Nannotax Enabling nannofossil research

USER GUIDE

You can, of course, just explore the site, but if you get confused or want to understand how it works a bit better, these notes should help. 

GEEK SYNTHESIS

Nannotax is a site being developed to allow online documentation of nannofossil taxonomy, collection of images of nannofossils, and commenting on them. It uses the content management system Drupal , as implemented within EDIT (European Distributed Institute of Taxonomy) and ViBRANT (Virtual Biodiversity Research and Access Network for Taxonomy) as a Taxonomy Information System - Scratchpads. The strengths of this system are that diverse information can be uploaded and dynamically linked to individual taxa (i.e. it can grow organically), that the commenting system allows users to readily share their own observations, and that contributors can edit and add to the content. In addition, the database structure makes Nannotax accessible as a web resource to other websites and projects. 

CREATING AN ACCOUNT AND LOGGING IN 

There is no need for an account if you just want to browse the site but to make comments, view revision history or make contributions you do need an account. Also the number of subscribed users (currently 382, May 2012) is one way we can record community interest, so you can regard it as a vote of approval. If you forget your password and/or user name then there is link for that below the log-in box, or ask Jeremy. 

WAYS TO CONTRIBUTE

There are various ways you can contribute, once your account has been created and you have logged on.

1. Add a comment to pages (all users) - this is very easy, there are comment boxes on most pages. This is especially suitable for adding subjective opinions or unpublished obsrvations, e.g. "In my experience in the Fictitious Basin the last occurence of D. surculus is unusable as a result of extensive reworking". or "I use S. neoabies for Pliocene Sphenolithus specimens <3µm long".
2. Use the forum (all users) to make any general comments on the site, suggest improvements etc.
3. Edit the text of pages (contributors only) - hit the edit button on the page, edit the text and submit. This is a bit more radical as a form of intevention but the site records changes so I can revert the text to a previous version if things go wrong. If you are adding information which is unpublished please add it as a paragraph in the remarks section and add your name in brackets after the observation. ...but the descrpitions I have given are short and doubtess flawed so if you are confident that you can improve them please do.
4. Add images (contributors only) - use the Add Image item from the menu on the left hand side. Give the image a title which inlcudes its identification and your initials. Also be sure to assign the image to a taxon (using the Nannotaxonomy dropdown menu) and to an image gallery. Age, geographic location, scale etc. can be added to the image description and obvioulsy will increase the value of the observation.
5. Add bibliographic entries (contributors only) - use create content menu item and bibliography option (but please check that the item is not in the bibliography first as eliminating duplicates is not a painless task).
6. Add a nannotalk page (all users) of specialist content, linked to particluar taxa.

NB

1. When new users register I will by default assign basic user access (which allows commenting and forum contributions only). If you would like contributor access (which allows editing of text, image upload etc.) please ask me (Jeremy Young).
2. With all contributions (including comments) there is a submit button at the bottom of the page and nothing you do is uploaded until this button is clicked.
3. Mac users - to edit the site I strongly reccomend using Firefox rather than Safari (Safari works but not as reliably and it creates messy html code).

HOW DATA IS PRESENTED - PAGE vs PANEL VIEWS

There are two main ways that content is displayed on the Nannotax site, either as panel or page views (see image below). The panel view is a 'mash up' of content from Nannotax and other sources, with different types of content being displayed in separate panels. The page view, by contrast, displays a single web page. The panel view is a useful way to aggregate a lot of content and is the main way we display information about taxa. To add coments or to edit a page, however, you need to be in page view. To switch from panel to page view, click the large blue taxon name at the top of the page, or the comments link. To switch from page to panel view, click the small blue link at the bottom of the page.

HOW TO SEARCH THE SITE

Two types of search are possible from the search box in the left hand margin. With Taxonomy search, start typing a taxon name then select from the dropdown menu, which gets shorter as you type more letters, and hit the Go! button. This takes you to the panel view for the taxon. With Simple search, enter a search term in the box and hit go. This takes you to a list of content types (taxon pages, images, bibliography entries, etc.) with your search term. The list can be very long, but usually the most relevant are near the top. Simple search is good for finding synonyms, searching on a species epithet, or looking for author names, etc. If neither of those work, you can always try Google search - add the word 'Nannotax' to a Google search and you will get a listing from the site, and Google has indexed the site comprehensively.    

NAVIGATION - TAXONOMIC MENUS

The taxonomy menus provide a quick way to navigate the site, so long as you know nannofossil taxonomy. Use the little blue + boxes to navigate through the taxonomy, then click the name of the taxon you want to see information on. If you are not familiar with the taxonomy, then this system is less useful. We intend to make hyperlinked pages to guide you through it - the Neogene site contains examples of how these will work. Click on the Nannotax logo at the top left from anywhere to return to the Home Page.   

IMAGE GALLERIES

There are >5000 images in the Nannotax database. As well as viewing these by taxon, you can browse sets of images by gallery. This works best for the Mesozoic where we have separate galleries for different publications. Click on an image title to open the image and add comments.

CITATION

Journal instructions for citing websites vary but typical citations might be:

Styzen, M. Comment on Discoaster musicus. Nannotax website. 21 Sept 2011. <http://nannotax.org/content/discoaster-musicus>

Young, J.R., Bown P.R., Lees J.A. (eds) 'Calcidiscus macintyrei' Nannotax website. 21 Sept 2011. <http://nannotax.org/content/calcidiscus-macintyrei>

Young, J.R., Bown P.R., Lees J.A. (eds) Nannotax website. International Nannoplankton Association. 21 Sept 2011. URL: http://nannotax.org

Including the date on which a page, or the site, was viewed is essential, since the site is changing continuously. If you are logged in, then you can use the revisions buttons on each page to see what the page was like at any time through its development. You can also use WebCite to create a permanent archive copy of any page or panel view from Nannotax with a unique DOI. This is probably the most robust way to cite pages and is ideal for use in peer-reviewed journals. 

NB The author given at the top of a page is the most recent contributor to the page and is often a volunteer or technical support worker; this name should not be used in citations, use instead the website editors as listed at the bottom of each page, or a comment author. We may be able to change this in future to give meaningful authorship for each page, but this is not the case yet.

Jeremy Young (jeremy.young@ucl.ac.uk)