Editing the BIOTECH Glossary with VocBench 1.1

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Editing the BIOTECH glossary with VocBench 1.1

Training

FAORome, June 20-21, 2011

Day 1

Caterina [email protected]

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Objectives of the course

Enable editors to maintain the biotech glossary using VocBench

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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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Topics for tomorrow

1. Validation of changes in glossary

2. New web interface of glossary

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VocBench

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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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Basic terminology

Glossary entry = concept

Entry title = term, or concept label

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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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Sandbox version for training

There, you can do anything! Real data will not be affected

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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

http://code.google.com/p/agrovoc-cs-workbench/

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VocBench

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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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Example

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Accessing the VB

You need:A User account, a role, a data set:

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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

http://202.73.13.50:55481/vocbenchv1.2i/#Concepts

http://aims.fao.org/website/The-VocBench/sub

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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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Your role(s)

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This is what I see

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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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How it appears to an editor in ZH

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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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Look at your Preferences

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You can edit your Preferences

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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

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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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Term editor

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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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Validator

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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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Validation

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Publisher

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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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Administrator

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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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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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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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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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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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Exercise 17

Chose a concept and add at least one relation to another concept

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History

Recap of history of changes of the concept

Automatically generated by VB

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History

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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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Hierarchy

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Editing the BIOTECH Glossary with VocBench 1.1

Education

workflow vb

editing validation

vb users

vb user community http

inside vb

concept entry title

vb documentation user

languagesa concept