Site Guide

In this book you'll find what can be expected of this site, the content it can offer and, if you're registered, how to add or modify any kind of content. Everything is quite simple, just follow the instructions and we hope you won't have to read this twice!

What's this site about?

This site is about ants. As obvious as it seems, we prefer to think of this site as a community-based tool about ants. The final goal is to provide the tools needed for any myrmecologist to curate their collection, identify the ants, check the ID with quality images, compare the data in distribution maps and know if the finding is new for a given region.

To achieve this, we need to:

define the different regions to study
create a list of existing ants for the region
develope identification keys
image specimens of all the existing species, three castes [at least!]
create a web-based database to store the data
...

This work is huge, but we think its achievable if we work together. We are developing several tools that will let us:

belong to this community
add their own info to the web [photos, database distribution records, stories, bibliography, videos, etc...]
comment/participate in the info offered by others
develope shared projects with other members
....

In the next pages we will try to explain how to use the different tools to perform the tasks above.

Do I want to join the community?

If you just want to enjoy the information offered here, you need no registration. All of the published information is public. We keep nothing for ourselves, as we believe that knowledge is valuable only if it's shared.

But...

If you think this tool is a real need and you want to participate in the project, register and become an active member

How can I help?

There're a lot of things to do. For example:

Image and load specimens
Prepare and upload keys
Write articles about biology, distribution, taxonomy, etc.
Update distribution lists
Update taxonomy
Prepare and translate pdf keys
Curate a collection and share the data
Participate in debates/common projects
Help us design and implement new tools
...

So, if you're a professional myrmecologist or a passionated amateur, and you're willing to help, do not hesitate, your place is here.

By the way, Drupal/PHP programmers are welcome too!

Exploring the site

This site has many use levels depending if you are a registered user or not, and, if you are, depending on your role. We will set some concepts about what you can expect and how to do it. All the explanations shall define the kind of user allowed to do the task.

Screen areas

Intro

You'll access a maximum of seven main areas in the screen. Not all of them are shown at once, but they can appear and dissappear depending on the content shown. When accesing the "home page", you'll discover five of them:

Zone 1: Logo area

Areas 1, 2 and 3 appear in every page, no matter the content. Zone 1 is the logo. Clicking on it will take you to the home page

Zone 2: Taxon Search

Zone 2 carries the "Taxon Search" widget. If you want to know if a taxon is available to use, write here any part of the name. Let's say I'd like to introduce an story about Cataglyphis albicans, but I'm not sure if it's available. Typing "albic" and clicking on "Search" will offer:

Clicking in any name shall show the results page for that taxon. If the one you're searching for is not listed, you'll need to add it to the taxa list before submitting any content related to it.

Zone 3: Main Menu

A quite complex tool which varies depending on the user role. Its functionalities are explained in detail here

Zone 4: Left bar

Helpful zone to show different blocks containing submenus or information related to the content shown. Its content varies depending on the section, and does not appear in some cases as in distribution maps.

Zone 5: Main content

The desired content is shown here. Sometimes it expands to cover the whole width and sometimes it shrinks when the Right and Left bars are populated, as in the next example:

Zone 6: Breadcrumbs

This line appears in some cases to make easier to jump to other parts of the site. For example, when viewing a camponotus species, this is the breadcrumb shown:

Clicking in any term will take you to the summary page of that particular issue

Zone 7: Right bar

With the same characteristics than the Left bar, it shows some useful tips on the content shown, but not navigational aid. In the image above, a Gmap of the specimen is shown, but other tips can appear.

One menu to rule them all (the main menu)

In this section we'll try to explain the functions and tools you can manage via the main menu. This is thought so you won't need any other tool to access the main funcionalities of the site. This is the actual look (by now!)

Please, have into account that this menu changes depending on the role of the user. Some of them are availble for registered users only, or for taxonomists or for admins. The images shown in this section are for the Admin user, an if you're missing something in your menu, is because you have not the permits to do the task. For example, if you're a visitor, you won't have the "My content" submenu.

Please report us if you are missing something or some explanation is not clear enough.

Specimens image comparison tool

This tool filters the images by taxa, body part and caste, and shows the selection. You can filter to the depth you like, like showhing all the images available for Myrmicinae or just viewing the lateral view of the Camponotus abjectus and Camponotus cruentatus males.

To view enlarged images, click on the thumbnail, as usual.

Distribution

This menu is the same for all the users, registered or not.

Have into account that in this version no records can be added to the database. We are working to implement this feature in the near future.

If you want your data to appear now in the database, contact us

Distribution Maps

This is the tool to picture Distribution Maps at the moment. It's quite powerful, and we've tested it with up to 1.000 dots in it, and works quite fast. This is a 1.0 version. Next versions will have:

Improved layers
Direct link to database queries instead of showing all of the records in the database
An option to copy the map to paste it anywhere. This option is now available only by the "Print Screen" option.

Although everything is quite obvious, we have prepared this video (4:56 minutes) to make things easier.

Useful tips

In this section we'll explain some tricks to make life easier

Keeping track of the new content

Registered users can be kept updated of the new or updated content in the site. To do so, we've created a "New Content" block, that can be activated at the user profile [My Content-> My account]

Editing my profile, and behind the "Picture", a "Block configuration" section appears. The optional blocks can be switched on and off here. In this example, two blocks appear, the "New Content" and the "Who's Online".

If the "New Content" block is on, every time that a new content is added or modified, the title shall appear in a block at the upper left. Once the content is viewed, or remains more than four weeks unseen, it is deleted from the list. If you want to be more selective on the contents to view, clicking on the "more" link will take to a page where the New Content can be filtered via the Content Type.

If you do not want to be advised of the new content any time it's created, but to check it now and then, you can access the "New Content" page directly from [My content->New or updated content].

The first time that the New Content page is checked, the results comprises the last four weeks.

Quick access to a taxon summary

To access the summary view of a certain taxon, just type the name with spaces replaced by "-". For example, www.formicidae.org/messor will take you to the Messor summary page, and to access Messor barbarus type www.formicidae.org/messor-barbarus

If typing the name results in a "Page not found", several things can be happening

The most probable thing is that we do not have that species in the list as it is a non Palaeartic species or not listed under any region covered by us.
The status for that taxon is different from the one typed. For example, www.formicidae.org/diplorhoptrum-robusta will have no results, but www.formicidae.org/solenopsis-robusta will take us the that page, as this is the criteria followed by us.
We have missed that taxon
If you're sure that the taxon is correctly spelled, it should be listed and you obtain no results, please type any part of the name at the upper right "Taxon search" widget. If the name is not listed, or listed but clicking results in a "Page not found", please report us

Other ways to access the taxon summary page are:

at the main menu: Taxa->List available taxa
via the "Taxon search" widget

Creating content

Creating content for the site is quite easy. Once that the "Content Type" you want to add is selected, you'll be carried to a data-entry form, where you'll have to fill some fields. Some of the tasks to fulfill are common, and other are quite specific for every content type.

Just to explain some concepts on what really is "Creating content". What you're are creating is a node. And every node has a workflow. This didn't help much, but we are entering into it right now. The workflow is the different stages that a node can have. To set things more clear. When you create a node, the last part of the creating form is always the same:

If a node is submitted but not published, the node is not public, and the information shall be available only for the user that has created the node. This is useful when you haven't finished it or when you want somebody else to revise it before going public. What's more, all of the nodes created but not published are listed here.

Set clear that if a node is not published, it shall not be found and therefore listed by any of the tools in the site. Once the content has been published, it's available in the site for the different tools, as listings, filters, etc.

The other three options are easier, and with almost no use for us.

"Promoted to front page" means that the node shall be listed in the "Home" page.
"Sticky..." shall make it appear in the top of the listings that it's included.
And "Create new revision" allows to modify a published node and let the system to keep track of all the versions of the node, showing differences among nodes if requested.

Adding Bibliographical references and footnotes to a Story

To add a Biblio reference, first thing you should check is that the referenced article is present in our database (Browse->Bibliographical references). If it is not, just create it.

There's a faster way to know if the article is listed in the database. When adding the Story, check the field "bibref" above the "Body" field.

In that field type part of the title for the searched reference:

Select the article to be referred. You'll see something like:

Now, the tricky part. In the Body field, write your article. To add the reference, click the upper-left "Fuente HTML" or "HTML Source" or whichever it is in the language you have the browser on. And everything becomes a litlle messy, as what you're looking into now is the real HTML code for what you're writing. Doing it for this article:

Don't panic (although this code can become really messy, the text can be easilly followed for a typical article) and look for the place where to add the reference. Once located, add <bib>2789</bib>, being "2789" the "nid" given in the bibref field for your article. It will look like 1

And that's it. Click on the upper-left "Fuente HTML" or "HTML Source"again and the tick is done. When you publish the article, an ordered sequence of references shall be created. One last thing, delete the content in the "bibref" field, if you do not want that messing in your article everywhere.

The best part is that references are integrated with footnotes. To add a footnote the process is the same, but instead of typing <bib>2789</bib>, type <fn>TEXT OF THE FOOTNOTE</fn>, and reference numbers shall be created and ordered. Doing it2

We're working on the messy part to make it more efficient, but that's how it has to be done by now.

1. Espadaler X . 2007. The ants of El Hierro (Canary Islands). Memoirs of the American Entomological Institute. 80:113-127.
2. Easy,uh?

Submitting "Biblio"

Next thing you find is a dialog box asking for the type of biblio you want to add. There are four types available, and all of them are filled in almost the same way.

If "Journal Article" is selected, you'll enter the submitting form. Everything is quite straightforward, except the Authors field. The biblio content type comes with an integrated feature that selects the different formats of a name and changes them in the presentations and filtering options. For instance, if I enter "John Doe", "J. Doe" or "Doe, J.", the system will present them always as "Doe, J." and shall filter any biblio reference with any of the three names under "Doe, J.".

But to do this, we must tell the system when a name begins and finishes. This is done separating the different names by semicolons in a format like this:

X. Espadaler; Cagniant, H.; Barry Bolton

The system recognizes the different names between the semicolons and translates it to:

Espadaler, X.; Cagniant, H.; Bolton, B.

And lists the article under any of these three authors, no matter the name structure you gave them in the authors field.

The "Journal Title" tries to match your words to the existing journals already existing in the database. if you find one in the list shown below the field, just select it.

From "Pages" and below there are some fields that in most of ocassions shall not be filled, as they are "Journal Date", "ISSN Number" and "ISBN Number" and others. We'll just note here the two most important of them, as they are "URL" and "File attachments".

"URL" is the link to the location where the full article can be found. We've decided to link our database to the magnificent database of antbase. So please, if the reference you're entering is available there, just add here the link to the pdf.

If not, you can always add a pdf to the biblio, via the "File attachments" tool. Just browse it and upload it. Please: DO NOT UPLOAD ANY COPYRIGHTED MATERIAL unless you've the permit of editors and/or authors.

The rest of the options are common to all the content types and explained in other sections of this book.

Don't forget to Publish it before submitting.

Adding a link to a certain taxon

Let's suppose that I'm writing a story and I want a link to a certain species appear. Well, just type the plain name. If the species is listed in the system as valid, a link will be automatically created. If it is listed as a synonym, it will take you to the valid species summary page. For example:

Please, have into account that the system is quite clever, but some weird things can happen, as this:

Anergates barbarus

The system recognizes Anergates as valid, and will create a link to that genus, but will not be capable to tell you that such an species does not exist

How does this site works?

This site manages information added by registered users. This information can have several formats (Images, videos, text, links, etc...). The way to manage the information is adding categories to the information, and browsing it via these labels. So, we are mixing three things: Users, content and labels.

Registered users, and only these, can add information. There are three types of users, depending on the expertise and knowledge area. We'll explain it in detail here.

The content is the information that can be added to the site. It can adopt several formats (images, database records, keys, articles, etc.) and to make life easier, we have prepared some "Content types" to automatize its load and management. It's really simple to do and quite similar for all of them (won't take you more than five minutes to learn it!).

Each "content type" is managed via labels or "categories". For example, if we add the images for a worker of Camponotus piceus, we need to tell the system that the images added:

belong to the taxa "Camponotus piceus"
belong to the section "Worker"

For a better explanation on the categories, click here

And that's it. The site combines different tools to manage, filter and present this information via maps, summaries, listings, queries, etc.

User types

This site is thought to be used by five user types: Visitors, Registered Users, Writers Taxonomists and Admins.

Visitors can access all of the published info in this site but can not collaborate adding info. They just enjoy. No registration is needed, and they'll have access to the same published information than registered users.

The other four user types (Registered Users, Visitor, Taxonomist and Admins) can log in the site. To be one of these, you need to be provided with a user name and a password.

Registered Users have access to all the information, but improved with some blocks offering different functionalities as "New content" that lists all the unseen information added or modified in the last month. Once this information is viewed, dissapears from the block, so it's a practical tool to keep updated. They can comment any piece of info in the site.

Writers are the blocks on which this community is based on. They can add and categorize content, modify their own content or comment any kind of information

Taxonomists can perform all the tasks available to Registered Users, revise the content and also manage the taxa structure. They can:

Modify any content, posted by them or by others
Add new taxa
Modify taxa tree
Modify taxonomic information for the taxa, as synonims, parents, etc.
Modify regional lists or taxa dsitribution

Admins have access to the whole site and are the only ones that can implement new tools for the web. This is a role obviously more suited to programmers than to taxonomists

Content types

The content that users can add to the web is formatted in several "Content Types". Each one is a preformatted schema where you will add the content itself and the categories the system needs to manage it. We have:

Story
Book Page
Specimen
Keys, with two different kinds, "Key cover" for general information and "Key step" for dichotomies
Biblio, to manage bibliographical references
Weblink
Image

All of these are introduced or edited in a very similar way.

Images

To upload one or more images, taxa related or not. Notes can be added to the image, as well as categories. Curiously enough, this content type is not of much use to this site, as the taxonomical images are better added via the Specimen type, and the story and other content types support the attaching of images or they can be inserted into the "body" field, so they usually form part of other content types.

We'd like to underline an special case, and it's when you upload an Specimen content type. The attached images are automatically processed and each of them generates an "Image" content type inheriting the propierties (categories, author, etc.). So, let's say that you upload an Specimen with two images. The system will generate three nodes, one for the specimen and other two one for each uploaded image, the three nodes with the same categories given to the "Specimen" node.

Story

The "Story" content is thought to add any taxa-related written content. It can carry:

Taxonomy information: Via categorization, you can tell the system the taxa and the Section that this Story is about. For example, if you want to add a story about the dulosis on Strongylognathus, you'll have to add to the content the labels"Strongylognathus" and "Tetramorium" for the Taxonomy information and "Biology" for the "Section" category.
The content itself, in the "body" field. It can have links, photos, videos, etc, and other tricks that we'll explain in detail.
Related links
File atachments (Images, pdf, txt, doc, etc...)

Once the Story is created, the system keeps track of the author, dates, etc, and also keeps a history record of the changes made to the document.

Book Page

The "Book" is a compilation of "Book pages" where each page can be added by an author. The pages can be ordered via an schema (let's say you can append it to a tree branch). It's not categorised under any category, and it's thought to develop common contents as a "Sampling methods" book or any other subject not strictly related to taxa.

The node you are reading now is a book page. The block on the upper left, to navigate the book is generated automatically by the system, and it's authomatically shown when some part of a book is opened.

As the "Story" content, it can carry written content (with media), related links and uploaded files.

Specimen

The way to add quality images of a given ant is via the "Specimen" type content. The goal is that once an specimen is identified with the keys, it can be cheked with these images. So, no biology or other kind of images are thought to be added in this content type, only taxonomical ones.

The information offered is:

Title: ususally the code on the collection it's curated and the caste. , to be easily identified in lists, where only the title is shown
Categories: Taxon and caste the images belong to. This obviously are very important field as they're used by the several different searching tools
Text field to add any relevant information
Location, via Google Maps. With this information the system shows a map on the upper right with the place the specimen has been captured, and it offers some new tricks to find specimens via it's geographical location, or in a world map.
Images

As this is a key content type in this site, a lot of searching tools are based on this. We'll talk about them later.

There's an special type of specimens, that can be found here. These are the specimens that do not have a valid ID, and are offered to the community to search them one. Everybody, registerd users and visitors, can comment the specimen, until a final ID appears.

Keys

No need to explain that in a site like this, keys are one of the main tools. There are two kind of keys in this site.

In-Built keys. They are created and maintained by our community. They should be updated, and if not, a note should appear noting the fact. All the steps should be imaged.
External keys. These are not created or maintained by our community, and can have two different main sources: other web pages (with a link to the page) or published articles (with a pdf or at least a reference to where it can be found). They maybe outdated, and listed by historical reasons. Notes assesing its real validity should appear.

The information offered contains:

Taxa the key is valid for, and is given via categories. For example, if the key is to identify Iberian Ponera, the Taxon category is "Ponera".
The taxa the key can be used to reach an ID. For example, in the former example, these should be Ponera coarctata and Ponera testacea.
Geographical Region where the key is valid. It's given via categories and is used to filter the keys valid for a given region. In the Ponera example, this validity comprises "West Palaeartic" and "Macaronesia". The system uses this information to show this key when a region included in one of these is listed. For example, when asking about "Iberian Peninsula", all the keys tagged with "Iberian Peninsula" or any region that contains it appear. In the Ponera key case, as it's tagged with "West Palaeartic", this key shall be listed as valid in any region inside "West Palaeartic" as "Europe" or "Slovenia"
Notes

Biblio

Used to manage bibliographical references. Offers all the typical information on authors, title, etc. It can offer the full text via an uploaded pdf or a weblink (to the fantastic www.antbase.org repository, mainly).

Once the biblio is submitted, the system offers a lot of tools to index, filter and show the information. For example, for each registered user a tab is shown with a list of his/her bibliographical references present in the database.

Weblinks

This content type carries information on the taxa and section, and is filtered and offered in the summaries for a taxon. Besides this info, a "notes" field can be filled with information about the link, it's validity, personal impressions, etc. When the weblink is shown, it can be commented by visitors or registered users.

There is another source of links in the system, and it is that any Story (or other content types) can have "related links" added to it for further information. The main difference is that these added links are not cathegorised (and thus, not filtered or searchable) and as they're not nodes, they can not be commented.

So, this content type is thought to offer information which we want to list when a taxon is selected.