Glossary

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The glossary of Scratchpad terms lists the definitions of the general terms used in the help wiki and within the Drupal community.

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A

Admin menu

Menu line at top of Scratchpad that gives access to administrative pages. The Admin menu is only visible to authenticated users who have logged in.

Anonymous

A visitor to a Scratchpad who is not logged in. Scratchpads consider any such visitor as being an anonymous user and belonging to the anonymous user role.

Authenticated

A visitor to a Scratchpad who is logged in. An authenticated user is able to access non-public content and create and edit own forum posts but no other content if he doesn't have an additional user role (see Roles).

Autotagging

An automated process that adds tags to content by analysing the text of content and searching for terms in a taxonomy.

B

Basic page

A standard content type in Scratchpads. Typically basic pages are used for static content that can (but are not required to) be linked into the sites’ menus. An example might be a general introduction to a taxonomic group or information about the contributors to a Scratchpad.

Biblio

The Scratchpad bibliography management module, used to add, organise and browse bibliographic content such as journal articles, books and monographs. Biblio nodes are a type of content and can be exported in different formats (BibTeX, RTF, Tagged (EndNote) and XML).

BibTeX

Pronounced Bib-Tech. One of several reference managers, notable because it is open source and freeware. Biblio can export references in BibTex format (*.bib)

Biodiversity Information Standards (TDWG)

A non-profit organisation (previously Taxonomic Databases Working Group) formed to establish international collaboration among biological database projects including the development of standards for the exchange of biological/biodiversity data. Scratchpads use TDWG standards for specimen, taxon descriptions and locality records (Darwin Core and the World Geographical Scheme for recording plant distributions). See http://www.tdwg.org/

Block

The ‘boxes’ visible in the sidebar of a Scratchpad and on taxon pages. Most blocks (e.g., taxonomies) are generated by various Scratchpad modules, but they can be created in the administer blocks area of a Scratchpad. See the documentation for more information on blocks.

Blogs

Blogs (contraction of “web” + “log”) are used to create and manage a series of regular content entries, like general status updates, a travel diary or a running commentary (e.g. http://iphylo.blogspot.com/). Readers can optionally comment on blog entries. They are a good way of communicating with the users of a Scratchpad.

Breadcrumbs

The section, usually near the top of the page and below the Main menu, that shows where you are in the sites’ navigation system. For example, it might show Home > Biology > Life Cycle > Mating, meaning that you are at the page on Mating, which is part of the Life Cycle section, which is in turn part of the Biology section. The term breadcrumbs is borrowed from Hansel and Gretel, who left crumbs of bread along their path so they could find their way back out of the forest.

Browser

See Web browser

C

CCK

Content Construction Kit. A module that permits site maintainers to create custom fields and content types. A variety of extension modules to CCK allow fields such as images and dates.

Character project

A module for managing taxonomic characters that can be exported in different standards. Data are managed in a matrix structure, comparable to a spreadsheet.

Child

For objects that can have hierarchical relationships, (such as taxonomies and menu items). A "child" menu item, for example, is nested under another menu item, which is referred to as the "parent" menu item.

CMS

Content Management System: a collection of tools designed to allow the creation, modification, organisation and removal of information. Drupal is the CMS used by Scratchpads.

Content

The text, images, and other information on a web site. Besides nodes a typical Scratchpad will contain other material, such as comments and files. Collectively these are content and are the intellectual property of the Scratchpad community that created them.

Content type

Every node belongs to a single "content type" (sometimes called “node-type”) that defines various settings such as the node’s fields, whether comments are permitted, who can see the node (see permissions) etc.

Controlled characters

Controlled characters can be used for phylogenetic analyses or interactive keys. The character is separated into two or more character states. Each characters state is attributed a number, starting with zero.

Countries map

The countries map content type can be used to produce shaded presence/absence maps for taxa. The map regions are based on the TDWG distribution standards.

CSV

Comma-separated values, a file where tabular data are separated with commas.

D

Darwin Core

Darwin Core (DwC) is a standard for sharing biodiversity information. Scratchpads use the DwC standard for location and specimen information. Read the introduction to the Darwin Core standard.

Dashboard

An easy to read user interface that gives an overview of important site information. You can access the Dashboard from the Admin Menu.

Drupal

A free and open-source content management system (CMS), used by Scratchpads. About Drupal

E

Editor

This term has two meanings in Scratchpads:

  • One of the categories of user permissions (see roles)
  • A program used for editing data. The most frequently encountered editors in Scratchpads are the WYSIWYG editor and the taxonomic editor.
EndNote 8+ XML

An EndNote file format used for exporting references from the bibliographic software, EndNote.

Entity

Any defined chunk of data in a Scratchpad. This includes things like terms in a taxonomy, users, files, etc.

EOL - Encyclopedia of Life

A project to provide global access to knowledge about life on Earth. EOL is a partner of the Scratchpad project. See http://www.eol.org.

eMonocot

eMonocot is a partner project that makes use of Scratchpads. eMonocot aims to create a global online resource for monocot plants. It will provide a focus for taxonomists working on monocots and will help people discover information about monocots by providing tools for identification, up-to-date checklists, descriptions and links to other resources. Read more about eMonocot.

F

Faceted browsing

!Add text!

Favicon

See Shortcut icon

Field

Elements of data that can be attached to a node or other Scratchpad entity. Fields commonly contain text, image, or numerical values, but there are many other data types. It is possible to create and customise fields in CCK.

Forum

A place in a Scratchpad where people can have online discussions by posting messages to each other. Forums (fora) are hierarchical and can contain subforums (subfora) with different discussion topics.

G

GBIF

The Global Biodiversity Information Facility (GBIF) promotes and facilitates the mobilization, access, discovery and use of information about the occurrence of organisms over time and across the planet. See http://gbif.org.

Git

A version control system used by Scratchpad developers to coordinate their individual code changes. Git records everyone's changes to a given project in a directory tree called a git repository. The Scratchpad source code is downloadable from our Git repository (https://git.scratchpads.eu/viewgit), which is publicly accessible.

Google Maps API key

A free key code that allows a Scratchpad to generate unique Google maps from its data.

Grid editor (Slickgrid)

An Excel-like matrix editor (Slickgrid) for bulk updating content.

Groups

Groups can be used to organise and control access to content. Groups can be visible and open for all users to join or hidden with membership controlled by the site maintainer.

GUID

GUID stands for Global Unique Identifier. GUIDs can be assigned by users for each term used in Scratchpad. GUIDs must be unique in the Scratchpad environment. If a user does not assign GUIDs to terms the system will generate them automatically. GUIDs of taxonomic terms are also displayed in the taxonomic editor on the left of the taxon name being edited.

H

HTML

Hypertext Markup Language, used for writing the basic parts of a webpage. Web browsers read and interpret HTML to compose web pages for a user.

I

Image

Individual or multiple images can be uploaded to a Scratchpad using the image module. Images can be classified using a taxonomy, linked to a specimen record or a publication and categorised by subject. Allowed file formats are GIF, JPEG, PNG and the default size limit is 50MB.

Integrated Taxonomic Information System (ITIS)

A partnership that maintains an online database of species names and their higher classification. ITIS is a member of the Catalogue of Life consortium. They have developed a data standard which is used by Scratchpads. See http://www.itis.gov.

Issue

Issues are used to report problems with the Scratchpads (e.g. a bug report, missing documentation) or to request a feature. Site maintainers have access to an issues tab on the right of their browser window through which they can examine issues already raised, their status and solution, or raise a new issue.

J

Javascript

A programming language used to perform actions on the user's computer, most commonly the mechanism by which web pages become 'dynamic' or interactive. JavaScript is a setting in your browser preferences and should be turned on for best performance of these pages.

L

Location

A location node stores information about a named locality. Location data may be linked to specimen data or other content types you create. Scratchpad location data conform to Darwin Core (version 1.2.1) and GBIF standards.

M

Main menu

The menu line below the header that gives access to Scratchpad content.

Maintainer

The site owner, responsible for moderating and maintaining the site (see ‘roles’).

Matrix editor (Slickgrid)

See Grid editor.

Media gallery

Media galleries are used to sort media into meaningful categories. The images in a media gallery can be viewed through a kind of slide show.

Menu

Refers to grouped clickable navigational elements on a page. They are often found in the sidebars or at the top of a page. Two default menus are displayed on a site and are referred to as Admin menu and Main menu. Menus are controlled by site maintainers.

Migration

The procedure of upgrading sites from Scratchpad v. 1.0 to Scratchpad v. 2.0. This procedure must be overlooked be a developer and cannot be completed by a Site maintainer. The global high-level procedure can be found at Migration Procedure

Module

Software that extends Drupal functionality to do a particular, well-defined task. Many modules exist in public libraries (http://www.drupal.org) and are known as 'contributed modules'. Scratchpads have developed many modules unique to the project. (see ‘Git’ above).

N

Newsletter

Newsletters can be used to keep a Scratchpad community informed about site-related matters. Newsletters can be distributed via email using a list of subscribers.

Nexus or Newick data

Phylogenetic data formats for constructing phylogenetic trees.

Node

A piece of content in a Scratchpad, typically corresponding to a single page on the site, that has a title, an optional body, and usually additional fields. Every node is of a single content type, and can additionally be classified using the taxonomy system. Examples of nodes are basic pages, bibliographic entries (Biblio nodes), localities, polls, specimens and images.

Node type

See content type.

O

Overlay

Editing as well as any administrative functions are done in an area superimposed over the page where this function was accessed from.

P

Page

See Basic Page

Parent

See child

Patch

A small piece of software designed to update or fix problems with a computer program or its supporting data. This includes fixing bugs, replacing graphics and improving the usability or performance. Patches are applied by the team maintaining a Scratchpad installation.

Path

In Scratchpad terms, a unique, last part of the URL for a specific function or piece of content. For instance, for a page whose full URL is http://example.com/node/7 the path would be "node/7". N.B. This is a slightly different usage to that normal in IT, see 'breadcrumbs' above.

Permission

In Scratchpads, a method for controlling access to content creation, modification and site administration. Many tasks (e.g. creating a node) require the user to have a certain permission in order for them to perform that task. Permissions are used to make pages invisible to certain groups, e.g. anonymous users, amongst other things.

Phylogenetic tree

A content type that displays relationships of taxa in a branching tree diagram.

Poll

The Poll module allows you to create multiple choice polls/questionnaires.

Profile

A set of fields containing information about each user. The minimum profile information is username and e-mail address and maintainers can set additional fields, either optional or required from everyone during registration. Additional information typically will include name and institutional address. Profiles are usually kept confidential to maintainers, but can be summarised for others (see Permissions). Profiles can also be used to contain bibliographic/historical information about non-users.

Published

A published node can be viewed by visitors to the website. An easy way to hide nodes from the public (i.e. anonymous role) is to make the node unpublished by unchecking "Published" in the node add/edit form.

R

Region

Defined areas of a page where content can be placed. Basic regions include: Header, Footer, Content, Left sidebar and Right sidebar. Content is assigned to regions via blocks. They can be ordered by weight within regions to define the order in which they display.

Regular expressions

Regular expressions are sequences of characters that form search patterns, mainly for use in pattern matching with strings, or string matching. To enable Scratchpads to read regular expressions (wherever applicable) append the character "/" at the start and at the end of your regular expression string.

Rich text editor

A tool to easily format text similar to a word processor. See WYSIWYG.

Roles

Sets of permissions that can be applied to individual users. Every user is assigned to at least one role that defines their rights to access and change areas of the site. The default roles are Maintainer (site owner), Editor (able to create, edit and delete content), Contributor (able to edit content), Authenticated user (able to access non-public content) and anonymous user.

RSS

Really Simple Syndication. A family of Web feed formats used to publish frequently updated content such as blog entries, news headlines or podcasts. An RSS document (which is called a "feed", "web feed" or "channel") contains either a summary of pages (see "teasers", below) from an associated web site, or the full articles. RSS is one of the many ways of connecting a Scratchpad with other sites, systems and data.

RTF

Rich Text Format – A file format for text documents that can be opened by most word processors. It allows a limited amount of text formatting (e.g. bold, italic, font colours). Biblio can export references as RTF files.

S

Sandbox

A test Scratchpad site where any user can experiment. Any content you put in the sandbox will be not be permanent as we automatically delete Sandbox content every 6 hours. Sandbox content can also be edited by other users. [Scratchpads Sandbox site]

Shortcut icon

A small icon representing the site that is shown in your browser or as the shortcut icon when you bookmark/favourite a page.

Shortcut menu

A customizable menu, located below the Admin menu, containing links to administrative pages that are frequently used.

Sidebar

A region to the left or the right of a page where blocks and/or content (often menus or links) are displayed.

Specimen

Specimen data that, usually together with a Location, is used in the creation of specimen records. Scratchpad specimen data conform to Darwin Core (version 1.2.1).

SPM

Species Profile Model (SPM) is a standard developed by Biodiversity Information Standards (TDWG) for information about taxa. It is used by Scratchpads for descriptive information about taxa. http://rs.tdwg.org/ontology/voc/SPMInfoItems

T

Tabs

Tabs refer to buttons that change the display of information on a page, without navigating away from it, in the same sense as most browsers. An example is the taxonomy editor interface, which has four tabs (Scientific Name, Usage, Reference and Vernacular Names) which display different data entry forms. Tabs are a specific type of menu.

Tag

A tag is a term used to classify content. Tags usually come from a taxonomy and can be added to content manually or automatically.

Tagged

Tagged may refer to:

  • (Endnote) Tagged files are used by the reference management program EndNote. Biblio can be export references as Tagged files.
  • The classification of content using terms, see Taxonomy. Some tags are added automatically, see autotagging.
Taxon Description

Content that provides descriptive data about taxa (not specimens). Scratchpads use the TDWG SPM standard for taxon descriptions.

Taxonomy

This term has two meanings in Scratchpads:

  • In IT, a taxonomy is a hierarchical organisation of "terms", i.e. organisational keywords known in other systems as categories, tags, or metadata. These terms are gathered within lists called "vocabularies".
  • The biological use of 'taxonomy' is a special application of this general term.

In Scratchpads the Taxonomy module has been modified to accommodate the biological use of the term ‘taxonomy’, while also providing the facility to create and manage these vocabularies. Most importantly, the terms in the vocabulary lists are attached to individual content elements as tags, allowing content to be assembled on a single page. There is an automatic process (autotagging) that adds tags to content by analysis of the content. Tags can also be added manually for enhanced linkage.

Taxon page

A page that can display multiple widgets that contain various data about a taxon. Users can control which widgets are displayed, their size and position.

TDWG

See Biodiversity Information Standards

TDWG regions

A standard for biogeographic regions defined by Biodiversity Information Standards (formerly TDWG). See http://rs.tdwg.org/ontology/voc/GeographicRegion or http://www.nhm.ac.uk/hosted_sites/tdwg/TDWG_geo2.pdf.

Teaser

A short introductory sentence or paragraph about a piece of content that informs readers about the subject of the content. By default, the first paragraph or two of the content is used (there is a setting for how much), usually with a link to the complete node. The intention is that teasers provide an expanded index to pages over a simple list of page titles.

Theme

A graphical package that changes the look and feel of a Scratchpad.

TID

TIDs (Term ID) is a unique sequential number given to each of the terms in the Scratchpads taxonomies. TIDs can be used in Excel templates to refer to taxonomic terms instead of the term name or the GUID. TIDs are being displayed in the taxonomic editor on the left of the term name being edited.

TinyMCE

A WYSIWYG editor.

Tinytax

A block which displays a classification in a graphical interface.

U

Unpublished

See published

URL

Uniform Resource Locator. Also known as a web address, a URL is a human readable address for content (like a page) on an Internet server e.g. http://www.scratchpads.eu/node/937

User roles

See Roles

V

Views

A module for controlling the presentation of lists and tables of content.

Vocabulary

See taxonomy

W

Web browser

Software for navigating, retrieving and displaying data on the World Wide Web. The major web browsers are Internet Explorer, Firefox, Google Chrome, Safari and Opera. Browsers vary in their capacities and facilities and not all pages will display or behave properly in all browsers. Scratchpads are developed in Firefox, which is the recommended browser for these pages.

Webform

Webforms are used to collect information from users. The completed form, when submitted, can be sent for processing, for example a survey, or processed locally, for example content creation.

Weight

A term used by Scratchpads to define the order of display in a block or node. For blocks the weight field is adjusted using a drag-and-drop interface. Note: A lower weight value (-10) will float to the top of lists, while heavier (+10) weights will sink lower in lists.

Widgets

Deprecated - Scratchpad 1.0 term Information panels found on a taxon page. The information used by widgets can come from Scratchpad data or external sources. Widgets are moveable and resizable.

World Geographical Scheme for recording plant distributions

A data standard published by TDWG that is used to record biological distributions (not limited to plants). http://www.nhm.ac.uk/hosted_sites/tdwg/geo2.htm

WYSIWYG

What You See Is What You Get. An acronym used in computing to describe a method in which content is displayed while editing in a format that closely resembles the final result. Most word processors are WYSIWYG.

X

XML
eXtensible Markup Language (XML) is a common standard for encoding data in a way that can be easily interpreted by computers and people. Scratchpads export data in XML for processing by external services, e.g. in the publication module.
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