Guide/Characters

From the initial list of characters (Fig. 2) you can either just browse and pick one or search by typing part of its name in the blue box, choose from the auto-complete picklist and click show. Having made your choice you will be taken to a new window looking something like in figure 11. There is a heading with the character name below which you will find first the states with any figure examples. This is intended to give you immediate access to the state definitions when you view a character. Hopefully you will not have to, but you can easily remove a state (the x to the right of Fig) or add a new one in the box immediately below the existing ones: Add new state.

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� Box 1. MorphBank: Biological image databasing @ http://www.morphbank.net/

MorphBank is an open web repository of images serving the biological research community. It is currently being used to document specimens in natural history collections, to voucher DNA sequence data, and to share research results in disciplines such as taxonomy, morphometrics, comparative anatomy, and phylogenetics. MorphBank can serve as a virtual reference collection of named organisms or a resource for comparative morphological study; new use cases are continuously added. Each image in the database is associated with fully searchable text information, and images can be downloaded in several different formats.

MorphBank is open to any biologist interested in storing and sharing digital images of organisms. A major advantage of MorphBank is that images and data associated with them are maintained in a system based on open standards and free software, facilitating the development of tools for image uploading, retrieval, annotation, and related tasks. The MorphBank team is currently working on a range of such tools. The MorphBank team is also working together with other developers on connecting their software to the MorphBank system.

Any image submitted to MorphBank is meant to eventually become available free for non-commercial use. There is a suggested maximum time-limit of five years during which you can chose to either keep the image to yourself or share it with other users via groups such as the HymAToL group. Currently, we are depositing all our images for use by the Heraty Laboratories group.

As of writing there are 57,687 images in MorphBank, of which 10,708 are of Hymenoptera. Each image, or collection of images, have their own unique ID which can be used for permanent links from another source such as a publication or mx. You can also link directly to actual image files, such as a jpgformat thumbnail or a fullscale TIFF. This last option is what can be used in mx. Note, however, that any such image used for our project has to be available for everyone directly from MorphBank; either by being fully published or belonging to a group accessible by all the chalcid project members.

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If you want to add a new figure and/or edit the existing ones, here is where you click on Fig located to the right of each state definition. A window will pop up, looking something like the one in figure 12. You can change the position or remove an existing figure by using the up, down and x links. To add a figure you search for it by finding the right OTU (and optionally also Part and View). After hitting Search you will be presented with any matching images immediately below. Click on the image of your choice, drag it to the topmost elongate window and drop it there when you see it being selected as indicated by changing color to green. Your chosen image will now appear next to any already existing figures where you can add a caption and change its position. Remember to click Edit to save before clicking close at the top of the pop-up. You will then have to refresh the page in order to view any changes.

A note about the unassigned character state: this is intended as a way of documenting why a specific OTU not is assigned any state. More on that in the section on coding. Further down on the page (Fig. 11) we find information about the character, the most important being the actual Document character description. It can be accompanied by a figure which you attach/edit/remove in a manner analogous to the state figures. To do so, you click the Fig link found in the lower part of the top left menu.

In order to edit states you choose Edit while the edit expanded is better suited for editing the actual character description text. Both options are found in the menu to the top left. The former should be fairly self explanatory (even though it is strongly recommended to read the online help before attempting to merge states/codings). The latter may need some further detailing. The layout is simple, since the idea is to facilitate text editing. Instead of allowing for the use of HTML (which could impose both layout and security problems) MX gives you the option to use Textile: http://en.wikipedia.org/wiki/Textile_(markup_language). This is an easy way to get access to things like

– 9 – Fig. 10. New mx image.

– 10 Fig. 11. Single character show.

Fig. 12. State figures.

bold and italics in the character description text. E.g., the previous sentence would be written like this using textile: This is an easy way to get access to things like *bold* and _italics_ in the character description text. You can read more and find links in the above Wikipedia-link on Textile.