Table of Contents
Data pages form the individual pieces of information that are woven together into species pages. All data pages have the same basic format, and can be used in the same way. The major data types are:
Taxon Concepts: The concept of a particular subspecies, species or higher taxon. Taxonomic concepts are used to distinguish taxonomic names (latin binomials, trinomials, and uninomials published according to one of the codes of nomenclature) from the different senses in which they are used.
Within CATE we're not especially concerned with curating multiple taxonomic hierarchies - instead, we aim to deliver a single, consensus classification. By identifying the fact that we're defining species as taxonomic concepts, we are able to distinguish our concepts from other concepts in use.
Taxonomic Names: A particular latin binomial, trinomial, or uniomial as recognised by one of the codes of nomenclature. Taxonomic names are goverend by the codes of nomenclature and are created and altered through publication.
The codes of nomenclature only really deal with the objective relationship between taxonomic names and individual organisms through explicitly stated relationships in print (for example, typification and lectotypification), and objective relationships between names (for example, homonymy and basionymy), but not wider subjective relationships (e.g. identification, determination, and subjective synonymy) which are relationships between specific taxonomic concepts.
Descriptions of Taxonomic Names and Taxonomic Concepts: Structured and unstructured facts about a taxonomic name or a taxonomic concept. Each "description" is composed of one or more elements. Each element has a subject (i.e. it is about a particular aspect of the name or concept - distribution, uses, discussion, typification, leaf length, growth habit), and can be associed with references and images.
Elements can consist of unstructured text (including markup), or can be structured: Distributional Data, Common Names, Categorical or Quantitative Data where the subjects, regions, characters and states can be drawn from user-defined controlled vocabularies.
Literature: Articles, Books, Chapters, Proceedings, Personal Communcations, Web Pages, Databases, Maps and other literature that form part of a reference, or which are the nomenclatural reference for one or more names.
Specimens and Observations: Specimens, observations, Living Beings, Fossils, Dna Samples and other derived artifacts. In addition, CATE can store information about the determination and derivation of the artifacts.
Images, Identification Keys, & Phylogenetic Trees: These data types represent binary files that are stored on the server. Only the metadata is actually stored in the database itself
CATE will process images in different formats (gif, png, jpeg, tiff, bmp), and store them efficiently as JPEG 2000 images, delivering them using an open-source JPEG 2000 image server that will deliver them in a number of formats, and sizes. Other media are delivered using in-browser plugins (such as lucid player, Xper2 and Phylowidget).
Biological Collections:Natural History Museums, Herbaria, Botanic Gardens, and Zoological Collections.
People, Teams of People, and Institutions: CATE refers to people in several places - as Authors of books and Articles, as Authorities for Names, Artists for Images, Collectors or Determiners of Specimens.
All data pages share common properties that are displayed at the bottom of each page.
Figure 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.
The date the record was created, and the username of the account which created the object are displayed at the bottom of the page. If the object has been updated, the date that it was last updated, and the user account responsible for the update are displayed as well.
Figure 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).
The citation information provides metadata about the specific record to allow it to be referenced and cited properly. The permanent URL, LSID, date of creation and modification, and the list of users who created or modified that record are displayed.
At the bottom of the page, the reference for the record is given in several common citation styles, to allow the page to be easily referenced in a printed publication.
Figure 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
Selecting the "history" link at the bottom of the page displays a list of changes to the object, the date, the title of the object, and the user account responsible for the change. Typicay, this list is sorted in date order, with the newest edits first. The versioning functionality in CATE is described in detail in a later section
Figure 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.
To the right of the page, in the collumn on the right, comments and tags are displayed. The most recent comments and most popular tags are displayed by preference. To display more tags or comments, or to search through them, select "More comments" or "More tags". If you want to add a comment to a page, or tag a page with a certain term, select "Add a comment" or "Tag this page". Comments and tags are described later.
Figure 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.
CATE aims to make high quality information available for use by taxonomists to further the understanding of the biodiversity and evolution of the group of plants or animals. By registering for an account on the website, and submitting content to CATE, you are certifying that you have the right to publish the content on the CATE site, and furthermore, you agree to license the content under one of the license selected by the project. If you don't specify a license, the default license will be displayed.
If you want to, you can choose another license for your content. If you know the copyright holder of the content, you can indicate them too. In addition, you can reference the original source(s) of the content.