This document provides an overview of the process for publishing biodiversity data from the Hindu Kush Himalaya (HKH) region on the HKH Biodiversity Information Facility (HKH-BIF) platform and making it globally accessible through the Global Biodiversity Information Facility (GBIF). It outlines the key steps, which include preparing the data using standardized templates, uploading it to HKH-BIF, filling out detailed metadata, mapping data fields to Darwin Core terms, and publishing the data to make it publicly available. The presentation provides guidance on preparing different types of biodiversity data like occurrence records, checklists, and using the GBIF spreadsheet processor and mapping tools.

1. Technical session II
Day 1
Publishing HKH Biodiversity
Data Globally
Deependra Tandukar, Suman Jaiswal, Bandana Shakya
23-24 August 2012
International Centre for Integrated Mountain Development
Kathmandu, Nepal

2. Outline
• Using HKH-BIF
• Processes for publishing the data
– Preparing the data
– Uploading data
– Filling Metadata
– Mapping
– Publishing

3. Platform
Data
HKH-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

4. 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

5. Step 1
Data Preparation

6. Step 1: Data preparation
Data resource
Data
resource = Dataset + Metadata
Collection of data records Information about
the dataset
Occurrence data + Metadata
Checklist + Metadata

7. Step 1: Data preparation
Templates
• Standardized templates (based on Darwin core)
• Glossary (location, scientific name, family, etc.)

8. Step 1: Data preparation
Template types
• Metadata
• Occurrence data
• Checklists
– Checklist 1
– Checklist 2
– Checklist 3
Download from:
http://tools.gbif.org/spreadsheet-processor

9. Step 1: Data preparation
Templates: Metadata
• Readme sheet
Readme sheet gives the
general instruction on
what and how to fill the
metadata sheet

10. Step 1: Data preparation
Templates: Metadata
• Metadata sheet Metadata sheet has number of
fields for information to feed in,
and some of the fields marked by
* are mandatory

11. Step 1: Data preparation
Templates: Occurrence
• Readme sheet This sheet is used to record species
• Metadata sheet occurrence data and is suitable for
recording basic natural history
• Occurrence sheet
collections specimen records or species
observations.
45 fields/columns in total

12. Step 1: Data preparation
Templates: Checklist1
• Readme sheet This sheet is used to record the species
• Metadata sheet lists where you are not sure of higher
• Classification sheet classification

13. Step 1: Data preparation
Templates: Checklist2
• Readme sheet
This sheet is used to record the species
• Metadata sheet lists where you are not limited to strict
• Classification sheet Linnaean classification

14. Step 1: Data preparation
Templates: Checklist3
• Readme sheet This template is used to record species
• Metadata sheet checklists in a simple columnar format that stores
the basic taxonomic data in the columns
• Classification sheet
(Kingdom, Phylum, Subphylum, Class, Order,
Family, Genus, Species, etc.).

15. Step 1: Data preparation
Hands-on session
• Use checklist 3 for data preparation
• Enter mandatory fields in metadata
• Fill in classification sheet

16. Step 1: Data preparation
Metadata
• Enter fields in metadata

17. Step 1: Data preparation
Checklist data fields
• Classification field
Kingdom Animalia
Phylum Vertebrata
Class Amphibia
Order Anura
Family Ranidae
Genus Amolops
Scientific name Amolops ricketti
Countries China

18. Step 1: Data preparation
Process the template
Spreadsheet
processor
Archive file

19. Step 1: Data preparation
Process the template
• Go to spreadsheet processor
(http://tools.gbif.org/spreadsheet-processor/)

20. Step 1: Data preparation
Process checklist template
• Click on ‘Choose File’ and select your prepared
checklist template, it gets uploaded
• Click on ‘Process File’

21. 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>

22. Step 2
Upload your data

23. Step 2: Upload your data
Go to HKH-BIF
• http://192.168.10.19/hkh-bif
• Enter your username and password
• Click on ‘login’

24. Step 2: Upload your data
Create New Resource
• 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’

25. Step 2: Upload your data
New resource created
4

26. Step 2: Upload your data
Source data

27. Step 2: Upload your data
Source data

28. Step 3
Metadata

29. Step 3: Metadata
Over view page

30. Step 3: Metadata
Basic metadata

31. Step 3: Metadata
Geographic coverage
• Geographic area covered by the resource

32. Step 3: Metadata
Taxonomic coverage
• Information about one of more groups of taxa covered
by the resource

33. Step 3: Metadata
Keywords
• One or more sets of keywords about the resource.

34. 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

35. Step 3: Metadata
Project data
• Information about a project under which the data in
the resource were produced/generated

36. Step 3: Metadata
Sampling methods
• Information about sampling methods in general, and
about specific sampling steps

37. 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

38. 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

39. Step 3: Metadata
External links
• Links to the home page for the resource, links to the
resource in alternate forms (database, spreadsheets, etc.)

40. Step 3: Metadata
Additional metadata
• Extra information e.g. logo, copyright information, etc.

41. Step 4
Mapping

42. Step 4: Mapping
Mapping

43. Step 4: Mapping
Mapping
Source data fields
Darwin core terms

44. Step 5
Publishing

45. Step 5: Publishing your data
Publish

46. 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

47. Step 5: Publishing your data
Visible
• Make it public for sharing

48. Step 5: Publishing your data
Visibility

49. Step 5: Publishing your data
Visibility

50. Technical session II
Day 2 (Hands-on)
Publishing
non-template data

51. Xls to csv format
• Open your excel file
• Save as ‘comma delimited csv’ format in your desktop, give
a name ‘my_first_data’

52. Go to HKH-BIF
• http://192.168.10.19:8080/hkh-bif
• Enter your username and password
• Click on ‘login’

53. Create New Resource
• Click on ‘Manage Resources’
• Give a short name for your data/resource
• Press on ‘Create’
my_first_data

54. Create new resource
• Click on ‘choose file’ under source file and select your .csv file

55. Create new resource

56. New resource

57. Mapping

58. Mapping
• Select ‘Darwin Core Mappings’ type from the drop down – in
our case it is ‘Darwin Core Taxon’
• Then click on ‘Add’

59. Mapping
• Auto mapped 1 column

60. Mapping
• At the bottom of the page, a list of the unmapped fields are
displayed

61. Mapping
• Let’s start mapping now
• Auto mapped Kingdom = Kingdom
• Map ScientificName = Sname, class = C according to our data
Source data fields
Darwin core terms

62. Filter
Exclude the records that do not
match the criteria using filter

63. Mapping
• Once all the known fields are mapped, click on save button

64. • On the top of the page, click on ‘back to resource over view page’

65. Metadata
• Now enter the metadata

66. Metadata

67. Publish
• Click on publish to publish your data

68. Make it visible
• Make it public for sharing

69. 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/

70. Thank you