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Editing the BIOTECH Glossary with VocBench 1.1

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  • 1. Editing the BIOTECH glossary with VocBench 1.1
    Training
    FAO
    Rome, June 20-21, 2011
    Day 1
    Caterina Caracciolo
    Caterina.caracciolo@fao.org
    1
  • 2. Objectives of the course
    Enable editors to maintain the biotech glossary using VocBench
    2
  • 3. Topics for today
    User roles and workflow
    Managing concepts, terms, definitions of the BioTech glossary
    3
  • 4. Topics for tomorrow
    Validation of changes in glossary
    New web interface of glossary
    4
  • 5. VocBench
    5
  • 6. 6
    VocBench functionalities
    • Web-based
    • 7. supports distributed collaboration
    • 8. organized in an editorial workflow
    • 9. Supports management of multilingual data
    • 10. Export data as SKOS, SQL
    ottimo,
  • 11. 7
    1
    5
    4
    5
    ottimo,
    2
    3
    5
  • 12. 8
    Legend
    Log in details
    Concept area – glossary entries
    Details about concepts
    • Titles, definitions, relations,history
    Operations that may be applied to concepts
    Navigation options
    ottimo,
  • 13. 9
    Basic terminology
    Glossary entry = concept
    Entry title = term, or concept label
  • 14. Scenario 1
    • Editing
    • 15. E creates an entry in EN
    • 16. Validation
    • 17. V validates it and approves it for translation
    • 18. Editing
    • 19. Translations into Chineese, Arabic, …
    • 20. Validation and Publishing
    • 21. P validates everything and publishes
    10
  • 22. Scenario 2
    • Editing
    • 23. R creates concept in RU, EN translation
    • 24. Validation, Publishing
    • 25. Editing
    • 26. Translations into A, C, …
    • 27. Validation, Publishing
    • 28. Editing
    • 29. More translations
    11
  • 30. 12
    Sandbox version for training
    There, you can do anything! Real data will not be affected
  • 31. 13
    VB documentation
    • User manual
    • 32. accessible from inside VB, link Help
    • 33. These slides
    • 34. will be made available
  • How to keep in touch with VB users and managers
    • To communicate with the VB User community
    http://aims.fao.org/community/group/vocbench
    • To report issues
    http://code.google.com/p/agrovoc-cs-workbench/
    • To comment on generic topics, use “Contact us” page from VB
    • 35. Email to any of us
    14
  • 36. VocBench
    15
  • 37. 16
    Managing the glossary in VB
    An entry in the glossary is a concept, which is titled by means of a term in a given language
    In any language, a concept must have one primary title, called preferred term
    Other titles, if any, are non-preferred
    Preferred titles are used to “call” concepts – see Concept Hierarchy Area in VB
  • 38. 17
    Managing the glossary in VB
    Concepts have definitions, which may be available in any languages
    A concept may be in a relation with another concept
    ottimo,
  • 39. 18
    Example
    ottimo,
  • 40. 19
    Accessing the VB
    You need:
    A User account, a role, a data set:
    ottimo,
  • 41. 20
    User accounts and roles in the workflow
    • VB implements a workflow of actions, typically:
    • 42. Editing -> Validation -> Publication
    • 43. Actions are performed by users playing a given role, at any given point of time
  • 21
    User roles in VB
    Term editor
    Ontology editor
    Validator
    Publisher
    Administrator
    Ontology editor and Administrators are not covered by this training
    ottimo,
  • 44. 22
    Your roles in this training
    For training purposes, each of you is given a user account, with possibility of playing any role in the workflow
  • 45. 23
    Exercise 0
    Go to VB 1.2 Sandbox
    http://202.73.13.50:55481/vocbenchv1.2i/
    FAO page where you can always find pointers to latest VB versions
    http://aims.fao.org/website/The-VocBench/sub
    You can get to the same FAO page by searching for “FAO AIMS VocBench”
    You may want to bookmark the URL
  • 46. 24
    Exercise 1
    • Login with your account (see next slide)
    • 47. Chose role Term Editor
    • 48. Note that User group stands for user role
  • 25
    Your role(s)
    ottimo,
  • 49. 26
    This is what I see
    ottimo,
  • 50. 27
    Exercise 2
    • Look at your VB
    • 51. In what language do you see the concepts?
    • 52. Do you see some warning saying “No term available in selected language”?
    • 53. What color?
    • 54. Have you noticed the Legend at the bottom of the screen?
  • 28
    How it appears to an editor in ZH
    ottimo,
  • 55. 29
    User and languages
    • The Biotech Glossary is a multilingual resources
    • 56. Different users may have different languages shown
    • 57. Note the difference between:
    • 58. The language(s) that you may edit
    • 59. The language(s) that you can visualize
    • 60. Elements in the glossary may have different “status”
  • 30
    Edit and visualize languages
    • Languages to edit
    • 61. Assigned by Administrator, Publisher
    • 62. You can request languages from Preferences -> Pending language request.
    • 63. Language for content display
    • 64. You can chose from button Content Language
    • 65. Selection is valid for current session
  • 31
    Look at your Preferences
    ottimo,
  • 66. 32
    You can edit your Preferences
    ottimo,
  • 67. 33
    Exercise 3
    • Go to your Preference, and update your email address
    • 68. You need to write in field “New email”
  • 34
    Exercise 4
    • Consider what languages you normally edit in the BioTech
    • 69. Compare with the languages you have granted right now
    • 70. Then go to your Preferences, and request the one(s) missing
    Your requests will be approved during our next coffee break 
  • 71. 35
    Exercise 5
    • Now consider which languages you normally need to take visualize when working with the BioTech
    • 72. For example, if you normally translate from English to Arabic, you need to visualize/edit Arabic, and visualize English
    • 73. Now change language display, by using Content Languages
  • 36
    Exercise 6
    Can you input non English characters using your keyboard?
    • If not, set up the appropriate virtual keabord
    • 74. Go to:
    • 75. Control panel -> Regional and Language options -> keyboards and languages -> change keyboard
    ottimo,
  • 76. Editorial workflow
    37
  • 77. 38
    Editorial workflow
    • Editorial actions needed to produce the final results
    • 78. Important to assure quality control
    Example: in a publishing house: writing, proof reading, editing, … publishing
    In Biotech:
    • Management of content by editors
    • 79. Validation by senior editors
    • 80. Publication by Biotech managers
  • 39
    Terminology
    • Role = function of a user in a workflow
    • 81. Determines what the user may or may not do in a given moment
    • 82. Rights = permission to execute actions
    • 83. Associated to roles
    • 84. e.g. a term editor may add terms
    • 85. Status = status of an element in a workflow
    • 86. An element may be a concept, a term, …
    • 87. Status may be draft, published, …
    ottimo,
  • 88. Roles in a workflow
    Editors
    Validators
    Publisher
    Creates new entries
    Add definitions
    Accept
    or
    rejects
    changes
    Edit entry title
    or definition
    Decides
    what
    goes public
    Establish relations
    between entries
    Revise relations
    Propose deletion
    40
  • 89. 41
    Workflow roles by content and languages
    • Editors are specialized by language and area, e.g. animal, plants…
    • 90. Validators too may be specialized by language and area(s)
    • 91. Publishers are responsible for the general quality of the product that is published
  • Term editor
    42
  • 92. 43
    Actions permitted to Term editors
    • Create new concepts, providing labels in the languages assigned
    • 93. Create/edit/delete/revise terms and definitions for concepts in the language assigned
    • 94. Created/edited by any editor
    • 95. Add/edit relations between concepts
  • 44
    VocBench
    ottimo,
  • 96. 45
    Exercise 7
    • One EN editor adds concept:
    “Amplified ribosomal DNA restriction analysis (ARDRA)”
    • Place it under concept “biotech glossary”
  • 46
    Exercise 8
    • Other editors check that a change has been made to the glossary by looking at section Recent Changes
    • 97. Can you read the table?
    • 98. Click on the concept name
    • 99. What do you see?
  • 47
    How to see “news” in VocBench
    • Log in and check section Recent Changes
    • 100. Log in and subscribe a RSS feed (link available in top stripe of the interface)
    • 101. Then you will get notifications without having to be logged in
    • 102. Notification can be via:
    • 103. Email
    • 104. Your browser
    • 105. On your desktop (using dedicated programs, called RSS feed readers)
  • 48
    Alphabetical order in VB 1.2
    • You should have noticed that after your last action, the list of entries is no longer in alphabetical order
    • 106. This is not a problem with AGROVOC, but it probably is with the Biotech glossary
    • 107. Plan to address this issue after this training
  • 49
    Exercise 9
    • An EN editor (different from the previous one) adds a definition to “Amplified ribosomal DNA restriction analysis (ARDRA)”
    • 108. The others see what has happened
    • 109. Now do it by searching
    • 110. Search for “amplified”
  • Validator
    50
  • 111. 51
    Actions permitted
    • Accepts or rejects proposals made by editors
    • 112. E.g. creation of a new concepts, revision of a definition, deletion of a term
    • 113. Validation actions are done in section Validation
    • 114. Validators are typically domain experts who ensure quality of the content
    • 115. Currently, if you log in as Validator, you have validation rights on all language
  • 52
    Validation
    ottimo,
  • 116. Publisher
    53
  • 117. 54
    Actions permitted
    • Have all rights as Validators
    • 118. May also create and edit relationships between concepts
    • 119. Approve new user accounts, grant rights on languages and data sets
    • 120. Publishers have overview of the entire glossary and have last say on what is going to be published
  • Administrator
    55
  • 121. 56
    Action permitted
    • Administrator rights stay with VocBench managers
    • 122. This role is not covered in this training
  • 57
    Status of elements
    Proposed
    Proposed deprecated
    Revised
    Validated
    Published
    Deprecated
    ottimo,
  • 123. 58
    Proposed element
    • Element that has been newly added
    • 124. Pink
    • 125. A proposal of deletion makes the element get status Proposed Deprecated
    • 126. Grey
    • 127. Status Proposed is independent of the role of the user of makes the proposal
  • 59
    Revised element
    • Any elements that have been edited
    • 128. Red
    • 129. If the editing consists in a suggestion of deletion, the status is Proposed Deprecated
    • 130. Grey
    ottimo,
  • 131. 60
    Validated element
    • Element approved by a Validator
    • 132. Green
    • 133. Validators may also reject change, then:
    • 134. The element goes back to previous status
    • 135. Approving an Proposed Deprecated element makes it Deprecated
  • 61
    Published and deprecated element
    • Elements published to the outside have either Published or Deprecated status
    • 136. Published
    • 137. Element approved by a publisher
    • 138. Deprecated
    • 139. Element discarded
    • 140. Kept for backward compatibility
    • 141. However, you can exclude deprecated elements from visualization (in Preferences)
  • 62
    Exercise 10
    • Go back to concept “Amplified ribosomal DNA restriction analysis”
    • 142. In which color does it appear?
    • 143. In which color do its terms and definition appear?
  • 63
    Exercise 11
    • Edit a term of the concept “Amplified ribosomal DNA restriction analysis”
    • 144. Now, in which color does the concept appear?
    • 145. And the edited term?
  • 64
    Exercise 12
    • Pick up a concept from the list (in blue) and delete it
    • 146. What is the meaning of the error message you get?
    • 147. Observe the new color of the concept, and the color of its terms
    • 148. Now delete also one of its terms
  • 65
    Exercise 13
    • Search for “acceptor control”
    • 149. What result do you get?
    • 150. What languages are selected in your Content Language?
  • 66
    Search
    • Search if against the entire data set, independently of which languages are selected in “Content language”
    • 151. But if languages are not selected, you cannot see the corresponding labels
  • 67
    Create a new concept step by step
    You may only add concepts in the language of your competence
    Click button “+” (Add new concept)
    A little window appears, asking for:
    Term
    Language
    Then click create, asks for position
    Child of the selected concept
    Same level as the selected concept
    Top concept
    Preferred term
    ottimo,
  • 152. 68
    Concepts and glossary entries
    • When entering a new concept, the Term assigned should be marked as preferred
    • 153. Because preferred terms are used for display in concept hierarchy!
    • 154. Definitions may be given at a later stage
  • 69
    Preferred terms
    • No more than one preferred term per language should be given
    • 155. But there is no automatic check in VB, so be careful!
  • 70
    Preferred terms
    • You can decide to show or not also non preferred terms
    • 156. However, the glossary only has preferred terms
  • 71
    More information about a concept
    Can be specified in the corresponding tabs:
    Terms
    Definitions
    Note
    Attribute
    Relationship
    History
    Image
    Hierarchy
    ottimo,
  • 157. 72
    Terms
    • Correspond to the title of the concept
    • 158. May be added either when creating a concept (to provide labels to the concept), or later on
    • 159. For example, when a translation is made
  • 73
    More information about a concept
    Can be specified in the corresponding tabs:
    Terms
    Definitions
    Note
    Attribute
    Relationship
    History
    Image
    Hierarchy
    ottimo,
  • 160. 74
    Definition of a concept
    • If you create a concept in a language other than English, VB requires that an EN definition be provided
    • 161. For each definition, a source and its URL must be given
    • 162. Right now there is no authomatic control on the URL, so be careful!
    ottimo,
  • 163. 75
    Definitions and translations of definitions
    • A concept may have one or more definitions
    • 164. A definition may be translated into several languages
    • 165. Source and URL are for Definition (not for its translations)
    ottimo,
  • 166. 76
    Sources of definitions
    Currently you can chose among:
    FAOTERM
    NAL
    WIKIPEDIA
    MeSH
    Other
    Book
    Journal Article
    AGROVOC
    WordNet
    ottimo,
  • 167. 77
    Exercise 14
    • EN editor add at least 3 of the following concepts:
    Cisgenetic
    Competitive ELISA (c-ELISA)
    DIVA vaccine
    Monosex population
    Omics
    Morula
    Probiotic
    Sperm mediated gene transfer (SMGT)
    Transcriptomix
    ottimo,
  • 168. 78
    Exercise 15
    • Editors in other languages translate terms and definitions
    • 169. You have 10 minutes
    • 170. This is not a race! Our goal is that you become confident with the tool, and suggest us where and how to improve it!
    ottimo,
  • 171. 79
    More information about a concept
    Can be specified in the corresponding tabs:
    Terms
    Definitions
    Note
    Attribute
    Relationship
    History
    Image
    Hierarchy
    ottimo,
  • 172. 80
    Notes
    Editorial note
    • To add information or remarks useful for editing purpose
    Scope note
    • To specify the field of validity of a concept
    • 173. These notes are not part of Biotech Glossary
    ottimo,
  • 174. 81
    More information about a concept
    Can be specified in the corresponding tabs:
    Terms
    Definitions
    Note
    Attribute
    Relationship
    History
    Image
    Hierarchy
    ottimo,
  • 175. 82
    Attributes
    • To specify information that is not relevant to a glossary
    • 176. You may find interesting the notion of subvocabulary
    • 177. A way to create sublists of concepts
    ottimo,
  • 178. 83
    Subvocabularies
    • Currently, 5 subvocabularies:
    Chemical
    Geographical country level
    Geographical above country level
    Geographical below country level
    Fishery related term
    • Subvocabularies may be defined in section Relationships, by Publishers
  • 84
    More information about a concept
    Can be specified in the corresponding tabs:
    Terms
    Definitions
    Note
    Attribute
    Relationship
    History
    Image
    Hierarchy
    ottimo,
  • 179. 85
    Relations between concepts
    • It is possible to establish relations between pairs of concepts
    • 180. Many relationships are available
    • 181. For the Biotech Glossary, it is recommended to use only Has related concept
    • 182. Very general, like “see also”
    ottimo,
  • 183. 86
    Exercise 16
    • Go to advanced search
    • 184. Search for all pairs of concepts linked by relation “Has related concept”
    • 185. How many have you found?
    • 186. Click on one of the related concepts
    • 187. If concept A is realted to concept B, is it true also teh opposite?
    • 188. navigate the concepts before answering
  • 87
    Exercise 17
    • Chose a concept and add at least one relation to another concept
  • 88
    More information about a concept
    Can be specified in the corresponding tabs:
    Terms
    Definitions
    Note
    Attribute
    Relationship
    History
    Image
    Hierarchy
    ottimo,
  • 189. 89
    History
    • Recap of history of changes of the concept
    • 190. Automatically generated by VB
    ottimo,
  • 191. 90
    History
    ottimo,
  • 192. 91
    More information about a concept
    Can be specified in the corresponding tabs:
    Terms
    Definitions
    Note
    Attribute
    Relationship
    History
    Image
    Hierarchy
    ottimo,
  • 193. 92
    Image
    • It is possible to add images to better explain a concept
    • 194. Currently, the glossary does not include images
    • 195. Consider pros/cons of having this
  • 93
    More information about a concept
    Can be specified in the corresponding tabs:
    Terms
    Definitions
    Note
    Attribute
    Relationship
    History
    Image
    Hierarchy
    ottimo,
  • 196. 94
    Hierarchy
    ottimo,
  • 197. 95

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