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]]
  
==System Installation and Administration==
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==The reBiND workflow==
* Installation
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* [[Overview_rebind_workflow#Overview_of_the_reBiND_workflow|An overview of the reBiND pipeline]]
** [http://wiki.bgbm.org/bps/index.php/Installation Installing BioCASe Provider Software]
 
** 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 Archiving==
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==System Installation and Administration (Technical information for administrators and IT specialists)==
*Workflow ([[Architecture-Concept#Overview|An overview of the pipeline]])
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* [[Installation]]
** Data Preparation
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* [[Administration]]
***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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* [[Data Rescue - outdated software and hardware]]
***ABCD Mapping (see BioCASE documentation) plus additional examples
 
** XML Export from BioCASE provider software (mention other like Pentaho Kettle?)
 
** Import to reBiND Framework
 
*** Import from XML file system
 
*** Connect to BioCASE and upload XML
 
** Validation and Corrections ([http://rebind.bgbm.org/first_screenshots 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 ([[Architecture-Concept#Manual_Review_and_Corrections|Some notes on manual review]])
 
** Entering metadata ([http://rebind.bgbm.org/metadata_capture An overview of the different forms in the Metadata Editor tool])
 
** Publishing the dataset
 
  
==Data Access and Search==
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==Data Archiving (Information for content administrators and contributing scientists) ==
* Search via reBiND web interface
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* Search via Biodiversity networks (GBIF)
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* [[Data_preparation|Data Preparation]]
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* [[Creating_new_rebind_project|Creating a new project]]
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* [[Data_upload_to_rebind_framework|Uploading data to the reBiND data portal - files less than 1000 ABCD units]]
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* [[Exporting_XML_files_from_BPS| Uploading data to the reBiND data portal - files greater than 1000 ABCD units]]
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* [[Validation_and_Corrections |Validation and Corrections]]
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* [[Manual_review_of_data |Manual review of the data file]]
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* [[Entering_metadata |Entering metadata]]
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* [[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
 
 
 
==Data Rescue (outdated software and hardware) ==
 
*Software
 
** [[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]]
 
  
 
== Supporting data preparation  ==
 
== Supporting data preparation  ==
* Software Products
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* [[Supporting_data_preparation_software|Software Products]]
** Data Splitter
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* [[Supporting procedures|Supporting data preparation procedures]]
** Character Encoding Correcter
 
** Stand-alone Correction Manager
 
* Supporting procedures
 
** [[Retrieving Geocoordinates From Points In Images]]
 
  
 
==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
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*[[Ecologial Metadata Language]]
*ABCD [[ABCD in reBiND]]
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*[[ABCD Access to Biological Collection Data, Standard]]
*EML [[Ecological Metadata Lanuage]]
 
 
 
==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