Technical session IIDay 1Publishing HKH BiodiversityData GloballyDeependra Tandukar, Suman Jaiswal, Bandana Shakya23-24 Au...
Outline • Using HKH-BIF • Processes for publishing the data   –   Preparing the data   –   Uploading data   –   Filling Me...
Platform Data                                 HKH-BIF     GBIF        • for easy and efficient access          and sharing...
Processes for publishing data • Prepare your data     – Data resource     – Templates     – Processing with spreadsheet pr...
Step 1Data Preparation
Step 1: Data preparationData resource       Data     resource         =           Dataset               +     Metadata    ...
Step 1: Data preparationTemplates  • Standardized templates (based on Darwin core)  • Glossary (location, scientific name,...
Step 1: Data preparationTemplate types  • Metadata  • Occurrence data  • Checklists      – Checklist 1      – Checklist 2 ...
Step 1: Data preparationTemplates: Metadata  • Readme sheet                           Readme sheet gives the              ...
Step 1: Data preparationTemplates: Metadata  • Metadata sheet         Metadata sheet has number of                        ...
Step 1: Data preparationTemplates: Occurrence  • Readme sheet                This sheet is used to record species  • Metad...
Step 1: Data preparationTemplates: Checklist1  • Readme sheet           This sheet is used to record the species  • Metada...
Step 1: Data preparationTemplates: Checklist2  • Readme sheet                           This sheet is used to record the s...
Step 1: Data preparationTemplates: Checklist3  • Readme sheet           This template is used to record species  • Metadat...
Step 1: Data preparationHands-on session  • Use checklist 3 for data preparation  • Enter mandatory fields in metadata  • ...
Step 1: Data preparationMetadata  • Enter fields in metadata
Step 1: Data preparationChecklist data fields  • Classification field   Kingdom           Animalia   Phylum            Ver...
Step 1: Data preparationProcess the template                           Spreadsheet                            processor   ...
Step 1: Data preparationProcess the template  • Go to spreadsheet processor     (http://tools.gbif.org/spreadsheet-process...
Step 1: Data preparationProcess checklist template  • Click on ‘Choose File’ and select your prepared    checklist templat...
Step 1: Data preparationProcess checklist template  •   Download the processed archive by clicking on ‘Click to Download  ...
Step 2Upload your data
Step 2: Upload your dataGo to HKH-BIF  • http://192.168.10.19/hkh-bif  • Enter your username and password  • Click on ‘log...
Step 2: Upload your dataCreate New Resource • Click on ‘Manage Resources’ • Give a short name for your data/resource • Cli...
Step 2: Upload your dataNew resource created                           4
Step 2: Upload your dataSource data
Step 2: Upload your dataSource data
Step 3Metadata
Step 3: MetadataOver view page
Step 3: MetadataBasic metadata
Step 3: MetadataGeographic coverage • Geographic area covered by the resource
Step 3: MetadataTaxonomic coverage • Information about one of more groups of taxa covered   by the resource
Step 3: MetadataKeywords • One or more sets of keywords about the resource.
Step 3: MetadataAssociated parties • Information about one or more people or   organizations associated with the resource ...
Step 3: MetadataProject data • Information about a project under which the data in   the resource were produced/generated
Step 3: MetadataSampling methods • Information about sampling methods in general, and   about specific sampling steps
Step 3: MetadataCitations • Information about how to cite the resource as well as   a bibliography of citations related to...
Step 3: MetadataCollection data • Information about the physical natural history collection   associated with the resource...
Step 3: MetadataExternal links • Links to the home page for the resource, links to the   resource in alternate forms (data...
Step 3: MetadataAdditional metadata • Extra information e.g. logo, copyright information, etc.
Step 4Mapping
Step 4: MappingMapping
Step 4: MappingMapping                        Source data fields    Darwin core terms
Step 5Publishing
Step 5: Publishing your dataPublish
Step 5: Publishing your dataPublish  • Click on publish to publish your data     • generates a new dwca.zip file containin...
Step 5: Publishing your dataVisible  • Make it public for sharing
Step 5: Publishing your dataVisibility
Step 5: Publishing your dataVisibility
Technical session IIDay 2 (Hands-on)Publishingnon-template data
Xls to csv format  • Open your excel file  • Save as ‘comma delimited csv’ format in your desktop, give    a name ‘my_firs...
Go to HKH-BIF • http://192.168.10.19:8080/hkh-bif • Enter your username and password • Click on ‘login’
Create New Resource • Click on ‘Manage Resources’ • Give a short name for your data/resource • Press on ‘Create’    my_fir...
Create new resource • Click on ‘choose file’ under source file and select your .csv file
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 ...
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 = ...
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_sta...
Thank you
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Publishing hkh biodiversity data globally technical session ii

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

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  • 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

    1. 1. Technical session IIDay 1Publishing HKH BiodiversityData GloballyDeependra Tandukar, Suman Jaiswal, Bandana Shakya23-24 August 2012International Centre for Integrated Mountain DevelopmentKathmandu, Nepal
    2. 2. Outline • Using HKH-BIF • Processes for publishing the data – Preparing the data – Uploading data – Filling Metadata – Mapping – Publishing
    3. 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. 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. 5. Step 1Data Preparation
    6. 6. Step 1: Data preparationData resource Data resource = Dataset + Metadata Collection of data records Information about the dataset Occurrence data + Metadata Checklist + Metadata
    7. 7. Step 1: Data preparationTemplates • Standardized templates (based on Darwin core) • Glossary (location, scientific name, family, etc.)
    8. 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. 9. Step 1: Data preparationTemplates: Metadata • Readme sheet Readme sheet gives the general instruction on what and how to fill the metadata sheet
    10. 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. 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. 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. 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. 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. 15. Step 1: Data preparationHands-on session • Use checklist 3 for data preparation • Enter mandatory fields in metadata • Fill in classification sheet
    16. 16. Step 1: Data preparationMetadata • Enter fields in metadata
    17. 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. 18. Step 1: Data preparationProcess the template Spreadsheet processor Archive file
    19. 19. Step 1: Data preparationProcess the template • Go to spreadsheet processor (http://tools.gbif.org/spreadsheet-processor/)
    20. 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. 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. 22. Step 2Upload your data
    23. 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. 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. 25. Step 2: Upload your dataNew resource created 4
    26. 26. Step 2: Upload your dataSource data
    27. 27. Step 2: Upload your dataSource data
    28. 28. Step 3Metadata
    29. 29. Step 3: MetadataOver view page
    30. 30. Step 3: MetadataBasic metadata
    31. 31. Step 3: MetadataGeographic coverage • Geographic area covered by the resource
    32. 32. Step 3: MetadataTaxonomic coverage • Information about one of more groups of taxa covered by the resource
    33. 33. Step 3: MetadataKeywords • One or more sets of keywords about the resource.
    34. 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. 35. Step 3: MetadataProject data • Information about a project under which the data in the resource were produced/generated
    36. 36. Step 3: MetadataSampling methods • Information about sampling methods in general, and about specific sampling steps
    37. 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. 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. 39. Step 3: MetadataExternal links • Links to the home page for the resource, links to the resource in alternate forms (database, spreadsheets, etc.)
    40. 40. Step 3: MetadataAdditional metadata • Extra information e.g. logo, copyright information, etc.
    41. 41. Step 4Mapping
    42. 42. Step 4: MappingMapping
    43. 43. Step 4: MappingMapping Source data fields Darwin core terms
    44. 44. Step 5Publishing
    45. 45. Step 5: Publishing your dataPublish
    46. 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. 47. Step 5: Publishing your dataVisible • Make it public for sharing
    48. 48. Step 5: Publishing your dataVisibility
    49. 49. Step 5: Publishing your dataVisibility
    50. 50. Technical session IIDay 2 (Hands-on)Publishingnon-template data
    51. 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. 52. Go to HKH-BIF • http://192.168.10.19:8080/hkh-bif • Enter your username and password • Click on ‘login’
    53. 53. Create New Resource • Click on ‘Manage Resources’ • Give a short name for your data/resource • Press on ‘Create’ my_first_data
    54. 54. Create new resource • Click on ‘choose file’ under source file and select your .csv file
    55. 55. Create new resource
    56. 56. New resource
    57. 57. Mapping
    58. 58. Mapping • Select ‘Darwin Core Mappings’ type from the drop down – in our case it is ‘Darwin Core Taxon’ • Then click on ‘Add’
    59. 59. Mapping • Auto mapped 1 column
    60. 60. Mapping • At the bottom of the page, a list of the unmapped fields are displayed
    61. 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. 62. Filter Exclude the records that do not match the criteria using filter
    63. 63. Mapping • Once all the known fields are mapped, click on save button
    64. 64. • On the top of the page, click on ‘back to resource over view page’
    65. 65. Metadata • Now enter the metadata
    66. 66. Metadata
    67. 67. Publish • Click on publish to publish your data
    68. 68. Make it visible • Make it public for sharing
    69. 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. 70. Thank you

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