Web revisions output requirements

VERSION 1.0

The requirements of the 3 exemplar groups.

EXEMPLAR GROUP PORTALS DESCRIPTION AND FUNCTIONAL REQUIREMENTS (VER. 1, 19 Jun 2007) PDF

The exemplar group portals are intended as a source of authoritative and integrated taxonomic and diversity information about a taxonomic group, and an instrument to facilitate dissemination of new taxonomic resarch. Their content and organization as well as their functional requirements are described in this document. The focus is on the common features of the portals although the specific needs are mentioned.

Content:
1. Users.
2. Basic organization.
3. Main uses of the site.
4. Content.
5. Functional requirements.
6. Mock screenshots.

1. Users
Every person using the portal is an user. Upon registration, users will be able to access tools and edit the content of the portal, depending on the user role assigned.

2. Basic organization
The portal requires at least the pages shown in the table, but more pages may be added as the project develops:

 

 

 

 

 

 

 

 

 

 

 

 

The items in the main menu may include among others:

  • Home
  • Names lists
  • Keys
  • Authors
  • Register (changed to Mypage when author has logged-in)
  • Log in (changes to Log out when author has logged-in)
  • Download folder

These items may also slightly vary among exemplar groups.

3. Main uses (see functional requirements)
User will be able to:

  • Retrieve information about a taxon by browsing or searching.
  • Find out about the portal authors.
  • Explore content by navigating through cross-linked information.
  • Download information.
  • Register/unregister and change personal data.
  • Log in/out

4. Details of the content elements in a taxon page.
The content elements of a taxon page have two main features:

  • they may have multiple sources stored in different places (e.g. different databases)
  • most will consist of a combination of text, images and links to files, references and other online resources.

Content elements from all exemplar groups put together:

  • Classification: links to the parent taxa (e.g. in higher rank levels)
  • Nomenclature. Consists of:
  • Name
  • Complete nomenclatural reference. TDWG standards for abbreviations will be followed whenever possible although the system should be able to handle both abbreviated and full references.
  • Authors: as with the references, TDWG standards will be followed whenever possible and both abbreviated and full references will be considered.
  • Status
  • Type information (for valid taxon and all synonyms): for names above the rank of species, the type is a species name; for names at and below the rank of species, the type is a specimen or an illustration. Information required: kind of type, designation, specimen information, locality, number, sex, depository references, links to type images from different online databases.
  • Taxa lists. Should include:
    • Names accepted under a certain taxonomic concept at all ranks to subspecies level.
    • Hybrids (to be discussed. Hybrid parents are needed)
    • Cultivars (to be discussed)
    • Misapplied names. Can be entered with their respective sources. (maybe misapplied names should go somewhere else)
    • Excluded Taxa. (At all taxonomic levels).
    • Incertae sedis and taxa not sufficiently known.
  • Synonymy, specifying the type of synonymy (heterotypic vs. homotypic vs. unknown, or subjective vs. objective). The synonym lists should be sorted (homotypic synonyms grouped together and in chronological order).
  • Protologue (original description): whenever possible, as links in the nomenclatural references to scanned images.
  • Description: the actual description of the taxon.
  • Taxonomic discussion: generally, text discussing (1) taxonomic concept used, (2) inclusion and exclusion of taxa, (3) non-acceptance of taxa.
  • Full taxonomic treatments: the taxonomic account as published (searchable text or downloadable PDF?)
  • Distribution: it may be provided as a text description, TDWG units or both. It may include links to downloadable files (e.g. georeferenced data points), a reference and maps (published dot and grid maps). Ideally, user would be able to produce maps on the fly. It should also be possible to do regional contour map from the TDWG codes. The distribution description should include status information (e.g. endemic, native, etc).
  • Conservation: a combination of text description and dynamic links to IUCN site.
  • Phylogeny: may include a combination of links to relevant DBs (e.g. treebase), an image of a tree with a brief explanation and links to references.
  • Molecular data: obtain from GenBank (webservice).
  • Uses: content variable; text as well as illustrations of products; citation of historical sources.
  • Ecology: content variable, ranging from autoecological descriptions to phytosociological data and habitat, including illustrations and photos, if available.
  • Local names: in different character sets (Unicode).
  • Other data: a flexible category to hold different subjects as needed. For example:
  • Name etymology.
  • Anatomy and micromorphology: images and links to references.
  • Palynology: images, preferably by links to databases (e.g. PalDat, Vienna).
  • Cytology: preferably by links to databases (e.g. Watanabe, Japan), additionally photos and other illustrations of documented chromosome counts; maps on the distribution of cytotypes.
  • Biology.
  • Hosts.
  • Images: illustrations and photos of habit, morphological details, characteristic specimen, etc. All images must conform to a minimum set of metada which should include keywords.
  • Bibliography: a list of all references available for individual taxa.
  • Keys: in different formats (static, downloadable, interactive). Preferably illustrated and with links to the glossary.
  • Specimens: links to GBIF and other specimen databases. Also links to specimen-based DNA databases (e.g. BGBM).
  • Alternative taxonomic concept: mostly references of that concept.
  • Data sets: links to files with data sets such as population dynamics, life histories, etc.
  • Work in progress: a list of ongoing projects.
  • Credits: a list of content contributors for the taxon (with links to individual pages) and other data sources for that taxon.
  • Download button

5. Layout of the taxon pages
The taxon pages will concentrate most of the content of the portal. Figure 1 below shows an example layout with important elements.

Figure 1. An example of a taxon page layout with the key elements.

6. Functional requirements
The functionality refers to the way the users interact with the portal and is described as a series of use cases that correspond to the main expected uses of the site.

6.1 Retrieve information about a taxon.

Browse the classification tree.
The user selects a taxon in the accepted classification, displayed as expandable/collapsable blocks with the nested hierarchy of parent-child taxa. The system goes to the selected taxon page.

Search for a taxon.
The user enters the search criteria. The application displays the result page: the list of taxa found indicating their status, with links to their individual pages. Wildcard characters will be allowed to search for partial words. The search fields may include:

  • Scientific name (text field)
  • Local name (checkbox or text field)
  • Locality (text field for locality names or TDWG codes)
  • Free keyword (text field)
  • Search image option (checkbox). See below.

Searches may be refined by combining criteria (e.g. scientific name + locality).


Search image gallery.
The user enters the search criteria and clicks the checkbox “only images” in the search bar. The system displays the results page: a thumbnail index with an option to show images according to type (i.e. photo, illustration, etc) or subject. From the thumbnail the user may go to the taxon page or to the enlarged image page which shows the image metadata. The images for that taxon may be also accessed from its taxon page.


6.2 Find out about the portal authors.

Browse the authors pages.

The user selects “Authors” from the main menu and the list of authors is displayed. The user selects a name and the system opens the page for that author, which shows contact information, expertise and contributions to the website.


6.3 Explore content by navigating through cross-linked information
All citations in the text should be a link to the full reference and a pdf of that reference if it exists.
All terms in the glossary should appear in the text as a link to that entry in the glossary.

6.4 Download content.

Download data for a taxon.
The user marks the taxon pages for download. The pages are added to a list in the download folder. In that folder the user may select the content elements he wishes to download and the download format (text, pdf, xml, etc) and download the content marked by pressing a button. The download folder will be accessible from the main menu and the taxon page.


6.5 Register/unregister

New member
The user selects register from the main menu. The system displays the registration form. The user enter the data including a username and submits the form. The system generates a password and sends it to the user by email.

Change personal data
The author selects Mypage in the menu and the system opens the form with the contact data and options to change the password and unregister.

6.6 Log in
After logging in, some menu items should change to reflect the options available to registered users (e.g. option to update content which are out of the scope of this document), including access to the tools in the cyberplatform. It is preferable to request log in only once and allow users to move between the cyberplatform and the portal.

7. Mocks screenshots (see powerpoint file)

Scratchpads developed and conceived by: Vince Smith, Simon Rycroft, Dave Roberts, Ben Scott...