Publishing hkh biodiversity data globally   technical session ii
Upcoming SlideShare
Loading in...5
×
 

Like this? Share it with your network

Share

Publishing hkh biodiversity data globally technical session ii

on

  • 385 views

This is about how to publish your biodiversity data in GBIF portal through HKH-BIF

This is about how to publish your biodiversity data in GBIF portal through HKH-BIF

Statistics

Views

Total Views
385
Views on SlideShare
384
Embed Views
1

Actions

Likes
0
Downloads
2
Comments
0

1 Embed 1

http://www.docseek.net 1

Accessibility

Categories

Upload Details

Uploaded via as Microsoft PowerPoint

Usage Rights

© All Rights Reserved

Report content

Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
  • Full Name Full Name Comment goes here.
    Are you sure you want to
    Your message goes here
    Processing…
Post Comment
Edit your comment
  • 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.

Publishing hkh biodiversity data globally technical session ii Presentation Transcript

  • 1. Technical session IIDay 1Publishing HKH BiodiversityData GloballyDeependra Tandukar, Suman Jaiswal, Bandana Shakya23-24 August 2012International Centre for Integrated Mountain DevelopmentKathmandu, 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 1Data Preparation
  • 6. Step 1: Data preparationData resource Data resource = Dataset + Metadata Collection of data records Information about the dataset Occurrence data + Metadata Checklist + Metadata
  • 7. Step 1: Data preparationTemplates • Standardized templates (based on Darwin core) • Glossary (location, scientific name, family, etc.)
  • 8. Step 1: Data preparationTemplate types • Metadata • Occurrence data • Checklists – Checklist 1 – Checklist 2 – Checklist 3 Download from: http://tools.gbif.org/spreadsheet-processor
  • 9. Step 1: Data preparationTemplates: Metadata • Readme sheet Readme sheet gives the general instruction on what and how to fill the metadata sheet
  • 10. Step 1: Data preparationTemplates: 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 preparationTemplates: 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 preparationTemplates: 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 preparationTemplates: 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 preparationTemplates: 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 preparationHands-on session • Use checklist 3 for data preparation • Enter mandatory fields in metadata • Fill in classification sheet
  • 16. Step 1: Data preparationMetadata • Enter fields in metadata
  • 17. Step 1: Data preparationChecklist 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 preparationProcess the template Spreadsheet processor Archive file
  • 19. Step 1: Data preparationProcess the template • Go to spreadsheet processor (http://tools.gbif.org/spreadsheet-processor/)
  • 20. Step 1: Data preparationProcess checklist template • Click on ‘Choose File’ and select your prepared checklist template, it gets uploaded • Click on ‘Process File’
  • 21. Step 1: Data preparationProcess 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 2Upload your data
  • 23. Step 2: Upload your dataGo to HKH-BIF • http://192.168.10.19/hkh-bif • Enter your username and password • Click on ‘login’
  • 24. Step 2: Upload your dataCreate 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 dataNew resource created 4
  • 26. Step 2: Upload your dataSource data
  • 27. Step 2: Upload your dataSource data
  • 28. Step 3Metadata
  • 29. Step 3: MetadataOver view page
  • 30. Step 3: MetadataBasic metadata
  • 31. Step 3: MetadataGeographic coverage • Geographic area covered by the resource
  • 32. Step 3: MetadataTaxonomic coverage • Information about one of more groups of taxa covered by the resource
  • 33. Step 3: MetadataKeywords • One or more sets of keywords about the resource.
  • 34. Step 3: MetadataAssociated 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: MetadataProject data • Information about a project under which the data in the resource were produced/generated
  • 36. Step 3: MetadataSampling methods • Information about sampling methods in general, and about specific sampling steps
  • 37. Step 3: MetadataCitations • 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: MetadataCollection 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: MetadataExternal links • Links to the home page for the resource, links to the resource in alternate forms (database, spreadsheets, etc.)
  • 40. Step 3: MetadataAdditional metadata • Extra information e.g. logo, copyright information, etc.
  • 41. Step 4Mapping
  • 42. Step 4: MappingMapping
  • 43. Step 4: MappingMapping Source data fields Darwin core terms
  • 44. Step 5Publishing
  • 45. Step 5: Publishing your dataPublish
  • 46. Step 5: Publishing your dataPublish • 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 dataVisible • Make it public for sharing
  • 48. Step 5: Publishing your dataVisibility
  • 49. Step 5: Publishing your dataVisibility
  • 50. Technical session IIDay 2 (Hands-on)Publishingnon-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 fieldsDarwin 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