Scratchpads¶

Scratchpads are an easy and effective way to present your data online.

Whether you just want to publish on the web, construct a database or assemble a formal manuscript, Scratchpads are able to help!

Contents¶

Site setup¶

This workflow leads you through step-by-step the basic set up of your new site.

Click the dashboard link in the admin toolbar:

You can see your site’s setup status is 0%. Click Finish setting up the site

Click the Continue button to start the set up workflow.

Step 1: Front page welcome message

The first step is writing a welcome message that will appear on the front page of your site.

Images will appear separately on the front page, so don’t add them to the welcome message.

Enter a welcome message, and select continue.

Step 2: About your site

Enter text to create your sites About page.

Use the icons of the rich text editor to format your text or to add links or images

Step 3: Licence

Select a Creative Commons license to apply to the content of your site. The default license is “Attribution CC BY” but you can select a different license if you want.

See http://creativecommons.org/licenses/ for an explanation of licenses.

Step 4: Category

Select the appropriate categories for your Scratchpad.

Scope
Ecoregion
Geographical extent
Research domain
Taxonomic area

This information is used by the team to analyse Scratchpads usage.

Step 5: Tools

Tools turn on and off different features of Scratchpads. For this training course, don’t change any of the tools, just save. We will activate and use some of the tools later in the course. The less tools activated the easier sites are to use for people with little Scratchpad knowledge.

Finish

Click on the Finish button to complete the set up.

Admin menu¶

The administration pages are accessed via the Admin menu at the top of the Scratchpad.

The Admin menu will be present once you have logged in to a site. The menu items you see will depend on your access permissions.

The first of the admin links is the Home icon that will always bring you back to the front page of the site
The Dashboard gives administrators a customizable overview of important site information. You can add and remove items from the dashboard (see Customise dashboard), or you can disable the dashboard completely
Under Content you can create and view the content on your site
Structure has links to administer site taxonomies, content types, tools and the various site layout options like blocks
Appearance is where you can edit the theme of your site
Under People you can administer the site’s users, including adding or removing administration privileges
Configuration gives access to various advanced administration pages that you will need only rarely or not at all
The Import page is the place to go when you want to import any kind of data into your Scratchpad

Theming¶

Colour scheme¶

To differentiate the look of your site from other Scratchpads you can change the colour of the theme.

To change the theme colour, click on the Colours icon in the lower right corner of your Scratchpad, to reveal the colour palette options.
Select one of the colours.
Click Save.

Logo¶

Adding a logo¶

From the Admin menu go to Appearance > Settings
Disable Use the default Shortcut icon
Click Browse to find the desired logo in your computer
Click Save

What makes a good logo?¶

It’s not easy to design a custom logo. Some guidelines to consider:

Try to keep it relatively small so the header area is not too big. The header appears on every page and site content is displayed below the header.
The dimensions of the default Scratchpad logo are 71x70 pixels. We do not recommend creating a logo over 130 pixels high.
The ideal file format is Portable Network Graphics (PNG) as it supports transparency, something that JPEGs do not. If your header image/logo does not require transparent areas then a JPEG is fine to use.
We create logos as vector images then save them as raster images.

Pages¶

In Scratchpads you can create custom pages to present content in a static way.

You can embed text, images or other content.

Adding a page¶

From the Admin menu go to Content

Click Add next to Page

Enter a TITLE, e.g. “Introduction”, and some BODY text. The BODY text is the main content of the page. If you click Edit summary you can enter text to be used as a summary for the page content, displayed on search results or news pages.
Use the MEDIA field to link media (images, audio or video) to your page. These items will appear as links beneath the text of your page
To add images to your text, you need to add them using the Add media icon in the BODY field
In MENU SETTINGS select where you want the page to be placed by choosing the appropriate PARENT ITEM.

By default, a page will be set to Main menu (see above). A MENU LINK TITLE is required for each page. By default, the page title is used. You may want to replace the menu link if the page title is very long

It is not advisable to have all pages showing up in the Main menu, so before you add pages think about the hierarchy of menu items and start adding the pages that should show in the main menu first.

The WEIGHT defines where in a list of menu items this item is placed.

Click the Save button at the bottom left

Editing page¶

To edit an existing page you can either click the edit tab on the page, or find the page in the admin>content>page section.

Edit content on the page by clicking the Edit tab
The BODY field has a Rich text editor. Explore some of the features of the rich text editor by modifying the format of the text you have entered.
Click Save

Cloning a page¶

For cases where there are only slight differences between nodes you can create a duplicate:

Click on the Clone tab.
Change the Title of the page and some of the text
Change the menu link

Hierarchical pages¶

Often, it’s useful to create a hierarchical structure of pages.

Create a new page
In MENU SETTINGS select a previously created page as the PARENT ITEM.

Click Save

Instead of popping up in the Main menu, the menu link title now appears in a block next to the page. This block will fill with a hierarchy of menu items as you add more pages. You can use it to structure your pages in a way that helps users to find the information.

Adding a biological classification¶

Introduction

Before adding data other than static pages to a Scratchpad, we need to add the taxonomic names. This is done via the Taxonomy module, which contains controlled vocabularies.

A vocabulary is a list of terms. These do not have to be biological classifications. Country lists, keywords etc. can all be treated as “taxonomies” in the context of your site. Taxonomies are the backbone of a Scratchpad and link together the content. They are used to generate taxon pages. Before you add a set of taxonomic names to your Scratchpad you need to add the vocabulary for it.

Click on Structure in the Admin menu and click on Taxonomy near the bottom

“Structure” admin page, listing the menu options: Blocks; Contact form; Content types; Menus; Taxonomy; and Tools
Click on the Add vocabulary link

Taxonomy page showing “Add vocabulary” button near the page title
Enter the vocabulary Name.
Add a vocabulary Description.
Select which kind of biological classification you are creating (“Animal” in our example)

Add vocabulary form showing name, description and biological classification fields
Click Save

Adding terms¶

Having created a vocabulary you now need to add the list of terms (names).

This can be done by either importing a classification through the Scratchpads Classification Service (see Importing a classification), or by creating and importing your own classification from Excel (see Importing classification from Excel). Alternatively you can add terms one by one by clicking on Add terms when you are on the Taxonomy admin page or by using the taxonomic editor (see Editing classification).

Troubleshooting¶

Missing tab after creating classification¶

If after creating a classification and adding terms to it a tab does not appear for it in the main tab bar try clearing the caches:

Go to Admin > config > development > clearcache

Click Clear all caches - this will take a number of seconds to complete (likely more than 30 seconds)

Importing a classification¶

Scratchpads provides a service to import classifications from Catalogue of Life.

The names provided by this service are currently a little out of date, from 2014 and 2015, but will be updated soon.

From the Admin Menu go to Import
From the drop-down list select Taxonomy > Scratchpads Classification Service
Select the Taxonomy
Enter the root term (the highest taxon for which all children will be imported) of your classification (e.g. “Pediculus” or “Pinus”).
Choose which Catalogue of Life name list to use (we’d recommend the most recent), and select Import. This will import the complete classification into the Scratchpad (and may take a few minutes, depending on the number of names to import).

Classification import progress bar

When the import is complete, the overlay will report the number of terms created.

Viewing classification¶

To view your new classification and the taxon pages, close the overlay and go to the new tab with the classification’s name in the Main menu - see Viewing a classification.

Viewing a classification¶

To view your new classification and the taxon pages, close the overlay and go to the new tab with the classification’s name in the Main menu.

On the left side of the page you can browse the classification. Navigate by clicking on the plus icons to view child taxa and clicking on a taxon name to open the respective taxon page.

On the top right, click on the cog wheel icon next to the taxonomic name header to open the taxonomic editor - see Editing classification.

Editing classification¶

You can open the taxonomy editor either from clicking the cog wheel icon next to the taxonomic name header of a taxon page (see Viewing a classification), or from the Admin menu:

From the Admin Menu go to Structure > Taxonomies
Click Edit terms next to the biological classification you wish to edit.

Taxonomy editor¶

The taxonomic editor is divided into a left Tree side and right Form side.

On the Tree side you can add, edit, move, delete or search for taxonomy terms.
On the Form side you add/edit the data associated with a term.

Selecting a term¶

When accessing the taxonomic editor via the classification edit function, the respective term is already in edit mode.

If you instead access the editor via the taxonomy administration page or if you want to edit a different term, extend the classification to the correct term by clicking on the plus icons and select a term by clicking on the Edit link next to it.

Editing term form¶

When you select a term to edit, the term form opens on the right hand side
Make changes and Click Save

Scratchpad biological classification fields conform to the Integrated Taxonomic Information System (ITIS) standard. For more information on these fields see Itis standard fields.

Adding a term¶

Add a term by either clicking on the Add term icon in the upper right corner of the tree, or on the Add term tab above the right hand Form side.

The new term will be added as child of the selected term. If no term was selected the new term is added to the root of the classification.

Delete a term¶

Select a term to delete, and click the Delete term icon in the upper right corner of the Tree side of the taxonomic editor. Scratchpads will ask you to confirm the deletion before proceeding.

Itis standard fields¶

By default all Scratchpad taxonomies have three basic fields: the term name, parent and description. This is not really enough when dealing with biological classifications. We have therefore developed a special way to deal with biological classifications that follows the standards used by the Integrated Taxonomic Information System (ITIS) and is compatible with other initiatives.

The fields we use for biological classifications are:

Standard Scratchpad fields:

Term name: A combination of the different unit names and indicators.
Parent term name: An ITIS term denoting the taxon that is the next highest level from the subject valid or accepted taxon. The parent of a species is usually a genus; the parent of a genus is usually a family, and so on. This parent-child linkage between records is the basis for the classification hierarchy in ITIS.
Term description: The term description field is usually not used for biological classifications.
GUID: The global unique identifier for the term name. GUIDs can be used to compare/synchronise different databases. Adding a GUID is not required, you only need it if your names were generated from an established database and you want to be able to update your names from this database at a later stage. Note that the GUID really has to be globally unique, at least across the whole Scratchpad. So it is not enough just to start counting from “1”. Better is a combination like “Species2000-1”
Parent GUID: The global unique identifier for the parent term name. Adding a Parent GUID is not required.

ITIS fields:

Associated accepted_name: The scientific name of the valid or accepted taxon identified as the currently accepted name used for a given invalid or not accepted name. Each name that is in synonymy (junior synonyms, obsolete combinations, etc.) must be connected to one accepted or valid name.
Authors: The author(s) associated with the name of a taxon. This can include the year of publication and brackets, e.g. “(Quoy and Gaimard, 1832)”.
Page number: The page number the taxon was described on in the protologue. This field is not part of the ITIS standard.
Rank: The label associated with the specific level of a taxonomic hierarchy, e.g. “Family”, “Genus” or “Species”. For values check ITIS or the taxonomic editor for an existing classification on your site. Note that the spelling and capitalisation of the ranks in your import file must match the ranks in the Scratchpad!
Unacceptability_reason: An explanation regarding why a given scientific name is judged to be invalid or not accepted. Unacceptability reasons vary among kingdoms. For values check ITIS or the taxonomic editor for an existing classification on your site. Note that the spelling and capitalisation of the reasons in your import file must match those in the Scratchpad!
Unit indicator 1: Indicator of an occurrence of a plant hybrid at the generic level. The only value allowed is “X”.
Unit name 1: The singular or first part of a scientifically accepted label for an occurrence of Taxonomic Units. For uninomials (1-part names like family or genus names) this will be the only name field entered. For binomials/polynomials, this field will be used for the first part of the name (the genus name). The names in this position require the initial letter to be capitalized.
Unit indicator 2: A category indicator positioned between the first and second parts of a binomial/polynomial taxonomic name. The only value allowed is “X”.
Unit name 2: The second part of a scientifically accepted label for a binomial/polynomial occurrence of Taxonomic Units (the species epithet).
Unit indicator 3: A category indicator located within a polynomial taxonomic name. Allowed values are: “ssp.” (plants and fungi), “subsp.” (animals and monerans), “var.”, “subvar.”, “f.”, “subf.”, and “X”.
Unit name 3: The third portion of a scientifically accepted label for a polynomial occurrence of Taxonomic Units (e.g. subspecies name).
Unit indicator 4: Same as unit indicator3.
Unit name 4: The fourth part of a scientifically accepted label for a polynomial occurrence of Taxonomic Units.
Usage: Current standing of an occurrence of Taxonomic Units. Allowed values are: “accepted” (plants and fungi), “not accepted” (plants and fungi), “valid” (animals and monerans), and “invalid” (animals and monerans).
Vernacular names: Enter vernacular names for this taxon, comma-separated. This field is not part of the ITIS standard.

Importing classification from Excel¶

Taxonomic terms can be imported directly into a existing vocabulary through a pre-populated template excel file. This can be very helpful especially when large volume of terms has to be imported or when the imported terms are already in a structured (or semi-structured) format (e.g. an MS Excel file, an MS Access database).

Create the vocabulary¶

Skip this section if you already have a taxonomy you wish to update

From the Admin menu go to Structure > Taxonomy
Click + Add vocabulary
Provide the Name of your new classification
Select if the classification is Biological or non-biological. This is a very important step
Click Save

Downloading the template file¶

From the Admin menu select Import
Select Taxonomy: Excel file import
Select a vocabulary.
Download the Excel template.
- Select the first template file if you wish to replace all contents of an existing classification.
- Select the second template file if you wish to update (correct, add) terms in a existing classification

Editing the template file¶

Complete the columns as follows:

Term Name - Required field

Provide the full term without the authority. e.g. Thymus or Thymus longicaulis or Thymus longicaulis subsp. longicaulis Do not italicize.

Always start with the higher taxa of your classification first

Parent Term Name

Provide the term name of the immediate hierarchical parent in your classification. Provide the name as entered in the Term Name field

Term description

Provide some basic description for the term. This field should not be confused with the taxon description that can be entered in detail from the Taxon description content type

GUID

Provide a unique and at least 10 character long alphanumeric identifier for the term. This identifier will be used throughout Scratchpads to identify this term. If left empty the system will auto-generate one once the file is uploaded

Parent GUID

Provide the GUID of the parent term. This can be left empty if you have already provided the Parent Term Name or if the taxon is the highest in the hierarchy.

Associated accepted name (Name)

Provide the name of the term that is the currently accepted name if the taxon is not accepted. Should be left empty if the column Associated accepted name (TID) or Associated accepted name (GUID) is filled.

Associated accepted name (TID)

Provide the TID number of the term that is the currently accepted name if the taxon is not accepted. Should be left empty if the column Associated accepted name (name) or Associated accepted name (GUID) is filled.

Associated accepted name (GUID)

Provide the GUID number of the term that is the currently accepted name if the taxon is not accepted. Should

Importing the template file¶

Once you have made the desired changes and additions to the template file, you can import it back into your Scratchpad.

Select Browse, locate the file, and select Import.

_images/ClassificationImportExcelBrowse.png

When the import is complete, the overlay will report the number of terms created.

_images/ClassificationImportExcelResult.png

To view your new classification and the taxon pages, close the overlay and go to the new tab with the classification’s name in the Main menu - see Viewing a classification.

Deleting classification¶

From the Admin menu go to Structure > Taxonomy

Select Settings next to the taxonomy you wish to delete
Click Delete at the bottom.

This will delete the vocabulary as well as all the terms in this vocabulary.

Integrating external data¶

Scratchpads can integrate data from many important data providers on its taxon pages

IUCN¶

NCBI¶

Enabling the widget¶

From the administration menu bar got to Structure > Tools
Find the Widgets section
Click on the switch next to NCBI Widget to enable it (ON)
Click Save

Accessing widget results¶

Once enabled, the widget will be visible as a new section called NCBI in the Description tab of your taxonomy viewer.

A table will provide results associated with a taxon from all NCBI’s databases; including Nucleotides and Proteins.
Click on the Subtree or Direct links number to directly access the NCBI data

Click on External links to expand it. These links are taxon related links to other third party resources, as provided by the NCBI API.

When no data are returned from BHL this section will not be visible.

Filtering taxonomic terms¶

You can use filters to temporarily ‘clean’ a classification from unwanted terms. Some biological classifications include a lot of synonyms, often multiple times the volume of accepted names.

You may want to allow for users to temporarily browse only through the accepted terms of a taxonomy. You can also allow the exclusion of terms based on the rank they belong or the unacceptability reason.

While on the desired classification browsing page, click on the cog on the left top corner of the taxonomic tree (left side bar)
Select Configure block
Adjust the settings under the Toggle visibility of terms section as follows:
Select the Field to match against. E.g. select usage if you want to add a filter to exclude all not accepted terms

Select the Values to hide. E.g. select not accepted if you want to add a filter to exclude all not accepted terms
Click Save block

Enable or disable the filter¶

Go to the page with the classification
On the top of the block you will see a tick-box stating Hide xxxxxx terms
Select to enable or deselect to disable this filter

Showing Hide Genus terms filter

Locations and specimens¶

Specimen data in a Scratchpad conform to the Darwin Core (version 1.2.1) format recommended by TDWG (the Taxonomic Databases working group) and GBIF.

They are separated into two content types: location and specimen, which allows you to connect different specimens at the same location.

Adding a location¶

From the Admin menu go to Content

Click Add next to Location
Enter a LOCATION IDENTIFIER. The location identifier needs to be unique because it is used for referencing this location while adding specimens.

Either click on the Point tab for the map to add a point to the map with a left mouse click (delete is with right click) or enter the latitude and longitude in decimal degrees (coordinate system WGS84) in the field below the map.
Click on the Extra Fields tab for additional optional fields.

Select a COUNTRY from the drop down menu
Use the LOCALITY field to enter information that is not covered in any of the other fields
Click Save

Location node

Adding a specimen¶

From the Admin menu go to Content
Click the Add link next to Specimen/Observation.
There are five different vertical tabs:
- Required
- Taxonomy
- Collection
- Miscellaneous
- Location
Each of these tabs has different fields that can optionally be completed in order to create a new specimen record.
Fill out the fields under the Required tab. The two code fields together with the catalogue number generate a unique ID for this specimen record that is used as the specimen title
The Taxonomy tab contains the basic information about the identification of your specimen. The important field here is the second one, TAXONOMIC NAME, which is linked directly to all your site’s vocabularies
Fill in the information under the Collection and Miscellaneous tabs
Under the Location tab, select the location you created earlier.

If you haven’t created a Location previously you may add one here by clicking on Create a new Location and use it here option. This new Location will be available to use for other specimens/observations in the future.
In addition to the fields above, you can also add a media file to your specimen record
Click Save

You will be redirected to view your specimen, including thumbnails of any media you attached and a map of the location.

If you tagged the specimen with a taxonomy term, you can now find the specimen records under the Specimens tab of the classification view.

Cloning specimen¶

Click on the Clone tab to create a similar specimen from the same location by just changing the data in the CATALOGUE NUMBER field.

In practice most people will (at least initially) want to enter locality and specimen records in bulk - see Import specimens.

Media gallery¶

Media Galleries are used to organise Images or other media types in groups. You may use media galleries to organise your media thematically according to the your needs.

From the Admin menu go to Content > Media gallery
Click + media gallery
Enter a TITLE and a short description of the gallery in the BODY field
In the Media box click on Select media and either upload a new image or, if you already uploaded images, click on the Library tab and select the image(s) you want to link to this media gallery
Click Submit
To change the creative commons license (the default licence is the one you chose during the set up workflow) or annotate your image in other ways (taxonomic name, imaging technique, keywords, etc.) click on Edit media next to the respective image.

If you upload several images, it is faster to use the Grid editor to edit several images at once (see Edit content)

To add another image click the Add another item button and select another media file.
Click Save
After saving you will see your media gallery and images.

Troubleshooting¶

If the images are missing, refresh the page in your browser (Control+F5 on a PC) after a couple minutes.

Images & media¶

From the Admin menu go to Content
Click on the Add link next to Images in the Files section at the bottom
Click on Add files to select one or more files to be uploaded. You may also drag and drop files in the filename box from your file explorer (e.g. windows explorer).
After selecting your file(s) click Start upload and wait for the files to upload.
Click on Submit

Editing metadata¶

If you want to set image metadata (e.g. title, media gallery or taxonomic name), you will need to edit the image.

From the Admin menu go to Content
Select Image
Find the uploaded image, and click Edit
Change the TITLE if necessary and fill in the other fields as needed.
To link the image to the classification and have it show on taxon pages enter a name in the TAXONOMIC NAME field. After typing a few letters you will get a list of names starting with these letters. Choose one of these.

Click on the Misc vertical tab. Fill the Media Gallery you wish your image(s) to belong to
Click Save

If you upload several images, it is faster to use the Grid editor to edit several images at once (see Edit content)

Taxon descriptions¶

The Taxon description content type is based on TDWG’s SPM (Species Profile Model) standard.

Adding a taxon description with distribution map¶

Click Content in the Admin menu
Click Add next to Taxon description

Add the taxon name into the Taxonomic Name field (this will autocomplete once you start typing)
Fill the fields as needed. Use the Morphology field for the actual morphological description of the taxon and Diagnostic Description for the diagnosis
To add a distribution map click on the Ecology and Distribution tab
Click on the + Polygon tab to enter a custom shaped distribution. You can move the map by dragging and dropping. Click the map to add polygon points. Right click to stop adding points. To edit an existing point click on it and drag it to a new position or right click to delete.
Click on the + Region tab to select TDWG regions. Select the level of the region either by zooming in or out of the map or by clicking on the Selecting by … (Level …) field. Then click on the map to select the respective region of this level.
Click Save

Literature¶

Add a single reference¶

Click Content in the Admin menu and then on the Add link for Biblio.
Select the publication type Journal Article (or any type you prefer), and fill out the fields given. Remember to link this bibliographic reference to your classification by filling in the TAXONOMIC NAME field.
You can also add a bibliographic record by pasting the BibTeX or RIS record or looking it up.

Adding file attachments to a reference¶

It is possible add a file to a bibliographic record
Underneath the field bibliography fields there is a File attachments section
Click the Choose File button and select your file (default allowed files are txt, pdf, doc) then click Upload
Once the file has been uploaded click Save
You should now see the file at the bottom of the page when viewing the reference

Edit a reference¶

Click on the title of any biblio entry to go to the node page for that entry. Click on the Edit tab.
You can now edit this individual entry, changing any of the fields that you consider to need changing.
Tag this biblio node to the classification by adding the respective term in the TAXONOMIC NAME field.

Only references that are linked to the classification will show up on your taxon pages.
Press the Save button.

Blog¶

Blogs are used to create and manage a series of regular content entries, like general status updates, a travel diary or a running commentary. Readers can optionally comment on blog entries. They are a good way of communicating with the users of a Scratchpad.

Instructions¶

To enable the blog go to Structure in the Admin menu and click on Tools.

In the Blog section enable blog and save.
Click Content in the Admin menu and then on the Add link for Blog entry.
Enter the title and some body text
Click Save
You can find your newly created blog entry in the Blogs tab in the Main menu.

The Blogs tab shows the blog entries from all users. You can filter by user using the facets in the left hand column. You can also filter blog posts by clicking on the link to this users blog available at the bottom of a blog entry. Alternatively go the the user’s account and use the link there.

Forums¶

Forums are basic communication tools between Scratchpads community members. They facilitate public discussions on selected topics. To create forums you first have to enable this functionality from the Scratchpads administration menu.

Enabling the Forums module¶

From the Admin menu bar go to Structure > Tools
Find the Forum section and enable Forums
Click Save

Creating a forum¶

Click on Structure in the Admin menu and click on Forums
To add a new forum click on Add Forum, enter the name of the forum a description and a parent term if you want a hierarchy of forums.

Click Save

You can access the forum by clicking on the Forums link in the Admin menu.

Forum containers¶

You can add containers to group related forums together.

Click on Structure in the Admin menu and click on Forums
Click on + Add container

When creating/editing forums you can select the container as the forum parent, creating a hierarchy of forums.

Adding a forum topic¶

Every forum can have multiple topics, or discussions. To create a new forum topic:

Click Content in the Admin menu and then on the Add link for Forum topic.
Enter the SUBJECT and choose the forum in which you want to submit your topic. By default Scratchpads have only one forum that is called “General discussion”. Enter the text of the topic in the BODY field
Click Save
To reply to a forum topic, click to enter the forum topic discussion.

And reply using the comment form.

Publishing¶

Items of content on Scratchpads can be either Published or Unpublished. Unpublished content is not viewable by members of the public and is a good method of creating drafts before publishing them.

Publishing options¶

Every content type has a publishing checkbox as part of the Edit/Create form.

Default publishing option¶

You can set whether content is published/unpublished by default on the edit content form.

Under Admin menu go to Structure > Content types
Next to the content type, click the Edit link
In the Publishing options tab, change the Default options

Unpublished content¶

Unpublished content will only be available to the author of the content; it will not be public on the site.

When viewing unpublished content the background will be coloured pink:

Finding content¶

There are several ways to find specific content on a Scratchpad: Search, Faceted search, Main menu and Admin menu.

Search¶

The Search box in the header has different search options: All and Taxonomy.

All finds all content that includes the search term.

Taxonomy only searches for terms in one of the vocabularies and returns the matched terms.

The search functionality is aware of the content type you’re viewing: When you are viewing a page (“Page” content type) you will get an additional option to search only page content.

Clicking on the Search button when the search field is empty will lead to a faceted search page.

Faceted Search¶

Some pages provide the option of faceted search in a separate block on the left of the page. Faceted search can be used to filter the nodes of a content type (e.g. References) To use the faceted search:

Fields with less than 20 terms show up as a list. Click on a term to restrict results for this term

Fields with more than 20 terms also provide an auto-complete search box. Fill in the term and press enter or else select from the list

You can remove a filter by clicking on the (-) sign next to a selected term
You can filter the content based on multiple fields

Recent content¶

You can also view all recent content - see Recent content.

Recent content¶

Tracking all the new content of your site can be very useful, especially if you are participating in a large Scratchpads community.

The ‘tracker’ module allows users to keep track of the latest changes they made in the site.

Enabling the module¶

From the Admin menu go to Structure > Tools
Find the section called Core
Enable the Tracker module
Click Save

Track new content¶

Once the module is enabled a new “Track” tab will appear on every user profile page. Click the tab to view a list of all content created by that user.

Dashboard¶

Your Dashboard also provides a view of all recent content added to a Scratchpad.

Click on Dashboard in the Admin menu.

This dashboard can be customised to display other useful information - see Customise dashboard.

Custom content¶

So far we have only worked with predefined content types, but Scratchpads also let you defined custom content types. This allows you to create content in which the data are entered and saved in specific fields.

Adding content type¶

From the Admin menu go to Structure > Content types
Click + Add content type link at the top
Enter a NAME (“Literature mining”) and DESCRIPTION
Under the Submission form settings tab change the TITLE FIELD LABEL to Taxonomic name as cited
Under the Display settings tab choose the View display and select Display on species pages
Choose on which tab of the species pages the new content type should be visible
Select Own tab so that the new content type appears on a tab of its own
Click the Save and add fields button. This will lead to the Manage fields tab

Managing fields¶

By default every new content type has a title and a body field. In this example the body field is not needed, so click on delete for this field.

Term reference fields¶

First we want to add a field that links to the biological classification, so that we can tag our new literature mining content to one or more taxonomic names.

Like with other content types, the Taxonomic name field should be an autocomplete field. A field like this is already present in several content types, so we don’t need to create a new one, we can use the existing one. Because it links to taxonomy terms a field like this is called a Term reference.

Go to Add existing field. As Label enter “Taxonomic name”
In the Field to share drop down menu select Term reference: field_taxonomic_name (Taxonomic name) and in the Form element to edit the data drop down menu select Autocomplete term widget (tagging)
Click Save

NOTE: These existing fields are locked, so you will not be able to edit their settings (make them required, for example).

Node reference fields¶

Next we want to add a field that links to the biblio content type (References), so that we can select a biblio node. This field should be a dropdown menu. Again, a field like this is already present in other content types, so we can use the existing one. Because it links to a node in a different content type a field like this is called a Node reference

Go to Add existing field. As Label enter “Reference”, in the Field to share drop down menu select Node reference: field_reference (Reference) and in the Form element to edit the data drop down menu select Select list
Click Save

Text fields¶

Next we want to add a field for the page number on which the taxon is cited in the reference. A page field doesn’t exist, yet, so we need to create a new field. Since pages are numbers, we could use Integer as data type. However, in some cases we might want to add a range of pages and this would not be possible with “Integer”, so instead it is better to use the “Text” data type, which is for text that is up to 255 characters long.

Go to Add new field. As Label enter “Page”, in the Type of data to store drop down menu select Text and in the Form element to edit the data drop down menu select Text field
Click Save
Under Field settings enter “20” as MAXIMUM LENGTH. This should give plenty of space for adding the page number.

List fields¶

There are various options for adding keywords to our new content type. We can just link to the existing keywords on the site that are for example used for images. To do this we would add the existing “Term reference: Field_keywords (Keywords) field. We could also create a new non-biological vocabulary for our literature mining keywords and create a new term reference field linking to this vocabulary. With the right settings, new keywords can be added to this vocabulary by adding them to the literature mining node. Another option would be to create a list of literature mining categories to choose from and then enter additional information or keywords into a text field. We will do the latter now:

Go to Add new field. As Label enter “Literature mining category”, in the Type of data to store drop down menu select List (text) and in the Form element to edit the data drop down menu select Select list
Click Save
In the ALLOWED VALUES LIST enter a few categories, e.g. distribution, original name, type information, one line each
Click Save and Save on the next page also

Long text fields¶

For adding extracts of the cited paper, we need a text field that can hold more information then just 255 characters. So we will use a ‘Long text’ field.

Go to ‘Add new field’. As ‘Label’ enter “Text”, in the ‘Type of data to store’ drop down menu select “Long text” and in the ‘Form element to edit the data’ drop down menu select “Text area”. Save and save again.
As HELP TEXT enter “Enter keywords or text extracts from the mined paper” and under TEXT PROCESSING select “Filtered text”, so that it is possible to use italics and other formatting. Save settings.

Groups¶

To facilitate the entering and viewing of fields, they can be sorted into groups. Groups can be shown as boxes around the fields (Fieldset) or for example as horizontal tabs in the view and edit mode. For the few fields we have in this content type groups are not really necessary, but we will add two anyway to demonstrate horizontal tabs. Each horizontal tab (horizontal tab) is a group and all tabs together also form a group (horizontal tabs group). First we need to create a horizontal tab group to which we then each Horizontal tab.

Go to Add new group. As Label enter “Horizontal tabs” and as Group name enter “horizontal_tabs”
In the drop down menu select Horizontal tabs group
Click Save
Go to Add new group. As Label enter “Reference data” and as Group name enter “reference_data”
In the drop down menu select Horizontal tab
Click Save
Drop and drag the Reference and the Page fields into the Reference data group
Click Save
Create another horizontal tab called “Text mining” and move the Literature mining category and Text fields into it
Click Save
Drag the Reference data and the Text mining groups into the Horizontal tabs group
Click Save

Create a new node¶

Check out how your new content type looks by adding a literature mining node.

From the Admin menu go to Content > Literature mining > Add

If you do this in a separate browser tab you can play around with changing the settings and seeing how this affects the view.

Managing display¶

The way the node is displayed can be changed under the Manage display tab. Two things can be changed: The position and presence of the label and the format of the field. The field format largely depends on the field type

Change all the labels to “Inline” to save space and have a look at the format options for different field types but don’t change any
Click Save

At the point where a new content type has been saved a menu item is added to the Main menu. By default this page just lists the titles of literature mining nodes with a link to the respective node. To improve this page and change it into, for example, a matrix, you need to edit the view. See Adding and editing views for more info

Phylogenetic tree¶

Scratchpads provide a custom field formatter for displaying NeXML as phylogenetic trees. NeXML is an exchange standard for representing phyloinformatic data.

This field formatter can be added to existing or custom content types - in this example we’ll use a custom *Tree content type.*

Creating a new ‘Tree’ Content Type¶

From the Admin menu go to Structure
Click Content Types then Add content type
Enter a TITLE, e.g. “Tree” and click Save and add fields
In the section Add new field provide a label, e.g. “Tree”
Select the Field type “Long Text” then click Save
Under Manage display you should set the Format to Newick/NeXML tree
Under Display type choose from either Rectangular or Circular
Click the Save button at the bottom left

Changing Phylogenetic Tree Display Options¶

From the Admin menu go to Structure
Click Content Types then manage display for your tree content type
Set the Display type to either Rectangular or Circular

Creating a new Phylogenetic Tree¶

From the Admin menu go to Content > Tree > Add

In the Tree field, enter some valid neXML data. For more information and some example NeXML files, see NeXML Github.

Edit content¶

Content can either be edited by going to the respective node and clicking on the Edit node tab or by using the Grid editor to update several nodes at once.

Edit node¶

When viewing any editable Node, an Edit tab will be available.
Click the Edit tab to open the edit overlay form.

Bulk operations¶

Within Admin menu, select Content
Next to the content type, click View link.
This page lists all the content of that particular type. At the top of the page you can apply filters to search for particular items of content.
Under Operations you can select an action to run against these nodes, including:
- Change the author of content
- Delete item
- Make content sticky
- Make content unsticky
- Modify entity values
- Remove content from front page
- Unpublish content
Next to each content row, is a checkbox. Select the rows you wish to run the bulk operation against.
Select Execute

Grid editor¶

Click Content in the Admin menu
Click Grid next to the content type you wish to edit
You will see a matrix with a row for each node and columns for selected fields of this content type. The rows are ordered chronologically, with the most recent nodes at the top
If the fields of the respective content type are sorted into groups on different tabs, these tabs will show in the grid editor, too. To gain more space for viewing a certain column the column sizes can be adapted by moving the column separators or by hiding columns by right clicking on the column header and deselecting columns.
To edit contents of a single cell click into the cell, edit and click Save
To edit the same field in several nodes, select the respective nodes by checking the box to the left of the row. Then click into the cell you want to edit for one of the nodes, edit and click Save. The content of this field will change for all selected nodes
To filter for certain content click on the little magnifying glass in the upper right corner of the matrix and enter the search word in the search box that appears for each column. You can sort the rows by clicking on the column header of the field you want to sort by.
At the bottom of the matrix there are icons for cloning (creating a duplicate entry), deleting and undoing.

Revisions¶

Scratchpads can keep track of the changes made to a node of a content type. These changes are stored as different versions of the node called revisions. Revisions can be very useful when data are updated by different authors.

Enabling Revisions for content types¶

From the Admin bar go to Structure > Content types
Click Edit next to the content type you wish to enable or disable revisions for
Click on Publishing options and select Create new revision
Click Save Content type

If Create new revision is specified for a content type, every edit will, by default, create a new version of the page.

This can be overridden in the Revision information on a node - along with setting a more informative revision log message.

Node form Revision information

Comparing Revisions¶

Once you have created a new revision of a node in the content type you can compare their differences:

Locate and view the node you wish to see the revisions for.
Click on Revisions tab
Select the revisions you wish to compare and click Compare

Note: If a field accepts HTML input, it might be easiest to view changed without HTML tags - to remove the HTML tags click on Marked down

Ordering content¶

There are two methods to control the order of nodes. Weight allows you to specify a weight for each node, so those with a lesser (lighter) weight float to the top of lists. The Sticky at top of lists setting is a simpler setting, where nodes can be ‘promoted’ to the top of a list*

Weight¶

Weight settings allow you to finely control the order of content. For example, if you have many taxon descriptions, you may want to control the order that they appear on the Descriptions tab on a taxon page.

Enable Weight¶

From the Admin menu go to Structure > Content types
Click edit next to the content type that you want to enable weight settings for (e.g. Taxon Description)
Click ‘Weight Settings’’ from the bottom left menu
Select YES under ENABLE to activate weight settings for that content type
Click Save content type

Set weight¶

Either Add or Edit an item of content for the node type on which you have enabled setting weight.

A new weight option is available in the node additional options.

Node edit form showing weight selection form

Sticky at top of lists¶

The Sticky at top of lists setting is a simpler setting to control node order. A node with Sticky at top of lists selected will appear at the top of all lists in which it appears.

For example, if you had multiple taxon descriptions for a single taxon and enabled Sticky at top of lists for one of these, it would be this one that appears on the taxon Overview page and would be first on the ‘Descriptions’’ page.

Set stickiness¶

Stickiness is enabled by default on all node types, and is available under publishing options on the Node edit form.

Node edit form with “Sticky at top of lists” checkbox

Import content¶

To import data into your Scratchpad they need to be in the correct format matching the fields, and in some cases the values within these fields.

To help prepare your data in the correct format you can export a template Excel file that includes all the fields and any pre-defined field values for the respective content type. Populate this file with your data and import into the Scratchpad.

Creating the template file¶

From the Admin menu go to Content
Click on Import next to the content type you want to create the template file for, e.g. Taxon description
Click on the Download link and open the file in Excel. You will see the different Scratchpad fields as column headers. Required fields are shown in Red

Fill the template file with your data and save

Create the pre-populated template file¶

From the Admin menu go to Content
Click Import next to the content type into which you want to import data, e.g. Taxon description.

From the Maximum number of rows drop down menu select the option that best matches your file. (e.g. for a excel file with 3500 rows, choose 5000)
Browse for the file and click on the Import button
View your imported data by clicking on the respective tab for the content type in the Main menu or by clicking on Content in the Admin menu and then on View next to the respective content type

Other Important Information¶

Always download an up-to-date template file - the Excel spreadsheets can be used for most content and are dynamically generated. This means that if you add fields you will need to use a new template.
Be patient with importing data - the Excel file needs to be uploaded, parsed, then saved in your Scratchpad. Upload speeds are usually much slower than download speeds, so depending on your internet connection this may take some time (especially for large files >1MB). Importing medium-sized (3000-6000 term) taxonomies with rich data can take 5-15 minutes.
Keep the browser window open when running an import - if you close the browser window the import will stop.
If a taxonomy imports in the wrong order, try running the import again - if you have defined parent child relationships and a child is imported before its parent, it will be placed at the root of a taxonomy. Running an import again will update the taxonomy and the hierarchical relationship should now be correct.
Use GUIDs if you have any - A GUID is a global unique identifier for a record/node. GUIDs can be used to compare/synchronize different databases. Adding a GUID is not required, you only need it if your records/nodes were generated from an established database and you want to be able to update your data from this database at a later stage. Note that the GUID really has to be globally unique, at least across the whole Scratchpad. So it is not enough just add a number. Better is a combination like “Species2000-1”.

Import specimens¶

Instructions¶

Excel file imports can be used either for creating new nodes or for updating existing. Please see the Import content page for more general info.

To download the template file (for new data or for updating your data)

Go to Import > Nodes > Excel file import
Choose specimen/observation from the second drop-down menu
Choose the template file you wish to work on (choose the first for creating new data or the second for changing or amending existing scratchpad data)
Open the downloaded excel file in your computer and edit it

Complete the columns as follows:

GUID:

Use Global Unique Identifiers for each one of your localities. These identifiers will not show up to users. Use complex combinations like DK-2012-05-20-1001

’Basis of Record:

This designates the type of record you enter. Please choose from: Fossil Specimen, Human Observation, Living Specimen,Machine Observation, Moving Image,Other Specimen, Preserved Specimen, Sound Recording, Still Image. Use Preserved specimen for herbarium or zoological museum specimens. This is a required field.

Catalogue number:

Provide the institution number of the specimen (accession number). This is a required field.

Collection code:

Provide the institution’s code for the collection in which the specimen is kept. This field is not to be misinterpreted as the institution code which is entered in a different field. This is a required field.

Collector (UID):

The Unique identification number of the collector as stored in your Scratchpad. Please note that collectors should first have been registered as persons in your Scratchpad. Leave empty if you do not know this number

Collector (Name on Site):

The name of the collector as it is registered in your Scratchpad. If you filled in the Collector (UID) you do not have to enter anything here.

Collector number:

The collector’s number for this specific entry.

Count:

The number of individuals present in the lot or container. Not to be used for observations

Date collected (Start):

The verbatim original representation of the starting date (and time) information for the collecting event. Enter dates as follows: for 25 January 1979 enter 1979-01-25

Date collected (End):

The verbatim original representation of the end date (and time) information for the collecting event. Enter dates as follows: for 25 January 1979 enter 1979-01-25

Date identified (End):

Date the specimen was taxonomically identified. Enter dates as follows: for 25 January 1979 enter 1979-01-25

GenBank number:

GenBank Accession number(s) associated with the specimen referred to by the catalogued object.

Identification qualifier:

A brief phrase or a standard term (“cf.”, “aff.”) to qualify the identification of the organism when doubts have arisen as to its taxonomic identity (determination). Example: 1) For the determination “Quercus aff. agrifolia var. oxyadenia”, the entry in this field would be “aff. agrifolia var. oxyadenia”

Identified by (UID):

The Unique identification number of the identifier (det.) as stored in your Scratchpad. Please note that identifiers should first have been registered as persons in your Scratchpad. Leave empty if you do not know this number.

Identified by (Name on Site):

The name of the identifier (det.) as it is registered in your Scratchpad. If you filled in the Collector (UID) you do not have to enter anything here.

Institution code:

The institution code that holds the specimen referred to by the catalogued object. This is a required field.

Lifestage:

The age class or life stage of the specimen

Location (NID):

The identification number of the location the specimen was collected from or the observation made in. You can find this number by browsing through your location list in your Scratchpad. Please note that entering the locations used in this field is a pre-requirement. You can see the permitted values for this field on the permittedValues tab of the downloaded excel file.

Location (title):

The title of the location the specimen was collected from or the observation made in. If you entered data in the Location (NID) field you should not enter anything here. You can see the permitted values for this field on the permittedValues tab of the downloaded excel file.

Field Notes:

Field notes associated with the specimen or observation

Field number:

An identifier given to the event in the field. Often serves as a link between field notes and the Event.

Other catalogue numbers:

A list (concatenated and separated) of previous or alternate fully qualified catalogue numbers or other human-used identifiers for the same Occurrence, whether in the current or any other data set or collection.

Remarks:

Comments or notes about the Event.

Sex:

The sex of the specimen. Permitted values:Female, Hermaphrodite, Indeterminate, Male, Multiple, Transitional, Undetermined, Unknown

Taxonomic names:

The taxonomic name the specimen or observation was identified as. Use a term from your existing biological vocabularies. Check permitted values on the same column of the PermittedValues tab in the downloaded excel file.

Type status:

Indicates the kind of nomenclatural type that a specimen represents. Permitted values: Holotype, Isotype, Lectotype, Neotype, Nontype, Not Provided, Paralectotype, Paratype, Syntype

Import literature¶

You can import a variety of reference data into your Scratchpad, including:

BibTex
Endnote XML
MARC
Pubmed ID List
Pubmed XML
RIS

Click Import in the Admin menu and select “Nodes: Biblio file import”.
Browse for the file and select the FILE TYPE.
Import.
Once the import has completed, a status message will show how many literature records have been created.
To view the literature references, in the Admin menu go to Content > Biblio > View

Troubleshooting¶

If the new records are missing when you click on Literature in the Main menu please give the system a few minuted to catch up. It needs to index all the new new references which can take a little time.

Import taxon descriptions¶

Excel file imports can be used either for creating new nodes or for updating existing. Please see the Import content page for more general info.

To download the template file (for new data or for updating your data)

Go to Import > Nodes > Excel file import
Choose taxon description from the second drop-down menu
Choose the template file you wish to work on (choose the first for creating new data or the second for changing or amending existing scratchpad data)
Open the downloaded excel file in your computer and edit it

Complete the columns as follows:

GUID:

Use Global Unique Identifiers for each one of your taxon descriptions. These identifiers will not be visible to users. Use complex combinations like TH-SIB-2012-001

Taxonomic name (Name):

Use the taxonomic name from your taxonomies the description refers to. The permitted values of this filed are located in column B of the PermittedValues tab of your downloaded Excel file. This is a required field.

Taxonomic name (TID):

Instead of typing the taxonomic name the corresponding Term ID (TID) can be used to identify a term in one of the taxonomies. TIDs are visible under the taxon name in the edit view of taxonomies.

Taxonomic name (GUID):

Instead of typing the taxonomic name the corresponding GUID can be used to identify a term in one of the taxonomies. Taxonomic names’ GUIDs are visible under the taxon name in the edit view of taxonomies.

Map:

You can set the geographic distribution of a taxon using specific values in this field.

To set distribution as predefined map polygon:
1. Use the LAT/LONG set of coordinates of each of the points that constitute your polygon in WGS84. Separate LAT and LONG with a space and each set with a comma.
2. Put your coordinates between the following strings POLYGON:POLYGON(( set of coordinates ))

For example to set a polygon distribution defined by the following points 27.42 44.65,17.66 39.36,20.30 36.80,24.25 34.45,27.33 36.31,29.79 37.85,27.42 44.65 you should put in the cell the following string POLYGON:POLYGON((27.42 44.65,17.66 39.36,20.30 36.80,24.25 34.45,27.33 36.31,29.79 37.85,27.42 44.65))

To set distribution as geographical or administrative units:
1. Use the REGION: prefix followed by the number of geographical unit according to TDWG controlled vocabulary on geographic regions
2. To select a Level 1 region use the REGION: prefix followed by the number of continent (e.g. REGION:2)
3. To select a Level 2 region use the REGION: prefix followed by the number of continent and number of sub-continent (e.g. REGION:1:13)
4. To select a Level 3 region use the REGION: prefix followed by the three letter alphabetical code of the country or state (e.g. for Spain REGION:SPA)
5. To select a Level 4 region use the REGION: prefix followed by the hyphenated
6. To set multiple regions of distribution for a taxon you must separate each REGION:… with a line break in the cell. To enter line breaks use Alt+Enter.

Associations:

Descriptions and lists of taxa that interact with the subject taxon. Includes explicit reference to the kind of ecological interaction: Predator/prey; host/parasite, pollinators, symbiosis, mutualism, commensalism; hybridisation etc.

Behaviour:

Description of behaviour and behaviour patterns of an organism, including actions and reactions of organism in relation to its biotic and abiotic environment. Includes communication, perception, modes and mechanisms of locomotion, as well as long term strategies (except mating and reproductive strategies, covered under reproduction).

Biology:

. An account of the biology of the taxon. E.g. behavior, reproduction, dispersal

Conservation status:

A description of the likelihood of the species becoming extinct in the present day or in the near future. Population size is treated under Population Biology, and trends in population sizes are treated under Trends. However, this is the preferred element if an object includes all of these things and details about conservation listings.

Cyclicity:

Description of biorhythms, whether on the scale of seconds, hours, days, or seasons. Those states or conditions characterised by regular repetition in time. Could also cover phenomena such as chewing rates. Life cycles are treated in the Life Cycle term. Seasonal migration and reproduction are usually treated separately.

Cytology:

Cell biology: formation, structure, organelles, and function of cells.

Diagnostic description:

Lists the characters that distinguish this taxon from its closest relatives.

Diseases:

Description of diseases that the organism is subject to. Disease-causing organisms can also be listed under associations.

Dispersal:

Description of the methods, circumstances, and timing of dispersal.

Distribution:

Covers ranges, e.g., a global range, or a narrower one; may be biogeographical, political or other (e.g., managed areas like conservencies); endemism; native or exotic; ref Darwin Core Geospatial extension. Does not include altitudinal distribution.

Ecology:

An overview of ecological aspects of the taxon.

Evolution:

Description of the evolution of the taxon.

General description:

A comprehensive description of the characteristics of the taxon. To be used primarily when many of the subject categories are treated together in one object, but at length. Taxon biology is to be used if a brief summary.

Genetics:

Information on the genetics of the taxon, including karyotypes, barcoding status, whole genome sequencing status, ploidy.

Growth:

Description of growth rates, allometries, parameters known to be predictive, morphometrics. Can also include hypotheses of paedomorphy or neoteny, etc.

Habitat:

Includes realm (e.g Terrestrial etc) and climatic information (e.g Boreal); also includes requirements and tolerances; horizontal and vertical (altitudinal) distribution.

Legislation:

Legal regulations or statutes relating to the taxon.

Life cycle:

Defines and describes obligatory developmental transformations. Includes metamorphosis, instars, gametophyte/embryophytes, transitions from sessile to mobile forms. Discusses timing. Morphology usually described in morphological descriptions.

Life expectancy:

Any information on longevity, including The average period an organism can be expected to survive.

Look alikes:

Other taxa that this taxon may be confused with. Useful for identification and comparison. Common in invasive species communities.

Management:

Describes techniques and goals used in management of species. May include management relative to a piece of legislation, e.g., a CITES list.

Migration:

Description of the periodic movement of organisms from one locality to another (e.g., for breeding). Usually includes locality, timing, and hypothesised purpose.

Molecular biology:

Includes proteomic and biochemistry (e.g Toxicity). Genomic information is usually treated under genetics.

Morphology:

Description of the appearance of the taxon; e.g body plan, shape and colour of external features, typical postures. May be referred to as or include habit, or anatomy.

Phylogeny:

Description of phylogenetic and systematic treatments of the taxon.

Physiology:

Description of physiological processes. Includes metabolic rates, and systems such as circulation, respiration, excretion, immunity, neurophysiology.

Population biology:

Includes abundance information (population size, density) and demographics (e.g. age stratification).

Procedures:

Deals with how you go about managing this taxon; what are the known threats to this taxon?

Reproduction:

Description of reproductive physiology and behavior, including mating and life history variables. Includes cues, strategies, restraints, rates.

Risk statement:

Negative impacts on humans, communities.

Size:

Average size, max, range; type of size (perimeter, length, volume, weight …).

Taxon biology:

Summary or overview of all aspects of an organism’s biology.

Threats:

The threats to which this taxon is subject.

Trends:

An indication of whether a population is stable, or increasing or decreasing.

Trophic strategy:

Summaries general nature of feeding interactions. For example, basic mode of nutrient uptake (autotrophy, heterotrophy, coprophagy, saprophagy), position in food network (top predator, primary producer, consumer), diet categorization (detritovore, omnivore, carnivore, herbivore). Specific lists of taxa are treated under associations (specifying predators or prey).

Uses:

Benefits for humans (e.g. in the field of Economic Botany). Can include ecosystem services. However, benefits to ecosystems not specific to humans are best treated under Risk statement.

Import locations¶

Excel file imports can be used either for creating new nodes or for updating existing ones. Please see the Import content page for more general info.

To download the template file (for new data or for updating your data)

Go to Import > Nodes > Excel file import
Choose locations from the second drop-down menu
Choose the template file you wish to work on (choose the first for creating new data or the second for changing or amending existing scratchpad data)
Open the downloaded excel file in your computer and edit it

Complete the columns as follows:

GUID:

Use Global Unique Identifiers for each one of your localities. These identifiers will not show up to users. Use complex combinations like EU-GB-S-DK-000-001

Title:

The title is the location identifier and will be used to refer to each specific location in your scratchpad. Make it human readable.

Continent/Ocean:

Select the continent or Ocean of your locality. Choose one from the following: Africa, Antarctic, Asia-Temperate, Asia-Tropical, Atlantic Ocean, Australasia, Europe, Indian Ocean, North-Central Pacific, Northern America, Northwestern Pacific, Pacific, South-Central Pacific, Southern America, Southwestern Pacific

Verbatim Coordinate System:

Provide the name of the system the coordinates of the locality were recorded. Choose one from the following: decimal degrees, degrees decimal minutes, degrees minutes seconds, UTM, CRTM.

Coordinate uncertainty in meters:

The upper limit of the distance (in meters) from the given latitude and longitude describing a circle within which the whole of the described locality lies. Leave the value empty if the uncertainty is unknown, cannot be estimated, or is not applicable (because there are no coordinates). The value should be greater than zero.

Country (ISO alpha-2):

Choose the administrative region (Country) the locality is in. Please fill in the the official ISO 3166-1-alpha-2 country code. An exhaustive list can be found here.

County:

Provide the the name of a second-level administrative subdivision of a country.

Geodetic datum:

Provide the geodetic datum of the locality coordinates. e.g. WGS84, NAD83, NAD27 etc.

Georeference protocol:

Give a citation (publication or URL) to the resource describing the methods used to determine the georeference (coordinates AND uncertainty, or footprint)

Georeference remarks:

Comments about the spatial description determination, explaining assumptions made in addition or opposition to the those formalized in the method referred to in Georeference Protocol.

Import users¶

Instructions¶

Excel file imports can be used either for creating new Users or for updating existing ones. Please see the Import content page for more general info.

To download the template file (for new data or for updating your data)

Go to Import > Users > Excel file import
Choose the template file you wish to work on (choose the first for creating new data or the second for changing or amending existing Scratchpad data)
Open the downloaded excel file in your computer and edit it

Complete the columns as follows:

Title: The title of the individual, either Mr, Mrs, Ms, Miss, Dr, Prof., or leave blank for no title.
Other/given name(s):
Family name:
Country (ISO alpha-2):
Homepage (URL):
Institution:
Area of Taxonomic Interest:
Mail:
Username:
Password:

Exporting data¶

Scratchpads support multiple ways of exporting your data. You can export data in specific content types as an .xls file or generate a standard compliant Darwin Core Archive file that includes all of your Scratchpads data.

Exporting as .xls¶

From the Admin menu go to Import
From the Select Import drop-down menu select accordingly
- Select Excel file Import under Files to export metadata of uploaded media files
- Select Excel file Import under Nodes to export data present of a specific content type
- Select Excel file Import under Taxonomy to export one of the existing classifications in your Scratchpad
From the second drop-down menu select the media type or content type you wish to export as .xls file
Click on Excel template file to populate and download the file

The .xls file will include all your data in rows under columns that represent the fields in the corresponding media type, content type or taxonomy

Exporting as DwC-A¶

Darwin Core archive files can be used to automatically feed your data to other web-services (e.g. EOL, GBIF).

Enabling the DwC-A module¶

From the Admin menu got to Structure > Tools
Browse through the page and locate Export
For both DarwinCore Archive (DwC-A) export and DarwinCore Archive (DwC-A) click the switch to the On position
Click Save.

Configuring & building DwC-A¶

From the Admin menu select Configuration > DwC-Archiver

Here you can Rebuild and Download the DwC-A.

Two default DwC Archive files are provided by Scratchpads, with content formatted for EOL and GBIF.

You can Override these implementations to create a custom archive, or Add DwCArchive to define your own.

Downloading the file¶

Note: before downloading the file, you must first go to :term:`Admin menu` > Configuration > DwC-Archiver and select Rebuild to crate the archive file.

Open a new browser tab and enter the address of your scratchpad site adding gbif-dwca.zip

For example, phthiraptera.myspecies.info/gbif-dwca.zip
You will be prompted to download a .zip file. Accept and save to your computer.

Please note that DwC-A files are not human readable, they are built to allow the sharing and re-use of biodiversity related information between machines over the web. You can use this archive file to contribute your scratchpad data to other Biodiversity information services like EOL or GBIF.

Exporting references¶

Scratchpads can export references in several formats (incl. BibTex RTF XML RIS)

From the Main menu, go to the literature page of your Scratchpad
Select the references you want to export through the available facets. If no filtering is used all references will be exported
Click on the export format file you want to populate and download next to Export selection as
You will be prompted to download a file, save the file in your local or network disk

Create backup¶

You can create a backup of all the content on your Scratchpad.

Creating the backup¶

From the Admin menu go to Configuration > Backup Scratchpad
Select Generate new backup

NOTE: Creating the backups is a resource intensive task, and are processed in the background by Cron. The backup will not be immediately available, so please check back later.

Hosting your own Scratchpad¶

You can very easily host a Scratchpad on your own server using our in-built Docker configuration.

This system architecture has been used to successfully run https://bio.acousti.ca, our most resource-intensive site, for many years.

If you need any help or support hosting your own Scratchpad, please raise a ticket on our issue queue https://github.com/NaturalHistoryMuseum/scratchpads2/issues

Finding a server¶

To host your own Scratchpad, you need access to a Linux Server (we prefer the Ubuntu distro) with admin permission so you can install packages.

There are plenty of companies providing this service - just search for Ubuntu Virtual Private Server. Or your institution might be able to provide a VPS for you.

Once you have a server, SSH in, and we’ll start installing the packages you need to run your Scratchpad.

Installing Docker¶

These instructions are based on https://docs.docker.com/engine/install/ubuntu/

1. Set up the repository¶

1.1 Update the apt package index and install packages to allow apt to use a repository over HTTPS:

sudo apt-get update
sudo apt-get install ca-certificates curl gnupg

1.2 Add Docker’s official GPG key:

sudo install -m 0755 -d /etc/apt/keyrings
curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo gpg --dearmor -o /etc/apt/keyrings/docker.gpg
sudo chmod a+r /etc/apt/keyrings/docker.gpg

1.3 Set up the repository

echo \
"deb [arch="$(dpkg --print-architecture)" signed-by=/etc/apt/keyrings/docker.gpg] https://download.docker.com/linux/ubuntu \
"$(. /etc/os-release && echo "$VERSION_CODENAME")" stable" | \
sudo tee /etc/apt/sources.list.d/docker.list > /dev/null

2. Install Docker¶

2.1 Update the apt package index:

sudo apt-get update

2.2 Install Docker Engine, containerd, and Docker Compose:

sudo apt-get install docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin

3. Install Scratchpads¶

3.1 Clone Scratchpads

git clone https://github.com/NaturalHistoryMuseum/scratchpads2.git /var/lib/scratchpads2

3.2 Update environment variables

cp /var/lib/scratchpads2/.env.template /var/lib/scratchpads2/.env

You must update the SQL default settings in the .env file (if you are recreating your site from an existing Scratchpads site, the settings.php will have sensible values to use).

MYSQL_ROOT_PASSWORD=root
MYSQL_DATABASE=drupal
MYSQL_USER=drupal
MYSQL_PASSWORD=drupal

3.3 Run docker images

cd /var/lib/scratchpads2
make up

4. Recreate from backup¶

If you want to recreate your hosted Scratchpad, first download the backup file following these instructions Create backup.

make site-from-archive archive=/path/to/backup/backup.myspecies.info-20230404.194808.tar.gz

5. Daemonize¶

To keep serving the site once you log-off from the server, you must daemonize the process.

make down
docker compose -f docker-compose.yml -f docker-compose.production.yml up -d

6. Set up cron¶

Scratchpads has tasks that run at intervals in the background (indexing for the site search, for example). To enable this, you must add a cron task.

crontab -e

And enter the text before saving the file.

0 3 * * * docker exec scratchpads.apache drush core-cron > /var/log/docker.cron.log 2>&1

You can also run Scratchpads without Docker, installing your own versions of PHP, MySQL, Apache and SOLR. It’s much more complex, but these instructions will help - https://www.digitalocean.com/community/tutorials/how-to-install-linux-apache-mysql-php-lamp-stack-ubuntu-18-04

Adding & editing users¶

You can control user access under People in the Admin menu. The People page allows you to list all users of your site and perform actions (upgrade, delete, edit) on them.

There are five user roles:

Anonymous A non-logged in user.
Authenticated (unblocked) user: Able to access non-public content, create and edit own forum posts
Contributor: Able to create content and edit own content
Editor: Able to create and edit own content, and also edit other people’s content
Maintainer: Like editor, but also has administration privileges

Adding a new user¶

Go to People in the Admin menu
Click Add user at the top of the overlay
For users that are allowed to log in, you need to check the Allow user to login? box at the bottom
Complete all the relevant boxes with example data (compulsory fields are marked with a red asterix)

Authorising new user accounts¶

All users of your Scratchpad have to be authorised by a site maintainer. When a new user creates an account the site maintainer will receive an email and will have to unblock them and add a user role before they can use the site.

Go to People in the Admin menu
Check the status and role of the user(s) you want to edit. Newly signed up users will have a status of “blocked”
Click the check box to the left of their username and select “Unblock the selected users” then click Update

Changing existing user roles¶

Go to People in the Admin menu
Check the role of the user(s) you want to edit
Click the check box to the left of their username and add or remove the required role then click Update

Permissions¶

Scratchpads let you control what features people can access on your site.

You can access the permissions from Admin menu go to People > permissions. Permissions can be set for each of the five user roles:

Anonymous A non-logged in user.
Authenticated (unblocked) user: Able to access non-public content, create and edit own forum posts
Contributor: Able to create content and edit own content
Editor: Able to create and edit own content, and also edit other people’s content
Maintainer: Like editor, but also has administration privileges

Biblio¶

If you do not want people to download files attached to Biblio references you can update the permissions:

Comments¶

By default, only users with an account (non-Anonymous) can create comments.

You can change this by checking the anonymous user option in the Post comments permission.

Node revisions¶

Node revisions are only viewable by the content authors, but you can grant other roles access to view the changes.

User biographies¶

The biographies module allows maintainers to add biographical information for existing people/users in a Scratchpad (e.g. date of birth, professional interests, example of handwriting etc). The module adds these fields to the editing environment of users and once enabled it also provides a direct link to a page with all the included biographies.

Enabling the module¶

From the Admin menu go to Structure > Tools
Enable Biography under the section called Features
Click Save

Adding a biography¶

From the Admin menu go to People
If the user to be updated exists already click Edit next to the name, otherwise select + Add user to add a new user. See more on how to add users at Adding & editing users page.
Fill in the fields accordingly and click Save

Viewing biographies¶

From the main menu select the new Biographies tab
All people that have biographies will be displayed in this page

Groups¶

Let’s assume you want to prepare data for a publication online, but you don’t want anybody to see these data, yet, except for yourself and maybe some co-authors. The best way to do this is by using a “Group”.

Groups are private areas on a Scratchpad which are only accessible to group members. A user can have a higher user role within a group. For example someone who is contributor to the main Scratchpad can be administrator for a group and edit group content created by other group members.

Content generated within a group can be publicly visible or hidden. The creator of a group is usually responsible for managing the group and its users, but he/she can give other users administrative rights.

Enabling the Group module¶

Before you can add a group you need to enable the Group module.

From the Admin menu go to Structure > Tools
In the Groups section turn the Group module On
Click Save
If a message appears that you need to rebuild the content access permissions, click on the Rebuild permissions link and rebuild.
Go to the front page. A new menu item called Group content will appear in the Main menu. As long as there are no groups, the Group content page will show all the content on the site. In addition to the new menu item, new fields related to groups will appear when you add or edit content.

Adding a new group¶

From the Admin menu click Content and then Add link for Group
Enter a GROUP NAME
In the BODY field you can enter a short description of the group that will be visible to users on general group pages
Select Group visibility - Public or private
Click Save

After saving you will see the main groups page which will show content linked to this group. It takes up to an hour for the Group name to actually show on this page and you will need to refresh the page to actually see it. However, you can already link content to the group or add members.

Add group members¶

Edit the group
Select the Members tab.
Click the Add people link.

Enter the USER NAME and click the button.

A user’s role is the same within a group as it is on the rest of the Scratchpad and the only option is to give a member the “administrator member” role, which can be done on the page. Administrator members can edit the group and manage the subscriptions.

Adding content to the group¶

Add a new page¶

In the GROUPS AUDIENCE box select the new group
In the GROUP CONTENT VISIBILITY drop down menu select Private - accessible only to group members. Group content can also be public or use the default. The default is on public and this can only be changed by members of the Scratchpad team.
Click Save

You are now viewing your private group page. Note that the menu item linking to this page is visible and the page also pops up in the Recent pages block on the front page.

When logged out the menu item disappears and the page is not cited in the Recent pages block on the front page any more. The page itself gives an “Access denied” message (after refreshing the browser window with Control+F5).

Adding and editing views¶

The views module allows you to create, manage, and display lists of content.

Each list managed by the views module is known as a “view”, and the output of a view is known as a “display”.

Displays are provided in either block or page form, and a single view may have multiple displays.

Enable views interface¶

To enable views go to Structure in the Admin menu, click on Tools, enable ‘Views’ and save.

Table view¶

We will create a table view for the custom literature mining content type we created in Custom content.

Views can modify how lists of content are displayed on your site. The default display format for a new content type is an HTML list, but this can be changed to a table, grid or for example a map to display your data in an optimal way.

For the Literature mining content type a table would be best, so that is what we are going to do:

Click on the LITERATURE MININGS tab in the Main menu and then on the cog icon to the right of the node title. Click on Edit view.

Literature mining page with default HTML list display, showing edit link (top right)

Tip: Can’t see the cog icon? Have you Enable views interface?

This will open the edit view administration interface.

Edit view administration page

Change Title¶

The system automatically added an “s” to the view title as well as the menu item. We will start by correcting this.

In the edit view interface, click Literature minings link in the ‘Title’ section.
Delete the “s” from the title.
Usually, when you edit any part of the view, you can decide whether you want to edit all displays and thereby change the default, or just the current page and thereby override the default settings only for this case. In our case we want to change the title for all displays, so click on the Apply (all displays) button.
A yellow message (“All changes are stored temporarily…”) appears at the top of the page to make you aware that your changes are not permanent yet.
Click on the Save button in the upper right corner to make your changes permanent. This will automatically bring you back to the page view where you can check the changes.

You will notice that the menu item in the Main menu is still with an extra “s”, so we need to change this, too.

Display Format¶

We want to change the default HTML list view to a table.

click on “HTML list” in the ‘Format’ section.

Edit view: Change format

Select Table.
Apply.

At the bottom of the ‘Edit view’ page you can now see an example of what our new view is going to look like. As you can see, only the title field is showing, so we need to add more fields. Before we do this however, save the view and edit again.

Fields¶

The table view display requires you to chose which fields to include - you can see a new section called Fields has appeared below the Format section.

Click on the Add link to add more fields.
Select Content: Literature mining category, and then select the fields:
- Content: Page
- Content: Text
- Field: Reference
- Field: Taxonomic name
Note that below each field name is a list of the content types in which it appears, so you can find fields by searching for the literature mining content type.
Click Apply
Now you can configure the fields you selected one by one. The default is usually fine, so you don’t need to change anything. However, you could for example make the column header (label) bold by clicking on Style settings , selecting ‘Customize label HTML’ and choosing “STRONG” from the ‘Label HTML element’ dropdown menu.

Table view
Change the field order by clicking on the arrow down icon next to the add link in the ‘Fields’ section. Click on the rearrange link. Drag and drop the fields into a better order. Apply.
Select Save to make the changes permanent.

Filter criteria¶

Filters restrict a view to a certain set of data. Filters can be hidden or exposed. Exposed filters can be used by the users to search for certain data.

Two filters are already present for this view. The “Published (Yes)” filter that ensures that only published content will be shown in this view and the “Type (= Literature mining)” filter that ensures that only literature mining content is shown.

To help users in finding certain literature mining content we are now going to add a few filters that are exposed to the users.

Click on the Add link in the ‘Filter criteria’ section.
Select the fields:
- Content: Literature mining category (field_literature_mining_category)
- Field: Taxonomic name (field_taxonomic_name)
- Field: Reference (field_reference)
Select Apply
Next configure each of the fields in turn. Adapt the labels and select “Expose this filter to visitors…” for all of them. For the taxonomic name filter also select “Expose operator” and “Allow multiple selections”.
Save the view.

Table settings¶

With the right settings, the table rows (items) can be sorted by clicking on the header of the respective column.

Edit view
Click on the Settings link next to Table in the Format section.
Check Sortable for the title, reference and category fields.
Click Apply
Save changes

Sort criteria¶

The default sort criterion is the creation date of the items, with the most recent nodes at the top. You can change the sort criteria or add criteria in the ‘Sort criteria’ section.

Additional displays¶

In addition to changing the existing display, you can add new displays.

Click on the Add button in the ‘Displays’ section near the top of the views administration page.
Select one of the display options:
- Attachment: With this display, you can attach one display of a view to another display. This allows you to group different views together.
- Block: Creates a block display.
- Data export: Creates a file.
- Feed: Creates a feed.
- Page: Creates a page display.
- References: Creates a references view that can be added for example as a field (e.g. node references view) to custom content types.

TIP: Take care when changing the settings of your new display that you only change the current display (override) and not all displays.

We will learn more about adding one of these displays in the next section - View blocks

View blocks¶

As we learnt in Adding and editing views the views module allows you to create, manage, and display lists of content.*

These views of content can be a Block - a small lists of information that can be embedded on other pages.

We will create a block to display the subordinate taxa of a classification term, and display it on species page.

Enable views interface¶

If you haven’t already, enable the views interface:

Go to Structure in the Admin menu, click on Tools, enable ‘Views’ and save.

Create block view¶

Within the Admin menu, go to Structure > Views
Select + Add new view
Enter the view name - for example “Species subordinate taxa”
In the Show section, select Taxonomy terms, and under Of type select the vocabulary you want to use.
Deselect Create a page
Select Create a block
Enter a block title - for example “Subordinate taxa”
Under display format, select Table
Select Continue & edit
Click Save to make changes permanent

Add relationship and contextual filter¶

We want to show taxa which are subordinate to the currently viewed taxon. To do this we need to add a relationship and contextual filter, so we can display terms based on their parent term.

On the edit view form, in the Relationships section click Add.
Filter the relationship types by ‘parent’, and select Taxonomy term: Parent term.
Select Apply.
On the next screen leave the defaults (Identifier=Parent), and click Apply.
In the Contextual filters click Add.
Filter the contextual filters by ‘parent’, and select Taxonomy term: Parent term.
Under Relationship, select “Parent” (or the identifier value from Step. 6 if you did not keep the defaults)
Select Provide default value
Select Taxonomy term ID from URL
Select Apply
Select Save to store your changes permanently.

The view is now ready to use, but we still need to add the block to the page. We’ll see how to do this in the next section - Enabling blocks

Enabling blocks¶

In the Admin menu go to Structure > Blocks
Scroll the page to find the Block you wish to enable.
Click on the Configure link
If needed, you can give a title for your block. This will replace the default title.
In the region settings select where you wish your block to appear:
- Select Sidebar if you wish the block to be visible as a right sidebar in one or more of your pages
- Select Footer if you wish the block to be visible in the footer area in one or more of your pages
- Select Menu if you wish the block to be visible in menu in one or more of your pages. Note: this option will not work with all Blocks.
- Select Main content if you wish the block to be visible in the main content section of the page.
From the Pages tab select on which pages you wish the block to appear/be excluded from.

You can target the pages by writing the paths, with multiple paths per line.
Click Save block

Additional options¶

Rather than specifying page paths to display the block on, you can set the block to be visible on certain content type pages.
Under Roles you can also restrict viewing the block to uses with a specific role.
Select Display as Tab in the Tabify the Block tab if you wish the content of the block to appear as a sidescreen tab (like the issues queue tab)

Create webform¶

Webform is the module for making forms and surveys in Drupal. After a submission customizable e-mails can be sent to administrators and/or submitters. Results can be exported into Excel or other spreadsheet applications.

In this example, we will create a webform for a conference registration. People can fill in the form without having to register or log in to the Scratchpad site.

Enable the webform module¶

In the Admin menu go to Structure > Tools
In the ‘Webform’ section turn Webforms on and save.

Create a webform¶

In the Admin menu go to Content
Next to Webform, click Add

Create a webform
Enter a TITLE and some BODY text. The body text will appear at the top of the form and can be used for an introduction.
Save. Now we can enter fields to your form.

Add webform components¶

Components is the webform terminology for fields. To start adding components start editing a webform, and select the Webform tab.

This opens the webform components interface:

Select the type of field you want (Text field, Date field, Number field, Select option field, File field, Grid field, Text area field, Private field) and click Add

Text field¶

Components of the type “Textfield” are for entering short text that is up to 255 characters long. Add a component for entering the full name.

Add “Full name” as the new component name and select the “Textfield” type. Check “Mandatory”. Mandatory means that the user has to fill in this field before he can submit the form. Click the button.

Webform component settings
Under ‘DESCRIPTION’ add a short instructions that help users in filling in this field.
In the ‘Display’ section you have several options for changing the display. For example if you add a field asking for the size of a poster, you could add “cm” in the ‘LABEL PLACED TO THE RIGHT OF THE TEXTFIELD’ field, so that users know to give the size in centimetres. By default the label is placed above the field. To save space select “Inline” as ‘LABEL DISPLAY’. For our “Full name” example component just select “Inline” display and none of the other display options. Save component.

Webform with introduction and one component
Click on the tab to check how your webform looks so far. Then click on the tab to add more components.

Email field¶

Add “Email” as the new component name and select the “E-mail” type. Check “Mandatory”. Click the button. Save.

Date field¶

Add “Arrival date” as the new component name and select the “Date” type. Enter “2000-05-29” as ‘START DATE’. Enable the pop-up calendar and choose “inline” for the label display. Save.

Number field¶

Add “Number of accompanying persons” as the new component name and select the “Number” type. Add. Check “Integer” in the ‘Validation’ section. Choose “inline” for the label display. Save.

Select option field¶

Add “Are you giving a talk?” as the new component name and select the “Select options” type. Check “Mandatory”. Add. Enter “1|No” and “2|Yes” in the ‘OPTIONS’ field in two lines. The ‘OPTIONS’ field uses safe keys. Safe keys ensure that each options is saved individually. For example if you publish a webform and at a later stage decide to change the wording of one of the options, you would only change the readable option, not the save key. That way the system recognises that this is still the same option and this will help you later when you evaluate the results. The safe key is always on the left side and separated from the readable option by a pipe character. Save.

File field¶

Add “Abstract” as the new component name and select the “File” type. Click the button. Add some instructions on what the abstract should contain in the ‘DESCRIPTION’ field. In the ‘UPLOAD DESTINATION’ section check “Private files” so that only user that have the right to view submissions can view the abstracts. Under ‘ALLOWED FILE EXTENTIONS’ unselect the web images extensions and choose several documents extensions instead. Save.

Grid field¶

Grid fields allow the user to select different choices for a set of questions. Grids are often used in questionnaires to for example state how good something is on a scale from 1 to 5. For our conference registration webform we will assume that participants numbers for symposia are restricted add a grid in which users can state how important the attendance at specific symposia is for them.

Add “Symposium choices” as the new component name and select the “Grid” type. Check “Mandatory”. Click the button.

Webform component settings for Grid fields
Add some options as well as the questions (both with safe keys) and a description. Save.

Webform administration page with various form components

Text area field¶

Text area fields are for longer text.

Add “Remarks” as the new component name and select the “Textarea” type. Click the button.

Private field¶

If you want to annotate the forms that users have submitted without having the annotation field showing up in the webform, check “Private” at the bottom of the component settings page.

Add “Private annotations” as the new component name and select the “Textfield” type. Click the button. Check “Private”. Save.
Click on the tab to have a look at your webform. For long forms you can add page breaks if needed. Log out of your Scratchpad and go to the webform page. You will notice that the “Private annotations” field is now hidden.

The webform is ready to to be used so lets setup a way to monitor responses and analyse the results - see Administer webforms.

Administer webforms¶

After Create webform we want to monitor responses and analyse the results.

Email settings¶

Notifications¶

Receive a notification every time the webform is submitted.

Locate the webform you wish to administer.
Select Edit
Select Webform tab.
Select +Emails
Enter the email address you wish to send notifications to.

Add an email address for webform notifications

Click Save configuration

Confirmation¶

Send a confirmation message to the user who submitted the form

Locate the webform you wish to administer.
Select Edit
Select Webform tab.
Select +Emails
Select Component value
Select the field that contains the email of the user and click on the button. This will only work if you have used an email type field in our webform.
In the ‘E-mail template’ section select “Custom template” in the drop down menu and enter some custom text in the field below, e.g. “Thank you for registering…”

Webform form settings page
Click Save configuration

Form settings¶

The form settings page allows you to add a confirmation message to the website and limit submissions.

Locate the webform you wish to administer.
Select Edit
Select Webform tab.
Select +Form settings
Add a confirmation message. This message will appear on the screen after the user has submitted the form.
Under PER USER SUBMISSION LIMIT limit each user to 1 submission ever.
Click Save configuration

Results¶

Submit the form a couple of times to test the confirmation message and notification emails.

On the webform, Select Edit > Results
On the + Submissions page you see a list of all submissions and can view, edit or delete single submissions.

List of webform submissions
Click on + Submissions and select the + Analysis option. You will be presented with statistics for each field.

Analysis of webform results
Click on + Analysis and select the + Table option to view all submissions in a table format.
Click on + Table and select the + Download option to download the results as a delimited text or Excel file. There are various option for selecting the fields and format for the download.
The last results option is + Clear. This will delete all submission, so be careful before you clear the form.

Managing comments¶

The commenting functionality in Scratchpads is a valuable system that enables registered and/or anonymous users to comment on a piece of content (usually a node). Maintainers and editors of a site can control the comment functionality per content type and per user role. This means that a Scratchpad site might have comments enabled for a content type (e.g. taxon descriptions) but not for another content type (e.g. specimens/observations).

Comments permissions¶

Maintainers can change the roles that are permitted to submit comments to a site.

From the Admin menu go to People
Under Comment select the user groups, according to their roles, that you wish to be able to post comments
If anonymous users are selected. Visitors of the site will be able to submit comments to be published. By default comments by anonymous users need the maintainer’s approval before published in the site
Click Save permissions

Enable comments for specific content types¶

Enabling comments for specific content types will not override the access level settings described in the previous section.

From the Admin menu go to Structure > Content types
Click edit next to the content type you wish to modify comment settings
Select Comment settings from the vertical tab menu
Set specific properties for the comments of this content type
- Closed: No comments can be submitted
- Open: Anyone can submit a comment provided they have given access, as described in the previous section
- Hidden: Comments can be submitted, but they are not published

Comment notifications¶

You can modify the settings that define when someone should be notified, via email, when a new comment is posted and also how the notification email is drafted.

From the Admin menu go to Configuration > Comment notify
Change settings accordingly and click Save configuration

Managing comments¶

Comments submitted by anonymous users are marked as unapproved by default and do not get published until a maintainer has approved them. To approve or delete comments go to

On Admin menu go to Content > Comments
All published comments are located and can be managed under Published comments

All unapproved comments can be managed (approved or deleted) under the Unpublished comments section
Numbers in brackets indicate the total number of comments under these two sections

Google analytics¶

Google Analytics helps you get an overview over the number of visitors on your site, where they come from and how they behave.

Go to http://www.google.com/analytics/features/index.html and create a Google Analytics account for your Scratchpad. You will be given a key that starts with “UA-”. Save this key or keep this page open while you enable the Google Analytics module on your Scratchpad.
In the Admin menu go to Structure > Tools.
Under the Statistics section enable Google Analytics and save.
Configure the Google Analytics tool by clicking on the Configure Google Analytics link that has appeared in the Statistics section. Alternatively go to Configuration in the Admin menu and click on Google Analytics.
In the WEB PROPERTY ID field enter the enter the UA number given by Google when you signed up.
Save configuration
After about a day you should be able to see the first data about your Scratchpad when you log into your Google Analytics account. You can only view these data via your Analytics account, not via your Scratchpad.

Citing Scratchpads¶

Scratchpads are a dynamic environment. Site maintainers, editors and contributors can modify the contents of a page at any point. However, as Scratchpads are being used as a source for information in scientific journals and other online resources it is necessary for a visitor to be able to capture the information provided in a page and be able to access this page at any point in time, even when the contents of the page have been modified at a later date.

The Cite this page functionality allows visitors to generate a snapshot of the page they visit that is being deposited in a separate secure Scratchpad server with a unique and stable URL. The stored snapshots will remain accessible even if the original source is no longer available.

Enabling the module¶

From the Admin menu go to Structure > Tools
Enable the Scratchpads Cite this page tool under the Sharing section
Click Save

Using the tool¶

This functionality, once enabled, is available to all registered and anonymous users of the site. Once enabled a Cite me button will be available to all pages in a site that have content that can be cited.

To create a permanent snapshot of a page click Cite me on the page you wish to store in our servers.
The original author as well as the subsequent editors of a node/page are included as authors of the node/page
The title of the node/page will be used as the title of the created snapshot
All snapshots are stored as PDF files with relevant annotation embedded

Customise front page¶

Click on the Home icon to go to the front page.

Welcome title & message¶

As part of the set-up workflow you will already have produced a welcome message for your front page.

To change this, click Edit.
In Welcome message enter the text you want to display
By default, the title will be Welcome to Scratchpad training site. You can change this by selecting Override welcome title and entering your new title.

Images¶

To the right of the welcome message is an image block. If you haven’t added any images, yet, this space will be empty. (See Images & media). The image block consists of four thumbnails and one larger image. The larger image changes to the image the mouse hovers over.

You can select which images to display on the home page by:

Under Admin menu go to Content > Image
Locate the image you wish to use, and click Edit
Select the option Promote to home page

If you would prefer to display a list of content rather than images:

On the home page select Edit.
In the Main block section, select Content
Select the content type to display
Select Save configuration

Content blocks¶

The home page also display three blocks of recent content - by default these blocks will show Page, Biblio, and Taxon description.

You can choose different content to display in these blocks.

On the home page select Edit.
In the Small blocks section, select which content type to show in each of the three blocks.

Customise dashboard¶

Instructions¶

In the Admin menu go to Dashboard.
By default the Dashboard shows the Recent content block. You can add more blocks by clicking on the Customise dashboard link at the top.

A selection of inactive blocks is shown in black at the top. Drag and drop these blocks into the columns below. The wider column to the left is the main dashboard area, the smaller column to the right is called the sidebar area.
Click the Done link to go back to view the dashboard.

Customise menus¶

In Admin menu go to Structure > Menus.
Next to Main menu click List links.
Drop and drag the menu items to rearrange into the preferred order
Click Save configuration.

Customise shortcut menu¶

The shortcut menu is the light grey bar beneath the Admin menu. If you use a particular administration page frequently, it can save time to add a shortcut link here.

Add a shortcut¶

To add a shortcut simply go to the administrative page you want to link to
Click on the plus icon in the upper right corner. This creates a link in the shortcut menu.

Edit shortcuts¶

To change the name of a shortcut menu item or the order of items, extend the Shortcut menu and click on Edit shortcuts on the right side.

Click on Edit to change a name. Click Save.
Drag and drop menu items to change the order. Click Save changes.
You can also add new shortcuts by clicking on Add shortcut and entering the name and path for the new shortcut. For example, if you frequently add pages enter the NAME Add page and PATH “node/add/page”. Click Save.

The default shortcut set is customised by the site maintainer but each user can create and customise his/her own set via the user account (Shortcut tab). The site maintainer also has the option to create different shortcut sets for different user groups.

Custom content type on taxon page¶

If you have a new content type you’d like displayed on the classification taxon page:

In the Admin menu go to Structure > Content types
Click Edit for the content type you want to display
Click on the Display settings tab near the bottom of the page and check Display on species page.
A new set of options appear in which you can check where the block is supposed to appear. It can either appear on its own tab or under one of the existing tabs. Select one option.
Click Save

TIP: The content type must have a taxonomic name field corresponding to the classification species page.

Formatting thumbnails¶

By default, thumbnail images on a Scratchpad are resized and cropped to fit an 85x85 pixel frame.

This provides a clean and easy way to browse thumbnail gallery - but does have the drawback that some image content will be missing from the thumbnail.

If this is a problem for your Scratchpad you can enable the Full thumbnails option which will display a miniature version of the entire image without cropping.

To enable Full thumbnails:

From the Admin menu go to Structure > Tools
Go to section Images
Turn the Full thumbnails on
Click Save

Nomenclatural status¶

Scratchpads follow the ITIS scheme (see Itis standard fields). When setting a term of a biological taxonomy as not accepted you are also expected to provide the unacceptability reason for it.

To accommodate the different nomenclature common practices followed by both IBN and ICZN, we provide adjusted lists of unacceptability reasons.

The following table illustrates how terms will be designated in the classification tree when a specific unacceptability reason has been selected.

Unaccepability reason	Mark in classification	Position in relation to term
database artifact	artifact	suffix
heterotypic (taxonomic) synonym	=	prefix
homonym (illegitimate)	nom. illeg.	suffix
homonym & junior synonym	= & nom. illeg.	prefix & suffix
homotypic (nomenclatural) synonym	≡	prefix
horticultural	horticultural	suffix
invalidly published, nomen nudum	nom. inval.	suffix
invalidly published, other	nom. inval.	suffix
junior homonym	homonym	suffix
junior synonym	=	prefix
misapplied	misapplied	suffix
nomen dubium	nom. dubium	suffix
nomen oblitum	nom. oblitum	suffix
objective synonym	≡	prefix
original name/combination	basionym	suffix
orthographic variant (misspelling)	nom. inval.	suffix
other	unplaced	suffix
pro parte	= & p.p.	prefix & suffix
rejected name	nom. rej.	suffix
subjective synonym	=	prefix
subsequent name/combination	comb.	suffix
superfluous renaming (illegitimate)	nom. illeg.	suffix
synonym	=	prefix
unavailable, database artifact	artifact	suffix
unavailable, incorrect original spelling	nom. inval.	suffix
unavailable, literature misspelling	nom. inval.	suffix
unavailable, nomen nudum	nom. illeg.	suffix
unavailable, other

Enable pretty URLs¶

Enabling Pretty URLs generates user-friendly URL aliases, based on the title of the content being edited/created.

For example, a page titled “About this site” will be accessible under the URL about-this-site, not just node/x. This also might help your pages rank high in search engine results.

To enable Pretty URLs on your Scratchpad:

In the Admin menu go to Structure > Tools.
In the Other section enable Pretty URLs
Click Save.

Bulk update existing content¶

If you have already created content, you can bulk update the URLs.

Under Admin menu go to Configuration
In the Search and metadata section, select “URL aliases”
Select the Bulk update tab.
Select the content types you want to to generate URLs for.
Select Update

Sitemap¶

The sitemap provides a way for people to more early find and navigate content on your Scratchpad.

Under Admin menu go to Structure > Tools
In the Other section turn the Sitemap on
Click save

You can view the sitemap at SCRATCHPAD_URL/sitemap

Help and support¶

If you have any issues with your Scratchpad, require any assistance, or would like to request a new feature, please use our Issue Queue. You will need to sign up for a user account on Github.

To make it easier to view and post new issues, you can do so from within your Scratchpad using the issue tab (no Github account required). This appears on the left hand side of your Scratchpad when you are logged in.

If you have specific questions or would like advice or help in how to best set up your site, please email the Scratchpad team at scratchpad@nhm.ac.uk.

Don’t be afraid to ask ‘stupid’ questions and don’t get hung up on a problem for hours. If you are having an issue it’s very likely others will have the same issue. By asking the question you’re helping the community and it will often lead to us fixing a bug or improving our documentation.

Service updates¶

For downtime or performance alerts, please see our Blog or Twitter.

Our blog is also a useful source of information on Scratchpad Releases and future plans for the platform.

Glossary¶

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.

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 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

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

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.

Cron

An automated command that is to be executed at a specified time.

CSV

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

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

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.

Encyclopedia of Life (EOL)

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.

Faceted browsing

Narrow down search results by applying multiple filters based on faceted classification of the items.

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.

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://github.com/NaturalHistoryMuseum/scratchpads2.

Google Maps API key

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

Grid editor

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.

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.

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.

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.

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.

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.

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).

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.

Overlay

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

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.

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.

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/

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 https://github.com/tdwg/ontology/blob/master/ontology/voc/GeographicRegion.rdf.

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.

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

Views

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

Vocabulary

See taxonomy

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.

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.

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.

Useful links¶

Scratchpads platform: Find information about Scratchpads, browse through sites and apply for a new Scratchpad site http://scratchpads.eu
Issues queue: Report an issue, ask your questions or find answers or to request a new feature https://github.com/NaturalHistoryMuseum/scratchpads2/issues
Sandbox: Experiment with all Scratchpads features through this fully functional test site that resets every 6 hours. http://sandbox.scratchpads.eu

For any other questions or queries, please contact as at scratchpads@nhm.ac.uk.

Scratchpads¶

Contents¶

Site setup¶

Admin menu¶

Theming¶

Colour scheme¶

Logo¶

Adding a logo¶

What makes a good logo?¶

Pages¶

Adding a page¶

Editing page¶

Cloning a page¶

Hierarchical pages¶

Adding a biological classification¶

Adding terms¶

Troubleshooting¶

Missing tab after creating classification¶

Importing a classification¶

Viewing classification¶

Viewing a classification¶

Editing classification¶

Taxonomy editor¶

Selecting a term¶

Editing term form¶

Adding a term¶

Delete a term¶

Itis standard fields¶

Importing classification from Excel¶

Create the vocabulary¶

Downloading the template file¶

Editing the template file¶

Importing the template file¶

Deleting classification¶

Integrating external data¶

IUCN¶

Enabling the widget¶

NCBI¶

Enabling the widget¶

Accessing widget results¶

Filtering taxonomic terms¶

Enable or disable the filter¶

Locations and specimens¶

Adding a location¶

Adding a specimen¶

Cloning specimen¶

Media gallery¶

Troubleshooting¶

Images & media¶

Editing metadata¶

Taxon descriptions¶

Adding a taxon description with distribution map¶

Literature¶

Add a single reference¶

Adding file attachments to a reference¶

Edit a reference¶

Blog¶

Instructions¶

Forums¶

Enabling the Forums module¶

Creating a forum¶

Forum containers¶

Adding a forum topic¶

Newsletter¶

Enabling the Simplenews module¶

Configuring Simplenews¶

Create a newsletter¶

Create a newsletter issue¶

User subscriptions¶

Publishing¶

Publishing options¶

Default publishing option¶

Unpublished content¶

Finding content¶

Search¶

Faceted Search¶

Main menu¶

Admin menu¶

Recent content¶

Recent content¶