** [http://exist-db.org/exist/apps/doc/quickstart.xml Installing eXist]
 
** Installing reBiND Framework
 
** [[ReBiND Framework Configuration Steps|Configuring eXist/reBiND Framework]]
 
* Administration
 
** [[Architecture-Concept#Uploading_the_Data_to_eXist|Management of reBiND data in the eXist database]]
 
** Rights management
 
** Documentation of [[Correction Modules]]
 
** Writing Custom Correction Modules ([[Architecture-Concept#Automated_Corrections|How to modify the correction configuration file]])
 
** Using a different XML format
 
** Using a different metadata format ([[Metadata|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*Data Rescue (outdated software and hardware)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a core part of the workflow, however during the project we gained experience with tranforming data stored in old and outdated software and hardware formats.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 [[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) ==
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* [[Data_preparation|Data Preparation]]
*Workflow
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* [[Creating_new_rebind_project|Creating a new project]]
** Data Preparation
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* [[Data_upload_to_rebind_framework|Uploading data to the reBiND data portal - files less than 1000 ABCD units]]
***Prepare the content for ABCD mapping: resolve abbreviations, add units, concatenate atomised scientific name, additional information from data documentation, add metadata, denormalise
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* [[Exporting_XML_files_from_BPS| Uploading data to the reBiND data portal - files greater than 1000 ABCD units]]
***ABCD Mapping (see BioCASE documentation) plus additional examples
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* [[Validation_and_Corrections |Validation and Corrections]]
** [[Data_upload_to_rebind_framework|Creating a new project and uploading data to the reBiND data portal]]
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* [[Manual_review_of_data |Manual review of the data file]]
** [[Validation_and_Corrections |Validation and Corrections]]
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* [[Entering_metadata |Entering metadata]]
** Reviewing the XML file ([[Architecture-Concept#Manual_Review_and_Corrections|Some notes on manual review]])
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* [[Publishing_and_searching_the_data |Publishing and searching the data]]
** [[Entering_metadata |Entering metadata]]
 
** [[Publishing_and_searching_the_data |Publishing and searching the data]]
 
  
 
==Case Studies==
 
==Case Studies==
* Case studies with single data sets from different providers ([[ReBiND_Stories| reBiND stories]])
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* [[Case studies with single data sets from different providers ]]
* General observations
 
 
 
  
 
== Supporting data preparation  ==
 
== Supporting data preparation  ==
 
* [[Supporting_data_preparation_software|Software Products]]
 
* [[Supporting_data_preparation_software|Software Products]]
* [[Supporting procedures|Supporting_data_preparation_procedures]]
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* [[Supporting procedures|Supporting data preparation procedures]]
  
 
==Technical Background==
 
==Technical Background==
*eXist ([[Architecture-Concept#eXist|The role of eXist in the reBiND project]])
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*[[eXist_and_xquery|eXist and xquery]]
*XQuery
 
 
*[[Ecologial Metadata Language]]
 
*[[Ecologial Metadata Language]]
 
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*[[ABCD Access to Biological Collection Data, Standard]]
==FAQ==
 
  
 
==Glossary==
 
==Glossary==
  
* [[Architecture-Concept#Terms|A description of some of the terms used in this manual]]
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* [[Glossary|A description of some of the terms used in this manual]]
  
 
==References==
 
==References==
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* Güntsch, A., Fichtmüller, D.,  Kirchhoff, A. & Berendsohn, W.G.: Efficient rescue of threatened biodiversity data using reBiND-workflows. In: Plant Biosystems, 146(4) (2012), S. 752-755, DOI:10.1080/11263504.2012.740086
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* The BioCASE Provider Software Documentation: http://wiki.bgbm.org/bps/index.php/Main_Page
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* BioCASE Biological Collection Access Service: http://www.biocase.org/
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* ABCD Schema (Access ot Biological Collection Data); ABCD 2.0 Concepts: http://wiki.tdwg.org/twiki/bin/view/ABCD/AbcdConcepts
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* GBIF (Global Biodiversity Information Facility): http://www.gbif.org/

Latest revision as of 15:57, 14 January 2015

reBiND Best Practice Handbook

Introduction

The reBiND workflow

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

Data Archiving (Information for content administrators and contributing scientists)

Case Studies

Supporting data preparation

Technical Background

Glossary

References

  • Güntsch, A., Fichtmüller, D., Kirchhoff, A. & Berendsohn, W.G.: Efficient rescue of threatened biodiversity data using reBiND-workflows. In: Plant Biosystems, 146(4) (2012), S. 752-755, DOI:10.1080/11263504.2012.740086