Intern:Terminology Editor

The Terminology Editor (also called Term Editor, or Feature Editor) has been implemented into 4D to manage and structure all terms (vocabularies) of the PANGAEA Terminology Catalogue.

This Wiki page summarizes the most important functions of the Terminology Editor and shall provide starting help for working with it. For more elaborate information, the documentation can be accessed here (work in progress document).

=The Terminology Editor window=

The Terminology Editor list tab
The list tab is the first window, when the terminology editor button is clicked on the side-bar.

It consists of four sections:
 * 1) Term entry window: Lists all details about the currently chosen term.
 * 2) Relation table: Lists all outgoing relations of the currently chosen term to other terms.
 * 3) Term list: List of all terms from a query-output or within a chosen ontology
 * 4) Hierarchy tree: Showing all “has broader term” relations. If synchronize-button is checked, currently selected term from the term list is shown.

The Terminology Editor search tab
The search tab of the term editor functions the same way as for tables like the dataset or parameter table. It allows more advanced searches, than the search slit in term list of the list tab.

The search results will then be displayed in the term list of the terminology editor window.

=Elements of a term entry=
 * ID = automatically assigned identifier within PANGAEA. Can not be changed.
 * Status = curational/review status of the term (default: pending)
 * Name = name of term
 * Abbreviation = abbreviation of term. Only assigned if commonly used.
 * Semantic ID = most commonly a uniform resource identifier (URI). Often, but not necessarily represents an URL (uniform resource locator) directing to a web-entry about the term
 * Web description = human-reabable web-entry (e.g. Wikipedia)
 * Description = short definition of the term, as understood within PANGAEA. Can contain own definitions by the team or foreign definitions (other ontologies, dictionaries, wikipedia etc.)
 * Comment = additional comments (e.g. short IDs, remarks for usage etc.)
 * Ontology = original ontology the feature comes from. A feature can only relate to one ontology.
 * Category = (description will follow)
 * Created = date of feature creation and responsible user
 * Updated = Date of update and responsible user

=Looking up terms and relations=

Searching for terms
A simple search slit for searching is given in the term list of the terminology editor.

There are three search options to be chosen from the drop down list: The full text search within the term editor functions similar to the full teyt search of the PANGAEA website, but does not sort the terms according to their search score. In contrast to a "contains"-search, not every query element needs to be present and the order of tokens may vary. Please note, that the full-text search only searches within the term name.
 * "contains" (term name contains a string)
 * "begins with" (term name begins with a string)
 * "full text" (full text search to find tokens within term name)

To restrict the term selection to one ontology, choose an ontology from the terminology field. The whole list of terms will appear.

Use the category field, to filter for terms belonging to the categories class, instance, systematics, grammar, attribute or quantity.

As long as a selection is done in the terminology or category field, search queries will only be performed within this selection.

The advanced search can be accessed via the search-tab of the terminology editor. Query results will be displayed within the term list.

Browsing through the tree
The hierarchy tree displays all "has broader term"-relations of a selected term. Other relation types like "is synonym of" are not shown.

Instead of using the search function, the hierarchical tree can be used to find terms and display their relations.

You can search for a broader term (e.g. enzymes) and display it in the tree view. Expand the tree to have a look at the subclasses. This can be especially helpful, if the allocation of the term is known, but the complex term name is not.

The hierarchy tree is only updated by a selection from the term list, as long as the "synchronize lists"-box is checked.

If you want to freeze the tree, uncheck the box!

=Term annotation=

=Creating and updating terms and relations=

Working with import files
Working with import files allow a fast and automated upload of new features or an update of existing ones.

The style sheet for the import file can be found here. Import files can be prepared with Microsoft Excel or a comparable program. The final import file should be saved as Unicode Text File (i.e. tab seperated) using UTF-8 character encoding.

The import file upload function can be found in 4D under: Import --> Features. (Ontology and Category need not be specified).

ID lists
Many columns within the import file work require IDs instead of names. All neccessary ID lists can be found below.