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This is about how to publish your biodiversity data in GBIF portal through HKH-BIF
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International Centre for Integrated Mountain Development
Kathmandu, Nepal
Technical session IIDay 1
Publishing HKH Biodiversity Data Globally
Deependra Tandukar, Suman Jaiswal, Bandana Shakya23-24 August 2012
Outline
• Using HKH-BIF• Processes for publishing the data
– Preparing the data– Uploading data– Filling Metadata– Mapping – Publishing
Platform
DataHKH-BIF GBIF
• for easy and efficient access and sharing of regional biodiversity information
• provisions for partners to publish and share their data
• for collaborative work e.g. data paper publication
Processes for publishing data
• Prepare your data– Data resource– Templates– Processing with spreadsheet processor
• Upload your data• Fill in metadata• Map the fields with Darwin core• Publish
– Make it public
Step 1
Data Preparation
Collection of data records Information about the dataset
Step 1: Data preparation
Data resource
Data resource
Dataset Metadata+=
Occurrence data Metadata+
Checklist Metadata+
Step 1: Data preparation
Templates
• Standardized templates (based on Darwin core)
• Glossary (location, scientific name, family, etc.)
• Metadata• Occurrence data• Checklists
– Checklist 1– Checklist 2– Checklist 3
Step 1: Data preparation
Template types
Download from: http://tools.gbif.org/spreadsheet-processor
• Readme sheet
Step 1: Data preparation
Templates: Metadata
Readme sheet gives the general instruction on what and how to fill the metadata sheet
• Metadata sheet
Step 1: Data preparation
Templates: MetadataMetadata sheet has number of fields for information to feed in, and some of the fields marked by * are mandatory
• Readme sheet• Metadata sheet• Occurrence sheet
Step 1: Data preparation
Templates: Occurrence
45 fields/columns in total
This sheet is used to record species occurrence data and is suitable for recording basic natural history collections specimen records or species observations.
• Readme sheet• Metadata sheet• Classification sheet
Step 1: Data preparation
Templates: Checklist1
This sheet is used to record the species lists where you are not sure of higher classification
• Readme sheet• Metadata sheet• Classification sheet
Step 1: Data preparation
Templates: Checklist2
This sheet is used to record the species lists where you are not limited to strict Linnaean classification
• Readme sheet• Metadata sheet• Classification sheet
Step 1: Data preparation
Templates: Checklist3
This template is used to record species checklists in a simple columnar format that stores the basic taxonomic data in the columns (Kingdom, Phylum, Subphylum, Class, Order, Family, Genus, Species, etc.).
• Use checklist 3 for data preparation• Enter mandatory fields in metadata• Fill in classification sheet
Step 1: Data preparation
Hands-on session
• Enter fields in metadata
Step 1: Data preparation
Metadata
• Classification field
Step 1: Data preparation
Checklist data fields
Kingdom Animalia
Phylum Vertebrata
Class Amphibia
Order Anura
Family Ranidae
Genus Amolops
Scientific name Amolops ricketti
Countries China
Step 1: Data preparation
Process the template
Spreadsheet processor
Archive file
• Go to spreadsheet processor(http://tools.gbif.org/spreadsheet-processor/)
Step 1: Data preparation
Process the template
• Click on ‘Choose File’ and select your prepared checklist template, it gets uploaded
• Click on ‘Process File’
Step 1: Data preparation
Process checklist template
• Download the processed archive by clicking on ‘Click to Download Archive’
• Save on your desktop (filename will be something like 503117a7e582a.zip>
Step 1: Data preparation
Process checklist template
Step 2
Upload your data
• http://192.168.10.19/hkh-bif • Enter your username and password• Click on ‘login’
Step 2: Upload your data
Go to HKH-BIF
• Click on ‘Manage Resources’• Give a short name for your data/resource• Click on ‘Choose file’ and select the ‘Archive’ that was
downloaded earlier • Press on ‘Create’
Step 2: Upload your data
Create New Resource
Step 2: Upload your data
New resource created
4
Step 2: Upload your data
Source data
Step 2: Upload your data
Source data
Step 3
Metadata
Step 3: Metadata
Over view page
Step 3: Metadata
Basic metadata
Step 3: Metadata
Geographic coverage
• Geographic area covered by the resource
Step 3: Metadata
Taxonomic coverage
• Information about one of more groups of taxa covered by the resource
Step 3: Metadata
Keywords
• One or more sets of keywords about the resource.
Step 3: Metadata
Associated parties
• Information about one or more people or organizations associated with the resource those not already covered on the Basic Metadata page
Step 3: Metadata
Project data
• Information about a project under which the data in the resource were produced/generated
Step 3: Metadata
Sampling methods
• Information about sampling methods in general, and about specific sampling steps
Step 3: Metadata
Citations
• Information about how to cite the resource as well as a bibliography of citations related to the data set, such as publications that were used in or resulted from the production of the data
Step 3: Metadata
Collection data
• Information about the physical natural history collection associated with the resource (if any) as well as lists of types objects in the collection, called Curatorial Units
Step 3: Metadata
External links
• Links to the home page for the resource, links to the resource in alternate forms (database, spreadsheets, etc.)
Step 3: Metadata
Additional metadata
• Extra information e.g. logo, copyright information, etc.
Step 4
Mapping
Step 4: Mapping
Mapping
Step 4: Mapping
MappingD
arw
in c
ore
term
s
Source data
fields
Step 5
Publishing
Step 5: Publishing your data
Publish
Step 5: Publishing your data
Publish
• Click on publish to publish your data
• generates a new dwca.zip file containing:• RTF file (draft of data paper)• eml.xml file describing the metadata of this resource• meta.xml file describing the mappings of DwC terms and
source data columns• Source data file
Step 5: Publishing your data
Visible
• Make it public for sharing
Step 5: Publishing your data
Visibility
Step 5: Publishing your data
Visibility
Technical session IIDay 2 (Hands-on)
Publishing non-template data
Xls to csv format
• Open your excel file
• Save as ‘comma delimited csv’ format in your desktop, give a name ‘my_first_data’
• http://192.168.10.19:8080/hkh-bif• Enter your username and password• Click on ‘login’
Go to HKH-BIF
• Click on ‘Manage Resources’• Give a short name for your data/resource• Press on ‘Create’
Create New Resource
my_first_data
• Click on ‘choose file’ under source file and select your .csv file
Create new resource
Create new resource
New resource
Mapping
Mapping
• Select ‘Darwin Core Mappings’ type from the drop down – in our case it is ‘Darwin Core Taxon’
• Then click on ‘Add’
Mapping
• Auto mapped 1 column
Mapping
• At the bottom of the page, a list of the unmapped fields are displayed
Mapping
• Let’s start mapping now• Auto mapped Kingdom = Kingdom• Map ScientificName = Sname, class = C according to our data
Dar
win
cor
e te
rms
Source data
fields
Filter
Exclude the records that do not match the criteria using filter
Mapping
• Once all the known fields are mapped, click on save button
• On the top of the page, click on ‘back to resource over view page’
Metadata
• Now enter the metadata
Metadata
Publish
• Click on publish to publish your data
Make it visible
• Make it public for sharing
Useful resources• Getting Started: Overview of Data Publishing through GBIF network
http://links.gbif.org/getting_started_publishing_en_v1 • Integrated Publishing Toolkit
http://links.gbif.org/ipt_user_manual • GBIF Spreadsheet Templates User Guide
http://links.gbif.org/dwca_spreadsheet_processor_guide • GBIF Metadata Profile How-To Guide
http://links.gbif.org/gbif_metadata_profile_how-to_en_v1 • GBIF Metadata Profile Reference Guide
http://links.gbif.org/gbif_metadata_profile_guide_en_v1 • Darwin Core Archive How-to Guide
http://links.gbif.org/gbif_dwc-a_how_to_guide_en_v1 • Publishing and Registering Your Data with GBIF
http://links.gbif.org/dwc-a_publishing_guide_en_v1 • Spreadsheet Processor and Excel Temp
http://tools.gbif.org/spreadsheet-processor/• Darwin Core Terms
http://code.google.com/p/darwincore/ • IPT Download link
http://code.google.com/p/gbif-providertoolkit/
Thank you