CATE - Creating a Taxonomic e-Science

List of Figures

1. The front page of a CATE site. A CATE web revision consists of a taxonomic checklist (arranged hierachically on the left) and a set of species pages (accessed by clicking on the species names). The checklist, names, literature, specimens, and other types of data can be queried and browsed in isolation (by following the links in the "Explore" sub-menu, on the left). Users can log in to the revision, allowing them to annotate and tag pages, edit pages, and administrate the web revision if they have appropriate permissions.

2. Species pages consist of four major parts: The section with diagnostic and distributional data at the top, a section containing links to structured information about the taxon such as the subordinate taxa, synonyms and so on, a section containing links to structured information about the nomenclature of the taxon (objective / nomenclatural synonyms, type specimens and hybrids), and finally a section containing discussion of the nomenclature and typifictation of the taxon

3. Data pages consist of at least one page, with more depending upon the type (or category) of data being displayed. Each page displays a title, the LSID of the object if assigned, and a menu of tabs linking to other information about the object. The core data is displayed in the middle of the page. Links to metadata including information about the copyright & licensing, provenance, citation of the page, change history and alternate formats are displayed at the bottom of the page.

4. Each type of data in CATE can be searched using 'google'-style free-text searching. Type a term or terms into the search box to filter the results that are returned.

5. In addition to searching the data, you can summarize it by selecting the 'summary' tab.

6. Data pages can be edited online provided you have been given appropriate permissions. In addition to editing individual pages, there are taxonomy-specific workflows for creating new child taxa, synonymising accepted names and raising names out of synonymy. CATE tries to validate objects prior to saving them to the database.

7. CATE provides an application programmers interface that allows you to store data in the CATE site programmatically, or to access data in the CATE site from another software application. This is based on a simple RESTful protocol that exposes data as XML or JSON.

1.1. CATE records your identity in as the creator or editor of an object when you add a new object or update an existing object. This data is displayed at the bottom of the page.

1.2. By selecting the 'cite' link, you display information that would help you cite the data (in a journal article, for example, or in another web page). This includes a permanent url, any GUID assigned to the object, and the authorship. At the bottom of the page the citation information of the object is given in several standard formats (such as the APA and MLA).

1.3. CATE tracks changes to data when you edit pages online. To view when changes were made to an object, the user who made those changes, and the type of change (creation, modification, or deletion), select the "history" link

1.4. All registered users can use the comment and tag functions to annotate objects. Comments are small, free-text annotations that allow users to state opinion without directly modifying the data. Tags are keywords belonging to a controlled vocabulary that can be attached to objects and used for searching.

1.5. By default, entries on a CATE site are licenced under a default licence (usually one which prevents commercial use, but which allows reuse of the information provided that the information is attributed). If you want to include specific rights statements (regarding the licencing, use, or copyright of an item of data), they are displayed by clicking on the "rights" link. The provenance of the data can be indicated using the "sources" page which allows you to add one or more links to publications, web pages, databases, and so on.

1.6. Data can be filtered by selecting a sub-category using the drop down list. In most instances, there will be several sub-categories of data - for example, taxa can be either Accepted Names or Synonyms. Taxonomic Names can be Zoological, Botanical, Bacterial, Viral and so on. To move through the results, select the page size and then select the forward and back arrows to move through the data.

1.7. CATE uses a powerful free-text query engine to allow you to search the data in your website. Typing keywords, and using boolean and wildcard queries quickly help you find the data you want.

15. CATE is a web application which consists of four separate layers or modules. Model data objects are exchanged between layers. Cross-cutting aspects, such as security, transactions, and caching are shared across layers.