Publishing hkh biodiversity data globally technical session ii
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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.
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Publishing hkh biodiversity data globally technical session ii
- 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
- 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
- 43. Step 4: Mapping Mapping Source data fields Darwin core terms
- 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
- 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
Notas del editor
- This sheet is used to record species occurrence data and is suitable for recording basic natural history collections specimen records or species observations. Occurrence sheetInstitution code, collection code, etc.Kingdom, phylum, family, scientific name, etc.Identified by, date identified, etc.Country, locality, latitude, longitude, elevation, etc.Event time, date, etc.