Taxon Entry Forms

Use taxon entry forms to make taxonomic descriptions and make them available as identfication keys in BIBE. This is a four phase process.

1. Copy a base form (template) for the group of objects that you are creating descriptions for. These base forms are available below. They are spreadsheets with appropriate characteristics listed in them to make description writing easier.
2. Edit the template
3. Upload the finished forms using the link at http://www3.isrl.uiuc.edu/~openkey/cgi-bin/upload.php
4. Wait up to two minutes and then search BIBE to view the results. Bibe is available at http://www.isrl.uiuc.edu/~telenature/projects/bibeDownload.html.
5. To change with the results, return to step 2 above and edit description.

Example Templates

Spreadsheets (use to make your own descriptions):

Programmer documentation for creating Spreadsheets is listed below.

Example XML and HTML Output:

The following is a list of all previously convered species pages for the Prairie Plant project. http://www.isrl.uiuc.edu/~openkey/prairieplant/Speciespages/species.html These are created through a series of operations but the first step is the description of a species description record as discussed below.

The XML files that were used to create these species pages can be found at http://www.isrl.uiuc.edu/~openkey/prairieplant/XML/. The Document Type Definition is at "http://www.isrl.uiuc.edu/~openkey/shared/Plant_description_2_21.dtd"

Notes on using these forms.

You should fill in the first several rows of the forms with Nomenclature information.

Most characteristic data can be filled in by selecting form lists on the spreadsheet. This is to help avoid spelling errors.

If there is more then one state associated with one character, for example the petals are both red and pink, the second color whould be placed on the row directly under the first color. Take as many rows as are necessary to finish the slections. Do not include nomenclature information at the beginning of rows that contain these additional states.

Numberic data from ranges also have validation functions built in. The Absolute minimum must be 0 or more if there is one. The minimum must be greater than or equal to the absolute minimum. The maximum must be greater then or equal to the minimum and so on.

Once you have created a set of taxon descriptions in the spreadsheets, save the streadsheet to your local disk to make sure you have a copy. Then convert the spreadsheet to a tab delimited format. Conversion to tab delimited files: After a file is created with all of the information that you want, save it in your native spreadsheet format using your spreadsheet “save” command. Then make a copy of the file as tab delimited. You do this by selection “file” then “save as.” There will be a “save as type” list at the bottom of the “save as” window that opens. Select “text (tab delimited file)” and save. The actual wording may vary slightly depending on your brand and version of spreadsheet.

A special note on the Prairi Plant and North Carolina collections: These collections have well over 500 characteristics per species. Microsoft excel can only handle 250 columns of data so we devided the taxon records into two different spreadsheets. When Excel exports tab delimited files it can only do so one spreadsheet at a time so you must save each file independently. This also means that you must be careful to insure that the rows in the two worksheets lineup with one another. If you have some species X on row 10 of the first spreadsheet, make sure that row 10 on the second worksheet is also species X.

Changing a taxon schema into a excel spreadsheet (for experts).

There are three files
1) Algae3.xsd : this is a schema and the most modern of this type. If we can use it this is better because it is compatible with most new business systems and biological standards as well. It has two main elements. The complex <taxon> element with the name forms and the like.

2) Algae3.dtd: This is a DTD created automatically by XMLSpy. By necessity, some information must be removed in the conversion because a DTD can not represent as much information as a schema. Only use this if you must. The DTDs are used in the current version of BIBE only because Karen could not write perl to read schemas. The Univ of north Carolina Group has been using schemas form the beginning. This is how they created their data records two years ago. They did not need to write a taxon input form. They used business tools to generate an input forms (XMLSpy). The problem with that approach is that you need to pay $2000 to use the form. Most teachers can not afford that!

3) TrentepohlisSpecies.xsl: The last item is an excel spreadsheet that I created for algae. I made it by hand so it may not be 100% consistent with the schema but I tried. Your program may find inconsistencies. Feel free to fix them just let me know here because I’ll be working on more algae species.

MAJOR problem: These are no state files in BIBE to match these characters. I think a good way to deal with this is to have other spreadsheets in the same files define the characters and the states that are used in the taxon description.

A1: Constant Green “DTD” in cell
A2: The path of where the schema is stored is places in cell
A3: Constant Red “DO NOT CHANGE ANYTHING IN BOLD
A4: Constant Yellow “Start Structure Section
The following section is an expansion of the Main “Plant_Description” Element
A5: “Plant_Description”
Lines 6-X. The names of the elements in the expanded hierarchy. Place the attribute <TYPE> right after the text for the element name followed by an “=”and then the type contents which will be “SelectionList”, “ImageSelectionList”, “String”, “Number” and maybe other things.
In out example A6 is “Taxon”
A7: “Name”
B7: Vernacular
All items on line 6 are at the same level of the hierarchy as Taxon. X is the last row in the hierarchy.
Determining row X+1 is a little difficult. You may want to do this while you expand the hierarchy because each element includes an attribute on each character called <DispalyName>. This attribute is what goes across the row to name the columns for the users. They are usually almost the character’s element name with underscores removed. Sometimes they are more complex wording.

Y is the beginning line of the description. It starts right after X’s In my example it is line 15.
The value of the attribute <TYPE> tells you what to put in the cells for this section. All items of type string you leave blank. All items of type number you restrict to numbers for user input. All items of type “SelectionList” or “ImageSelectionList” are a little more complex. These will have elements after them that are the legal state values that can go into these fields. These need to be put at the bottom of the column where this element occurs. The cells of the description sections should be pull down menus of the choices for the user. In our algae example, column E is the “Aplanospore Presence” character. The legal state values are, “Absent”, “present,” and “unknown.” These are stored in cells E36, E37 and E38 respectively. Cells E16-E32 are each filled with a Data validation pull down menu that references Cells E36-E38 to get its values. The data validation is set in excel using these steps: 1) select a cell to be validated (eg. E16), 2) select “Data” from the top row of excel commands (the row with “File,”) 3) Select “validation” from the pull down menu under “Data” You will get a data validation window. 4) In the data validation window, insure that the “settings” tab is selected. 6) In the “Allow:” dropdown pick “list” 7) In the “Source:” filed enter the cell list having the choices. In our example for Aplanospore Presence, pick “=E$36:E$39”. The E39 cell is included so that the user can enter blank. You can “drag and prop to select the list rather than type it by clicking on the piny spreadsheet next to the “Source” filed.

That is all there is to it.
There are also validations for numerics but none exist in the Algae example.

That is all there is to it! ?

Save the resulting file on the OpenKey server and mail Honyan Sun to let her know that the file is ready for processing.

Any comment or question? Contact Lilli Szafranski at (217) 333 - 7123