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1
Editing the BIOTECH glossary with VocBench 1.1
Training
FAORome, June 20-21, 2011
Day 1
Caterina [email protected]
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Topics for today
1. User roles and workflow
2. Managing concepts, terms, definitions of the BioTech glossary
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VocBench functionalities
Web-based• supports distributed collaboration• organized in an editorial workflow
Supports management of multilingual data
Export data as SKOS, SQL
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Legend
1.Log in details
2.Concept area – glossary entries
3.Details about concepts• Titles, definitions, relations,history
4.Operations that may be applied to concepts
5.Navigation options
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Scenario 1
Editing E creates an entry in EN
Validation V validates it and approves it for translation
Editing Translations into Chineese, Arabic, …
Validation and Publishing P validates everything and publishes
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Scenario 2 Editing
R creates concept in RU, EN translation
Validation, Publishing
Editing Translations into A, C, …
Validation, Publishing
Editing More translations
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VB documentation
User manual• accessible from inside VB, link Help
These slides• will be made available
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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
Email to any of us
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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
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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
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User accounts and roles in the workflow
VB implements a workflow of actions, typically:Editing -> Validation -> Publication
Actions are performed by users playing a given role, at any given point of time
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User roles in VB
1.Term editor2. Ontology editor3. Validator4. Publisher5. Administrator
Ontology editor and Administrators are not covered by this training
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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
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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
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Exercise 1
Login with your account (see next slide)
Chose role Term EditorNote that User group stands for user role
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Exercise 2
Look at your VB
In what language do you see the concepts?
Do you see some warning saying “No term available in selected language”?
What color?
Have you noticed the Legend at the bottom of the screen?
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User and languages
The Biotech Glossary is a multilingual resources
Different users may have different languages shown
Note the difference between:The language(s) that you may editThe language(s) that you can visualize
Elements in the glossary may have different “status”
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Edit and visualize languages
Languages to edit• Assigned by Administrator, Publisher• You can request languages from
Preferences -> Pending language request.
Language for content display • You can chose from button Content
Language• Selection is valid for current session
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Exercise 3
Go to your Preference, and update your email address
You need to write in field “New email”
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Exercise 4
Consider what languages you normally edit in the BioTech
Compare with the languages you have granted right now
Then go to your Preferences, and request the one(s) missing
Your requests will be approved during our next coffee break
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Exercise 5
Now consider which languages you normally need to take visualize when working with the BioTech
For example, if you normally translate from English to Arabic, you need to visualize/edit Arabic, and visualize English
Now change language display, by using Content Languages
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Exercise 6
Can you input non English characters using your keyboard?
If not, set up the appropriate virtual keabordGo to:
Control panel -> Regional and Language options -> keyboards and languages -> change keyboard
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Editorial workflow
Editorial actions needed to produce the final results
Important to assure quality control
Example: in a publishing house: writing, proof reading, editing, … publishing
In Biotech:• Management of content by editors • Validation by senior editors• Publication by Biotech managers
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Terminology
Role = function of a user in a workflow• Determines what the user may or may not
do in a given moment
Rights = permission to execute actions• Associated to roles• e.g. a term editor may add terms
Status = status of an element in a workflow• An element may be a concept, a term, … • Status may be draft, published, …
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Editors Validators Publisher
Creates new entries
Add definitions
Edit entry titleor definition
Establish relations between entries
Revise relations
Propose deletion
Accept or rejects changes
Decides what goes public
Roles in a workflow
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Workflow roles by content and languages
Editors are specialized by language and area, e.g. animal, plants…
Validators too may be specialized by language and area(s)
Publishers are responsible for the general quality of the product that is published
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Actions permitted to Term editors
Create new concepts, providing labels in the languages assigned
Create/edit/delete/revise terms and definitions for concepts in the language assigned
Created/edited by any editor
Add/edit relations between concepts
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Exercise 7
One EN editor adds concept:
“Amplified ribosomal DNA restriction analysis (ARDRA)”
Place it under concept “biotech glossary”
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Exercise 8
Other editors check that a change has been made to the glossary by looking at section Recent Changes
Can you read the table?
Click on the concept name
What do you see?
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How to see “news” in VocBench
Log in and check section Recent Changes
Log in and subscribe a RSS feed (link available in top stripe of the interface)Then you will get notifications without having to be logged in
Notification can be via:EmailYour browserOn your desktop (using dedicated programs, called RSS feed readers)
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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
This is not a problem with AGROVOC, but it probably is with the Biotech glossary
Plan to address this issue after this training
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Exercise 9
An EN editor (different from the previous one) adds a definition to “Amplified ribosomal DNA restriction analysis (ARDRA)”
The others see what has happenedNow do it by searchingSearch for “amplified”
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Actions permitted
Accepts or rejects proposals made by editorsE.g. creation of a new concepts, revision of a definition, deletion of a term
Validation actions are done in section Validation
Validators are typically domain experts who ensure quality of the content
Currently, if you log in as Validator, you have validation rights on all language
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Actions permitted
Have all rights as Validators
May also create and edit relationships between concepts
Approve new user accounts, grant rights on languages and data sets
Publishers have overview of the entire glossary and have last say on what is going to be published
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Action permitted
Administrator rights stay with VocBench managers
This role is not covered in this training
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Status of elements
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1. Proposed2.Proposed deprecated
3. Revised
4. Validated
5. Published6. Deprecated
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Proposed element
Element that has been newly addedPink
A proposal of deletion makes the element get status Proposed DeprecatedGrey
Status Proposed is independent of the role of the user of makes the proposal
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Revised element
Any elements that have been editedRed
If the editing consists in a suggestion of deletion, the status is Proposed DeprecatedGrey
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Validated element
Element approved by a ValidatorGreen
Validators may also reject change, then: The element goes back to previous status
Approving an Proposed Deprecated element makes it Deprecated
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Published and deprecated element
Elements published to the outside have either Published or Deprecated status
PublishedElement approved by a publisher
DeprecatedElement discardedKept for backward compatibilityHowever, you can exclude deprecated
elements from visualization (in Preferences)
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Exercise 10
Go back to concept “Amplified ribosomal DNA restriction analysis”
In which color does it appear?
In which color do its terms and definition appear?
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Exercise 11
Edit a term of the concept “Amplified ribosomal DNA restriction analysis”
Now, in which color does the concept appear?
And the edited term?
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Exercise 12
Pick up a concept from the list (in blue) and delete it
What is the meaning of the error message you get?
Observe the new color of the concept, and the color of its terms
Now delete also one of its terms
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Exercise 13
Search for “acceptor control”
What result do you get?
What languages are selected in your Content Language?
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Search
Search if against the entire data set, independently of which languages are selected in “Content language”
But if languages are not selected, you cannot see the corresponding labels
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Create a new concept step by step
You may only add concepts in the language of your competence
1.Click button “+” (Add new concept)2. A little window appears, asking for:1. Term2.Language3.Then click create, asks for position
1.Child of the selected concept2.Same level as the selected concept3.Top concept
4.Preferred term
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Concepts and glossary entries
When entering a new concept, the Term assigned should be marked as preferred
Because preferred terms are used for display in concept hierarchy!
Definitions may be given at a later stage
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Preferred terms
No more than one preferred term per language should be given
But there is no automatic check in VB, so be careful!
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Preferred terms
You can decide to show or not also non preferred terms
However, the glossary only has preferred terms
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More information about a concept
Can be specified in the corresponding tabs:
1.Terms2.Definitions3.Note4.Attribute5.Relationship6.History7.Image 8.Hierarchy
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Terms
Correspond to the title of the concept
May be added either when creating a concept (to provide labels to the concept), or later onFor example, when a translation is made
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More information about a concept
Can be specified in the corresponding tabs:
1.Terms2.Definitions3.Note4.Attribute5.Relationship6.History7.Image 8.Hierarchy
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Definition of a concept
If you create a concept in a language other than English, VB requires that an EN definition be provided
For each definition, a source and its URL must be given
Right now there is no authomatic control on the URL, so be careful!
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Definitions and translations of definitions
A concept may have one or more definitions
A definition may be translated into several languages
Source and URL are for Definition (not for its translations)
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Sources of definitions
Currently you can chose among:
FAOTERMNALWIKIPEDIAMeSHOtherBookJournal ArticleAGROVOCWordNet
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Exercise 14
EN editor add at least 3 of the following concepts:
1. Cisgenetic2. Competitive ELISA (c-ELISA)3. DIVA vaccine 4. Monosex population5. Omics6. Morula7. Probiotic8. Sperm mediated gene transfer (SMGT)9. Transcriptomix
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Exercise 15
Editors in other languages translate terms and definitions
You have 10 minutes
This is not a race! Our goal is that you become confident with the tool, and suggest us where and how to improve it!
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More information about a concept
Can be specified in the corresponding tabs:
1.Terms2.Definitions3.Note4.Attribute5.Relationship6.History7.Image 8.Hierarchy
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Notes
1.Editorial note• To add information or remarks useful for
editing purpose
2. Scope note• To specify the field of validity of a concept
These notes are not part of Biotech Glossary
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More information about a concept
Can be specified in the corresponding tabs:
1.Terms2.Definitions3.Note4.Attribute5.Relationship6.History7.Image 8.Hierarchy
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Attributes
To specify information that is not relevant to a glossary
You may find interesting the notion of subvocabularyA way to create sublists of concepts
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Subvocabularies
Currently, 5 subvocabularies:1.Chemical2.Geographical country level3. Geographical above country level4.Geographical below country level5.Fishery related term
Subvocabularies may be defined in section Relationships, by Publishers
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More information about a concept
Can be specified in the corresponding tabs:
1.Terms2.Definitions3.Note4.Attribute5.Relationship6.History7.Image 8.Hierarchy
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Relations between concepts
It is possible to establish relations between pairs of concepts
Many relationships are available
For the Biotech Glossary, it is recommended to use only Has related conceptVery general, like “see also”
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Exercise 16Go to advanced search
Search for all pairs of concepts linked by relation “Has related concept”
How many have you found?
Click on one of the related concepts
If concept A is realted to concept B, is it true also teh opposite? navigate the concepts before answering
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More information about a concept
Can be specified in the corresponding tabs:
1.Terms2.Definitions3.Note4.Attribute5.Relationship6.History7.Image 8.Hierarchy
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More information about a concept
Can be specified in the corresponding tabs:
1.Terms2.Definitions3.Note4.Attribute5.Relationship6.History7.Image 8.Hierarchy
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Image
It is possible to add images to better explain a concept
Currently, the glossary does not include images
Consider pros/cons of having this
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More information about a concept
Can be specified in the corresponding tabs:
1.Terms2.Definitions3.Note4.Attribute5.Relationship6.History7.Image 8.Hierarchy
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