TAXIS 3.5 Manual

TAXIS 3.
5
manual
© <2004> Evgeniy Meyke, Bio-Tools.Net
I TAXIS 3 Help
Table of Contents
Foreword 0
Part I Whats new in TAXIS 3.5 4

1 What's new ................................................................................................................................... 5
2 Bugs fixed ................................................................................................................................... 6
3 Updates history
................................................................................................................................... 6
Part II Introduction 11
1 What is TAXIS?
................................................................................................................................... 11
2 TAXIS licenses
...................................................................................................................................
and versions 12
3 Quick start ................................................................................................................................... 12
4 Using bars and
...................................................................................................................................
menus 21
5 Using TAXIS...................................................................................................................................
windows 22
6 Working with...................................................................................................................................
tables and trees 24
Printing .......................................................................................................................................................... 25
Searching .......................................................................................................................................................... 27
Sorting .......................................................................................................................................................... 28
Customizing .......................................................................................................................................................... 28
Navigating .......................................................................................................................................................... 29
Part III Database 29

1 Opening Database
................................................................................................................................... 29
2 Creating new...................................................................................................................................
database 30
3 Changing properties
................................................................................................................................... 31
4 Backup ................................................................................................................................... 32
5 Summary ................................................................................................................................... 33
6 Sections ................................................................................................................................... 34
Part IV Taxa 35
1 Editing ................................................................................................................................... 36
2 Images ................................................................................................................................... 37
3 Samples ................................................................................................................................... 37
4 References ................................................................................................................................... 38
5 Synonyms ................................................................................................................................... 39
6 GIS ................................................................................................................................... 40
7 Import/Export
...................................................................................................................................
species list 41
8 Import/Export
...................................................................................................................................
all taxa 43
Part V Samples 44

Contents II
1 Working with...................................................................................................................................
table 45
2 Add/Delete columns
................................................................................................................................... 46
3 Images ................................................................................................................................... 47
4 GIS ................................................................................................................................... 48
5 PRINTING LABELS
................................................................................................................................... 48
Part VI Identification builder 48

1 Character tree
................................................................................................................................... 49
2 Adding new characters
................................................................................................................................... 50
3 Images for character
...................................................................................................................................
states 52
Part VII Identification 53

1 Identification...................................................................................................................................
control 54
2 Characters tree
................................................................................................................................... 55
3 Used characters
................................................................................................................................... 57
4 Remaining taxa
................................................................................................................................... 57
5 Using images
................................................................................................................................... 58
6 Taxa for selected
...................................................................................................................................
state 60
Part VIII Localities 60

1 Images ................................................................................................................................... 61
Part IX References 61
1 RIS support ................................................................................................................................... 63
2 Linking to taxa
................................................................................................................................... 65
3 Organizer ................................................................................................................................... 65
4 Input form ................................................................................................................................... 66
5 External file link
................................................................................................................................... 67
6 Importing ................................................................................................................................... 67
7 Exporting ................................................................................................................................... 68
Part X Images 68
1 Images in other
...................................................................................................................................
sections 69
2 Import/Export
................................................................................................................................... 71
Part XI GIS 72
1 Working with...................................................................................................................................
maps 72
2 Map views ................................................................................................................................... 73
3 Legend ................................................................................................................................... 74
4 Layers (themes)
................................................................................................................................... 74
Properties (parameters)
.......................................................................................................................................................... 75
Metadata (attributes)
.......................................................................................................................................................... 79

III TAXIS 3 Help
Export .......................................................................................................................................................... 79
5 Editing vector
...................................................................................................................................
maps 80
6 Taxa distribution
...................................................................................................................................
maps 82
7 Plotting samples
................................................................................................................................... 82
8 Supported formats
................................................................................................................................... 83
Part XII Tools 83

1 Slide show ................................................................................................................................... 84
2 Web site ................................................................................................................................... 84
3 Designing and
...................................................................................................................................
printing labels 85
4 Import/Export
................................................................................................................................... 88
Part XIII Appendix 88

1 Bio-Tools.Net
................................................................................................................................... 88
2 Credits ................................................................................................................................... 88
Index 89

Whats new in TAXIS 3.5 4
1 Whats new in TAXIS 3.5

References
· !!! Compliance with RIS format 63 !!! (old format references converted automatically).
· RIS import 67
· duplicates treatment
· RIS export 68
· Input form 66
· external file link 67 (automatic execution from the table and form)
· !!! Organizer 65 !!!
· print selected
· multi assign of taxa 65
· row sizing
· !!! Searching 27
· taxa autosearch 27
· Taxa links 65 toolbar changed
Taxa
· redesigned and fixed export/import
· export references 38 (RIS) for selected taxon
· !!! autosearch 27
Samples
· row sizing
· table footer shows number of records
· !!! Searching 27
Identification builder
· Collapse/Expand tree
Localities:
GIS
· Layers properties 75 dialog improved with new features
Images
· Redesigned export/import 71 .
· Path to original image file is saved in the table.
· Preview thumbnails in the table ("Image" column).
· row sizing.
· footer record number.
Other:
· !!! Autosearching 27 tables and trees
· Export/Import menu moved to from Database to Tools.
· Navigation bar 21 redesigned.
· Reader 12 access provided.
· Database summary 33 report redesigned.
· Backup 32 procedure updated.

5 TAXIS 3 Help
Help
· Help files rewritten.

· Windows Help file is provided
· Online help updated.
· F1 activated help topics.
· "What's this?" help topics on mouse click.
· PDF manual for download.
Bugs fixed 6
Updates history 6
1.1 What's new

References
· !!! Compliance with RIS format 63 !!! (old format references converted automatically).
· RIS import 67
· duplicates treatment
· RIS export 68
· Input form 66
· external file link 67 (automatic execution from the table and form)
· !!! Organizer 65 !!!
· print selected
· multi assign of taxa 65
· row sizing
· !!! Searching 27
· Taxa links 65 toolbar changed
Taxa
· redesigned and fixed export/import
· export references 38 (RIS) for selected taxon
Samples
· row sizing
· table footer shows number of records
· !!! Searching 27
Identification builder
· Collapse/Expand tree
Localities:
GIS
· Layers properties 75 dialog improved with new features
Images
· Redesigned export/import 71 .
· Path to original image file is saved in the table.
· Preview thumbnails in the table ("Image" column).

· row sizing.
· footer record number.
Other:
· !!! Autosearching 27 tables and trees
· Export/Import menu moved to from Database to Tools.
· Navigation bar 21 redesigned.
· Reader 12 access provided.
· Database summary 33 report redesigned.
· Backup 32 procedure updated.
Help
· Help files rewritten.

· Windows Help file is provided
· Online help updated.
· F1 activated help topics.
· "What's this?" help topics on mouse click.
· PDF manual for download.
Bugs fixed 6
Updates history 6
1.2 Bugs fixed

Patch 3.5.2.1 (24 Oct 2004)
· Taxa: Export/Import of taxa is fixed

· GIS: TIFF does not load if the extension '.TIF' is in capital letters
Version 3.5 (27 Sep 2004)
· Full screen image preview stretching small images.

· Update database format is executed when new database is created
· Backup procedure improved
· Systematic order menu item removed (done via Taxa->View|Customize)
· Print menu item does not appear in all sections 34
· "New database" form - Cancel button missing
· Localities: button "New child" disabled when first record is made
· Localities: Samples Taxon field is not shown (empty)
· Samples: when new taxa added - they appear in the list only after TAXIS restart
· Tools:slide show stretching small images
· Taxa: GIS: coordinates on mouse move in status bar
· References: long pause when switching to References section
· GIS: map view background color not saved
· other minor fixes
What's new 4
Updates history 6
1.3 Updates history

TAXIS 3.0
07 January 2004

7 TAXIS 3 Help
· Professional version:
· GIS section added:
· Raster layer support (TIFF, JPEG)
· ArcView Shape files support.
· Tiff files support (georeferenced).
· Full featured GIS editor (adding, editing, deleting shapes, snapping to layer,
saving to *.shp files).
· Layer (theme) legend.
· Layer properties adjustment (colors, outlines, shapes, opacity, etc.)
· Thematic maps.
· SQL query for the shapes based on metadata.
· Advanced label placement, overlap avoidance, multi-field, formatted, and
support of practically any international language character set (Chinese,
Japanese, Arabic, Russian, Hebrew, etc.).
· Connection to Taxa section (creating distribution maps)
· Connection to Samples section (plotting samples on the map)
· Map export to image (tiff, jpeg), automatically georeferences exported images
(creates world files).
· Taxa:
· GIS subsection added.
· Interactive swapping distribution maps on background vector (*.shp) and/or
raster (TIFF, JPEG) background layers.
· Samples:
· GIS subsection added.
· Interactive plotting of selected samples on the map.
· Standard version
· Printing
· Web site creation
· Adding deleting columns for samples
· Labels design (user) and printing
· Overall interface improvements
· Bugs fixed:
· Library: disabled buttons.
TAXIS 2.12
08 March 2003
· Bugs fixed:
· Image library: Customize Button visibility.
· Export Images: Export button disabled.
· Import Images: Import button disabled.
· Species list printing: authors position.
· Bugs not yet fixed:
· Printing of species list resulted in wrong Author names positioning. This option was
Temporarily removed to provide with fixed and more advanced printing controls in the
next update.
TAXIS 2.11
25 February 2003
· Bugs fixed (nothing big - you probably haven't even noticed):
· Identification Builder: when characters folder is selected, numerical states panel was
not hidden.
· Identification Builder: Selected character changed its image.
· Identification: character tree was not visible under certain conditions.

TAXIS 2.1
03 February 2003
New features:
· General:
· customizing fields in the tables
· selecting taxa in taxa table
· copying selected taxa from table
· faster taxa display and manipulation
· enhanced taxa explorer
· dropdown list with all authors for rapid taxa editing
· drag and drop taxa in the Taxa Explorer
· specimens editing (drop-down trees with taxa and locations)
· New locations table structure (tree)
· Lit table customize
· Image copy to clipboard
· redesigned ID Builder section
· improved Image Lib table
· enhanced menus
· bugs
· some view settings
· data loss upon abnormal termination of TAXIS
· import species list (authors and years not imported)
TAXIS 2.06
27 November 2001
New features:
· General:
· Database splash. Window with selected image and database information is displayed
when the database is opened.
· Main menu, toolbars, and context menus are redesigned and are more convenient to
use.
· Accessory windows (e.g. displaying images) may now be integrated into the layout so
that they always occupy all the space available. NOTE: you can now move these
windows by their frame and resize them using their lower right corner.
· Slide show (first version of it) displays taxa images full screen. The only settings you
can control for now is displaying of the taxon name and the speed of the slide show.
· Help files are updated accordingly. Read step-by-step example if you have difficulties
starting with TAXIS.
· Library (screen shot).
· This is a new section which allows recording literature references and linking them to
taxa and synonyms.
· Taxa:
· Taxa tree. Allows faster navigation through all taxa by representing them in a
hierarchical order.
· Taxa editing table can be hidden leaving just a tree to navigate.
· Taxa library. Displays list of literature references attached to selected taxon and
synonym.
· Species list printing. Includes author, year, synonyms, library listing for both species
and synonyms. It is possible to print all species in the database or only those which
are under selected taxon. The order of species may be alphabetical or systematic.
· Specifying systematic order.
· Sorting taxa by systematic or alphabetical order.
· Identification builder:
· Characters can now be organized in a form of tree with free choice of tree levels. You

9 TAXIS 3 Help
can freely group the characters at any level by simply dragging it to the new location.
· "Move" button has to be pushed down to allow item dragging.
· Characters can be grouped by folders which are similar to Windows directory
structure.
· The description can be assigned to any item of the character tree, even if it is not a
character but a grouping folder.
· Identification:
· Last identification stage is saved and reopened automatically next time you start
TAXIS.
Bugs fixed:
· Synonyms. TAXIS have not been allowing synonyms with the same names.
· Taxa. TAXIS have not been allowing taxa with the same names under different higher taxa.
· Identification builder. Assigning states to taxa.
TAXIS 2.05
30 April 2001
Bugs fixed:
· Problems with accepting some numeric values.
· Images export problem.
31 March 2001
If you were bothered by delay when TAXIS is shutting down in the previous update, it is now handled in
proper way. The "saving settings" message is displayed and the time of saving is shorter.
· 25 March 2001
· Taxa
· synonyms (list of synonyms can be recorded to any taxon)
· common names (the desired language can be set)
· preview of all images of selected taxon (thumbnails)
· possibility to add any category between genus and species and any sub specific
category. That is, now you have no restrictions in creating or using category names
and combining them with each other.
· Export:
· species list to tab separated text file (genus, species, author, year)
· all taxa to a text file (to import to another TAXIS database)
· all/selected images to files (jpeg)
· Import:
· all taxa from a text file (exported from another TAXIS database or created manually
according to designated format)
· species list from tab separated text file (genus, species, author, year)
· all/selected images files (jpeg) from selected folder
· Locations
· Comments (text)
· Coordinates (global, UTM, source)
· Images
· Save selected image to file (jpeg)
· Export/import - selected and whole library
· Database backup
· Enhanced help (now included in TAXIS update file and installs automatically. Contains the
actual database structure. )
· Automatic installer for update file.
· known and fixed in this version bugs
· when loading image into image library - images appears deformed but when cursor is
moved away and back to the record, image shoes normally.
· help menu item reference wrong file in a help folder.
· error message displayed when recording specimen with taxon name not previously

recorded.
· Taxa search didn't work from the main menu
· in identification section (Identification control) when clearing a path the message of
invalid index popup.
TAXIS 2.04 (31 January 2001)

· numeric states handling
· identification
· identification control window
· all characters window
· simultaneous display of all images of all states for selected character
· selected taxon's image in separate window
· selected state's image in separate window
· list of used characters
· remaining taxa (sorted in the order of increasing probability)
· taxon deletion handling - all linked records are deleted
· subspecific categories handling
· statistics for taxa by categories
· more functions available on the adjusting to context tool bar
· switching on and off captions on the toolbar
· minor bug fixes
TAXIS 2.03 Beta (14 December 2000)

New
· Deletion trekking (maintaining integrity)
· Password protection
· Database properties (author, name, password)
· Database summary (number of records)
· Customizing view (fonts)
· Addition of free-moving windows for displaying images, comments characters, etc.
· Searching taxa
· Characters of selected taxon (optionally: including lower taxa)
· Location 'comments' field
Fixed bugs
· 'Load from file' - disabled for taxa images
· Number of images counter for taxa
· Edit menu didn't work
· In 'Character' section taxa table had wrong popup menu
· Other bug fixes
TAXIS 2.02 Beta (24 October 2000)

Fixed bugs
· Tool bar gets disabled after visiting sections under construction
· Check of loading the existing image
· Correct deletion of the image
· Dialog appears twice when image is loaded directly into im. library
· Table sort arrows
· Pop-up menu at 'Locations' table
· Faster appearance of specimens' table
· 'Institution' field title in Specimens' table
· Taxon status change (higher taxon appears empty)
New
· Characters' section

11 TAXIS 3 Help
· Specimens of selected taxon

· States table
· Taxa tree
· Image display
· Lock button to prevent accidental editing
· Full screen preview of any image
· Rearrangement of image input
· Status bar below image with navigation arrows and image info (author, number, etc)
· Locations: Pop-up menu
· Specimens: Pop-up menu
· Taxa: specimens are displayed only for the selected taxon but not for its subitems
2 Introduction
Welcome to TAXIS Help Topics!
It is strongly recommended to go through at least the Introduction topics:
What is TAXIS? 11
TAXIS licenses and versions 12
Quick start 12
Using bars and menus 21
Using TAXIS windows 22
Working with tables 24
The online copy of this help can be accessed at

http://www.bio-tools.net/products/taxis/help/
To get support, feel free to contact Evgeniy Meyke at http://www.bio-tools.net/contact.htm
Home page:
http://www.Bio-Tools.Net
Registration page:
http://www.bio-tools.net/products/taxis/register.htm
Forum:
http://forum.bio-tools.net/
TAXIS online help:
Last updated on 31 July 2004

Bio-Tools.Net
2.1 What is TAXIS?

TAXIS is a database management system designed for biologists (professionals as well as amateurs).
The main purpose of this software is to provide an interactive and user-friendly tool to facilitate
processing of taxonomic information: keeping records of biological collections, studying collected
samples by recording characters, photographs, drawings, maps etc.
TAXIS will automatically serve as an interactive identification system that make use of recorded
characters, taxa and images. The structure of TAXIS database makes it possible to use it for any
group of organisms.

Introduction 12
Please read about TAXIS license and versions here 12 .
2.2 TAXIS licenses and versions
Licenses:
Student - undergraduate students who hasn't yet obtained their Master's degree.
Private - Individual is registering a copy TAXIS.
Organization - Organization (or individual on behalf of organization) is registering a copy TAXIS.
Versions:
Standard - includes all features except GIS components.

Professional - includes GIS component
2.3 Quick start

Create new database:
To create a new database use menu item - Database|New
In the dialog that appears, type database title, your name, database folder (it will be created in the
specified folder), and a select a folder form the directory tree in which your database folder will be
stored.
If you type a password you will be prompted to enter it each time you (or somebody else) open this
database.

13 TAXIS 3 Help
Add taxa:
You can insert new taxon by:

· Press Ctrl+N
· Press a button 'New' on a tool bar ( ) or in menu 'Edit'
· Click right mouse button and select 'new' from context menu
After you perform this action new empty line appears in the list. Fill all the fields...
...and press 'Post' ( ) using the same options as mentioned above (pressing 'Cancel' ( ) at this
stage results in the canceling of the whole record). If this was a taxon first in the list (or first in the
database) you will be prompted to specify the category of the taxon.
When you use categories like Genus, Species or Subspecies, type them exactly as they are
here (do not use lower case or abbreviations!)
After that all other taxa will be assumed to be in the same category, which means that Category field
will be filled automatically for new taxa in the same level but you can always change it to any other
category.
if Taxon has no sub (child) item use "New child item" button (Ctrl+Shift+N) to add new sub item. If you
leave the category field empty you will be prompted to enter the category of new taxon.

Introduction 14
If the parent is 'Genus' or 'Species' then categories are assigned by default 'Species' and 'Subspecies'
respectively.
'Cancel' button cancels all changes after last pressing of the 'Post' button (NOTE: Record is posted
automatically when you move away to the next record).
For instance, if you pressed 'New', typed some thing, and pressed 'Cancel' - the whole record will be
cancelled. If you are editing the existing record, pressing 'Cancel' will result in restoring the record as it
was before you started editing.
To edit the contents of the tree simply click the cell you want to edit and either press Enter or click
again to enter the cell.
To delete taxon press Delete button
Images attached to deleted taxon are not deleted (they remain in the image library 68 ).
Taxon cannot be deleted if it has sub taxa.
Distribution layer 82 for the taxon will be deleted after a prompt (if confirmed).
samples of the taxon are also deleted (the message comes out before deleting each sample and, if
cancelled, the whole process of taxon deletion aborts).
Add image to taxa:
Displays images of the selected taxon.

Images can be loaded either from files or from the image library (read more 69 ).
Double-clicking the image displays it full screen.
If there are several images, Navigator at the bottom of the image window allows browsing through
them.
Use context menu to see available options.
Thumbnail list of images is displayed on the left of the image if button is pressed.
Shows thumbnails of all images loaded for selected taxon.

Is part of the Taxa images window.
If button is pressed. Images displayed include not only images linked to selected taxon but also
images linked to sub taxa of selected taxon.
Add characters and linking to taxa:
To edit the character tree use buttons on the toolbar and context menu:

15 TAXIS 3 Help
You can group characters by their similarity using folders. There is no limit of how many items can be
included in one another.
"Move" button, if pushed down, allows you to change the placement of the characters in the tree by
dragging them to a new location.
To move the item to the uppermost level drag it lower than the last item in the tree:
Use a set of small buttons at the bottom of Character states table (+,-,post, cancel) to edit the list of
states for each character and via context menu you can load images for character states:

Introduction 16
For Numeric character the following table appears:
If you have just a value (not range) you record it into the first column. If you have a range - enter both
values.
Note: These values are assigned directly to the selected taxon (while string states are assigned to
taxon only when the check box is clicked [details]
Identification:
Identification is managed in Identification control 54 window.

At any stage you can
· go back;
· restart;
· delete used characters from any point;
· use temporal identification paths;
· check image of any taxon;
· check image of any character state;
· view all image of selected character. i.e. conduct identification by comparing images
of character states;
· check taxa of selected character state;

17 TAXIS 3 Help
Working with Samples table:
Basic procedures are described in topic: Working with tables and trees 24 .
Two special column require a bit different handling when editing.

"Taxon" and "Locality" columns take their content from relevant sections 34 of database. Choose
values from drop-down lists that appear when you click the cell content.

Introduction 18
You can also type the beginning of the Taxon or locality and the rest of the word will be automatically
located:
References:
This section is a reference manager of TAXIS. The format in which references are stored is compatible
with other bibliography managing applications (EndNote, ProCite, etc.) via RIS support 63 .
Input form 66 is provided to facilitate manual data recording.
Reference records can be linked 65 to Taxa 35 . Table has common properties 24 with other TAXIS
tables.
"Organizer 65 " can be used to have more control over you references.

19 TAXIS 3 Help
Most important commands can be accessed via context menu (in addition to Main menu and toolbar):
· References 61
· RIS support 63

Introduction 20
· Taxa 35
· Linking references to taxa 65
· Synonyms 39
· Importing 67
· Exporting 68 Working with tables 24
·
· Searching 27
· Sorting 28
· Customizing 28
Printing 25
GIS:
GIS section of TAXIS is responsible for handling geographic data (supported formats 83 ).
The basic idea behind the implementation of GIS features in TAXIS is to facilitate the work for
researchers dealing simultaneously with biological and geographic data. TAXIS provides a way to link
taxonomic database entities and geographic maps in one application. Creating distribution maps 82 is
possible without leaving TAXIS and using the familiar tools available in other GIS applications.
Samples can be plotted 82 on the map on-the-fly while browsing through specimen data or taxonomic
data plotting all specimen records for selected taxon.
Handling of vector maps is organized in the same way as in popular GIS applications. Vector and
raster files can be loaded as map layers 74 . View properties can be adjusted for each layer and the
whole map view can be saved and opened later.
Built-in full featured editor allows creating and editing of vector layers without leaving TAXIS but in the
same time retaining the compatibility with other GIS applications.

21 TAXIS 3 Help
2.4 Using bars and menus

Commands of the program are accessible through:

Introduction 22
Navigation bar allows

browsing through main
sections 34 of the program:
Main menu provides access to ALL options available at the moment:
Toolbar show major important commands to be easily accessed:
Context menus depends on the place on the screen where you click
right mouse button:
2.5 Using TAXIS windows

Additional information, such as images, synonyms, taxa samples, etc. is located in special windows:

23 TAXIS 3 Help
These windows can be moved, resized, and aligned.

You can move the window by dragging it by its edge.
To resize the window use small darker area at the lower right corner:
These windows can be "aligned" inside the area where they are situated. The align of the windows can
be changed through the context menu:

Introduction 24
This means that each window can either be "floating" (it can have any shape and situate wherever
inside the area):
Possible "Align" options:

· None: window can be moved to any place and have any size.
· Client: window occupies all available space and resized if neighbouring components are
moved or resized.
· Top: window is aligned to the top of available area.
· Bottom: window is aligned to the bottom of available area.
· Left: window is aligned to the left of available area.
· Right: window is aligned to the right of available area.
If you have several windows at once you can combine these options for each window to use the space
more affectively.
2.6 Working with tables and trees

Please read this chapter to get familiar with common properties of data trees and tables throughout the
program. The same approach to basic functions makes using the software easier and more intuitive.
Trees have usually additional commands - Collapse all items and Expand all items:
Printing tables and trees 25

Searching contents 27
Sorting columns 28
Customizing visible fields 28

25 TAXIS 3 Help
2.6.1 Printing
In addition to specialized printed reports like Labels 48 TAXIS offers the possibility to print the contents
of main tables and tree as you see them on screen.
This means that all visual changes that you care to make to the tables' (trees') layout, such as
customizing 28 , sorting 28 , changing column width, etc. is replicated on paper with 100% accuracy.
Access main printing function in the menu:
Database|Print
Database|Print preview

Introduction 26
Database|Page setup

27 TAXIS 3 Help
2.6.2 Searching
Make sure that the cursor is in the column that you intend to search and you are not in editing mode of
cell contents.
Start typing the string that you wish to locate. Found combination is highlighted with different color and
table (or tree) is scrolled to located item.
If the combination you typed is repeated in other records, press Ctrl+Enter to cycle through repeating
combinations.

Introduction 28
Same method of searching is used in Samples 44 table.
2.6.3 Sorting
To sort the column click the column title. Small arrow indicating the sort direction will appear.
To change the direction of sorting click again.
To sort against several columns hold Shift and click.
2.6.4 Customizing
Moving columns
Click, hold and drag the column header to a new position:
Choose View|Customize to see the window with the list of hidden columns (now you can drag
columns to and from the list to show/hide columns):

29 TAXIS 3 Help
2.6.5 Navigating
Several tables have a Navigator control. It can be represented in two styles:
- allows editing of the table and appears usually at the bottom of the table
- navigation only
Main tables have buttons in the toolbar:
3 Database
These series of topics covers TAXIS database handling and other general issues.
TAXIS stores data in a relational database in Paradox format tables (Paradox is not required).
Borland Database Engine (BDE) required for database access is installed automatically with TAXIS.
TAXIS database is therefore consists of many files (tables, indices) that are situated in the same
folder. So 1 database = 1 folder.
Backup 32 procedure creates a copy of the whole folder.
When moving or copying the database make sure you copy all files from the folder.
3.1 Opening Database

To open previously created database use Database|Open. The database that was opened last before
you close the program opens automatically next time. You can also reopen previously opened
databases by choosing the title in end of the Database menu.

Database 30
3.2 Creating new database

To create a new database use menu item - Database|New

31 TAXIS 3 Help
In the dialog that appears, type database title, your name, database folder (it will be created in the
specified folder), and a select a folder form the directory tree in which your database folder will be
stored.
If you type a password you will be prompted to enter it each time you (or somebody else) open this
database.
3.3 Changing properties

To change database description (database author, database name, password, image) go to
Database|Properties:
Following window will allow to set database properties:

Database 32
Image to display in database splash window is selected from image library 68 .
3.4 Backup
Copies the contents of the database folder to specified destination folder.
Access this function through Database|Backup:
Select the folder in which the backup folder will be created:

33 TAXIS 3 Help
Backup progress is shown:
3.5 Summary
Summary of the number of records in the database can be checked in Database|Summary:
The report can be copied as normal text. Values are tab-separated, so that it pastes better to
applications like MS Excel.

Database 34
3.6 Sections
Sections of the program include:

35 TAXIS 3 Help
Taxa 35 Samples 44 Identification builder Identification

48 53
Taxonomic tree Samples Characters and Actual

records states for use in identification
Identification session
Localities 60 References 61 Images 68 GIS 72
Localities Reference Image library

Geographic
records library Information
System
To navigate through the program's sections use navigation bar 21 .
4 Taxa
This is the main section 34 of the program which all the other section build on.
Here you input taxonomic information in hierarchical manner.
Taxa are arranged in the form of tree in which levels and nodes are arranged with no fixed pattern.
Read more about working with tables and trees 24 .

Taxa 36
4.1 Editing
You can insert new taxon by:
· Press Ctrl+N
· Press a button 'New' on a tool bar ( ) or in menu 'Edit'
· Click right mouse button and select 'new' from context menu
After you perform this action new empty line appears in the list. Fill all the fields...
...and press 'Post' ( ) using the same options as mentioned above (pressing 'Cancel' ( ) at this
stage results in the canceling of the whole record). If this was a taxon first in the list (or first in the
database) you will be prompted to specify the category of the taxon.
When you use categories like Genus, Species or Subspecies, type them exactly as they are
here (do not use lower case or abbreviations!)
After that all other taxa will be assumed to be in the same category, which means that Category field
will be filled automatically for new taxa in the same level but you can always change it to any other

37 TAXIS 3 Help
category.
if Taxon has no sub (child) item use "New child item" button (Ctrl+Shift+N) to add new sub item. If you
leave the category field empty you will be prompted to enter the category of new taxon.
If the parent is 'Genus' or 'Species' then categories are assigned by default 'Species' and 'Subspecies'
respectively.
'Cancel' button cancels all changes after last pressing of the 'Post' button (NOTE: Record is posted
automatically when you move away to the next record).
For instance, if you pressed 'New', typed some thing, and pressed 'Cancel' - the whole record will be
cancelled. If you are editing the existing record, pressing 'Cancel' will result in restoring the record as it
was before you started editing.
To edit the contents of the tree simply click the cell you want to edit and either press Enter or click
again to enter the cell.
To delete taxon press Delete button
Images attached to deleted taxon are not deleted (they remain in the image library 68 ).
Taxon cannot be deleted if it has sub taxa.
Distribution layer 82 for the taxon will be deleted after a prompt (if confirmed).
samples of the taxon are also deleted (the message comes out before deleting each sample and, if
cancelled, the whole process of taxon deletion aborts).
4.2 Images
Displays images of the selected taxon.
Images can be loaded either from files or from the image library (read more 69 ).
Double-clicking the image displays it full screen.
If there are several images, Navigator at the bottom of the image window allows browsing through
them.
Use context menu to see available options.
Thumbnail list of images is displayed on the left of the image if button is pressed.
Shows thumbnails of all images loaded for selected taxon.

Is part of the Taxa images window.
If button is pressed. Images displayed include not only images linked to selected taxon but also
images linked to sub taxa of selected taxon.
4.3 Samples
Samples of selected taxon can be view by choosing View|Samples

Taxa 38
List of samples is updated as you move to the next taxon.

Samples are displayed only those that are assigned directly to the selected taxon (i. e. if the genus is
selected the samples assigned to the species of that genus are nor shown).
4.4 References
Literature references recorded in Library 38 and linked to selected taxon, can be view in Taxa section
using a button "Show library" on the toolbar or in context menu 21 .
Taxa library window is not for editing references but only for viewing those records which are linked to
selected taxon.

39 TAXIS 3 Help
These references can be exported to other Bibliographic application via RIS export 63 :
4.5 Synonyms
Use button on a toolbar to hide/show taxa synonyms window .

Use navigator at the top of the window to navigate and edit synonyms list. Synonyms are recorded to
the selected taxon.
Also, using tool bar or context menu 21 you can show/hide Literature references for synonyms.
References are linked to taxa and synonyms 65 in References 61 section.

Taxa 40
4.6 GIS
The GIS window in Taxa section serves a specific purpose of displaying a distribution map for selected
taxon (how to create distribution map 82 ).
Distribution layer is loaded dynamically into GIS view as the taxon is selected (if it has been created
before).
GIS view in Taxa section does not allow for editing (refer to main GIS section for editing 72 ) but you
can load different background layers (see here for file formats 83 ).
Distribution layers are stored under [Your Database Folder Path]\GIS\distributions in standard
shape file format (.shp) using taxon's internal ID number for the file name (you can use Layer|Export to
SHP command to save selected distribution under different path and name, but the original should
remain as it is used for automatic loading to the Taxa GIS view).
As for the rest, Taxa GIS view functions as normal GIS view with all parameters adjustable and other
commands applicable.

41 TAXIS 3 Help
· GIS 48
· Working with maps 72
· Map views 73
· Layers 74
· Taxa distribution maps 82
· Plotting samples 82
· Supported formats 83
· Using TAXIS windows 22
4.7 Import/Export species list

Exports/imports list of species to/from a text file.
Text file must contain fields in the following order:
Genus->Species->Author->Year
Can be used to import to another TAXIS database.
Can also be opened in other programs like MS Excel, MS Access, etc. which can import tab delimited
data.

Taxa 42
Example of exported Text file:
Genus SpeciesAuthor Year Comment

Parnassius tianschianicus Oberthür 1879 comments for this species
Parnassius staudingeri A. Bang-Haas 1891 comments for this species
Parnassius simonius Staudinger 1889 comments for this species
Parnassius simo Gray 1853 comments for this species
Parnassius patricius Niepelt 1911 comments for this species
Parnassius mnemosyne Linnaeus 1758 comments for this species
Parnassius maximinus Staudinger 1891 comments for this species
Papilio machaon Linnaeus 1758 comments for this species
Parnassius loxias Püngeler 1901 comments for this species
Parnassius jacquemontii Boisuval 1836 comments for this species
To export species list choose Tools|Export species list, select destination folder:
To import species list choose Tools|Import species list. When text file is selected it is checked for
correct format and preview in a form of table. Click Import to import marked "Import" records
(duplicates are not imported). Imported records are marked "Imported" after the procedure:

43 TAXIS 3 Help
4.8 Import/Export all taxa

Exports all taxa in a form of tree to a text file.
Can be used to import to another TAXIS database or in your text editing program for further use.
Example of exported Text file:
Papilio/Genus/Linnaeus/1758/
aleksanor/Species/Esper/1800/
machaon/Species/Linnaeus/1758/
Parnassius/Genus/Latreille/1804/
actius/Species/Eversmann/1843/
apollo/Species/Linnaeus/1757/
apollonius/Species/Eversmann/1843/
autocrator/Species/Avinoff/1913/
boedromius/Species/Püngeler//
cardinal/Species/Grum-Grshimailo/1887/
charltonius/Species/Gray/1853/
delphius/Species/Eversmann/1843/
honrathi/Species/Staudinger/1882/

Taxa 44
To export all taxa choose Tools|Export taxa, select destination folder:
To import taxa from such text file choose Tools|Import taxa. When text file is selected it is checked for
correct format and preview in a form of table. Click Import to import marked "Import" records
(duplicates are not imported). Imported records are marked "Imported" after the procedure:
5 Samples
Adding and deleting of the samples is in most part the same as adding and deleting taxa 36 . The
insertion of new sample results in copying the information from the currently selected sample.
To hide or show the image use tool bar button or context menu items 'Images'. Adding and deleting
images works in the same way as in Taxa 37 .
To specify the locality and taxon information for the sample record use drop down lists of respective
columns or start typing and auto-complete function will finish the text if the item is in the database.
Read more:
Working with table 45

45 TAXIS 3 Help
Add/delete columns 46
Images 47
GIS 48
Printing labels 48
Working with tables and trees 24
5.1 Working with table

Basic procedures are described in topic: Working with tables and trees 24 .
Two special column require a bit different handling when editing.

"Taxon" and "Locality" columns take their content from relevant sections 34 of database. Choose
values from drop-down lists that appear when you click the cell content.

Samples 46
You can also type the beginning of the Taxon or locality and the rest of the word will be automatically
located:
5.2 Add/Delete columns

You can add and delete columns in Samples sections (please, distinguish from hiding/showing column
through Customize 28 ).
Choose from View|Columns:

47 TAXIS 3 Help
Adding field:
Deleting field (columns that are not to be deleted will cause Delete button to be disabled if selected):
5.3 Images
You can load images to selected sample.
Working with Images for Samples is very similar to that for Taxa 37 .

Samples 48
5.4 GIS
Automatically plots sample on the map view if Coordinate fields (Coord_x, Coord_y) are not empty.
To add coordinates for each sample manually - edit columns "Coord_x", "Coord_y".
To add coordinates for each sample from the map go to GIS section 82 .
5.5 PRINTING LABELS

Read about printing labels in Tools chapter 85 .
6 Identification builder
In this section you can build the tree of characters 49 , link them to taxa 50 and load
images for character states 52 .

49 TAXIS 3 Help
6.1 Character tree

Characters are organized in a form of tree which may contain following items:
· Folders
· String characters
· Numeric characters
Before building a tree you have to carefully think through the organization of the tree. It is good to have
it on paper first to get the whole picture. Although, you can start filling the characters in right away,
because it is quite easy to make changes.

Identification builder 50
6.2 Adding new characters

To edit the character tree use buttons on the toolbar and context menu:

51 TAXIS 3 Help
You can group characters by their similarity using folders. There is no limit of how many items can be
included in one another.
"Move" button, if pushed down, allows you to change the placement of the characters in the tree by
dragging them to a new location.
To move the item to the uppermost level drag it lower than the last item in the tree:
Use a set of small buttons at the bottom of Character states table (+,-,post, cancel) to edit the list of
states for each character and via context menu you can load images for character states:

Identification builder 52
For Numeric character the following table appears:
If you have just a value (not range) you record it into the first column. If you have a range - enter both
values.
Note: These values are assigned directly to the selected taxon (while string states are assigned to
taxon only when the check box is clicked [details]
6.3 Images for character states

For each characters state (string characters) you can load image (either from the library or from disk).

53 TAXIS 3 Help
7 Identification
Identification is managed in Identification control 54 window.
At any stage you can
· go back;
· restart;
· delete used characters from any point;
· use temporal identification paths;
· check image of any taxon;
· check image of any character state;
· view all image of selected character. i.e. conduct identification by comparing images
of character states;
· check taxa of selected character state;

Identification 54
7.1 Identification control

New characters are added to identification to the point where the cursor is:
This means that at any point you can go back and go to the new direction. Remaining taxa 57 are
shown depending on the cursor position in the Identification tree.
The list of used characters 57 and the list with remaining taxa 57 are updated each time you move the
cursor from one node to another.
Use Character tree 55 to add characters to identification.
Identification control window has its own tool bar with following buttons:
· - Add selected character to current session.

55 TAXIS 3 Help
· - Expand all nodes in character tree.

· - Collapse all nodes in character tree.
· - New identification path. Results in adding new root item with date and time (later I will add
the possibility to save the identification for future use).
· - Delete node. Has two options - delete node with all children or just cut the node from the
tree keeping children.
· - Clear all identification.
· - Strip the current identification path of all branches which are not currently used (only the
selected item and its parents are kept).
· - Expand all nodes in identification tree.
· - Collapse all nodes in identification tree.
7.2 Characters tree

Characters are organized in the form of tree using 'Group' field to combine related characters:

Identification 56
Button 'Go' or double clicking on the string character state adds selected character state (for String
characters) to identification control window 54 as a child of selected item. Numeric characters are
handled in a different way:
If numeric character is selected (it has no subitems) the small edit box with measurement units
appears. After typing the number press 'Go' button to add the value to identification control:

57 TAXIS 3 Help
After adding new character to identification control the cursor shifts to last added character state and
used characters list 57 and remaining taxa list 57 are updated automatically. Used character is
marked by red color:
to indicate that it has been used.
7.3 Used characters

This list updates each time the cursor in identification control window 54 shifts.
Selecting one of the used states results in following changes:
· The character is located in Character tree 55 and this character is scrolled in view.
· The states' image window updates.
· The character images window updates.
7.4 Remaining taxa

This list updates each time the cursor in identification control window 54 shifts.
Selecting one of the taxa displays its image in taxa images window.

Identification 58
7.5 Using images

Use menu View to turn on and off images windows:
When taxon is selected in the remaining taxa 57 list its image is shown in a separate window:
When character is selected in the list of used characters 57 or in the Character tree 55 images of all
character states of the character are shown in a separate window:

59 TAXIS 3 Help
When character state is selected in the list of used characters 57 or in the Character tree 55 its
image is shown in State images window:

Identification 60
7.6 Taxa for selected state

If you press the State taxa button on the tool bar, window with the list of taxa for selected character
state appears:
8 Localities
This section holds database of localities.
Localities recorded here are used in Samples 44 section when entering sample's locality data.
The locality tree is constructed with no limitations on number of categories and sub items.

61 TAXIS 3 Help
8.1 Images
For each locality node in the tree (regardless of its category) you can load an image from the Image
library or from the file on disk.
9 References
This section is a reference manager of TAXIS. The format in which references are stored is compatible
with other bibliography managing applications (EndNote, ProCite, etc.) via RIS support 63 .
Input form 66 is provided to facilitate manual data recording.
Reference records can be linked 65 to Taxa 35 . Table has common properties 24 with other TAXIS
tables.
"Organizer 65 " can be used to have more control over you references.

References 62
Most important commands can be accessed via context menu (in addition to Main menu and toolbar):
· References 61
· RIS support 63

63 TAXIS 3 Help
· Taxa 35
· Synonyms 39
· Importing 67
· Exporting 68
· Working with tables 24
· Searching 27
· Sorting 28
· Customizing 28
Printing 25
9.1 RIS support

To provide compatibility with widely used bibliographic managers (e.g. RefMan, EndNote). TAXIS
offers the possibility to export 68 and import 67 RIS format files.
This means that you can continue using you favorite bibliographic application and when needed export
references to RIS format and than import them to TAXIS database.
To ensure full compatibility with RIS format the structure of References section is fixed. You can read
more about RIS format here (from Reference Manager website).
Reference "type" field has following predefined values to cover whole range of possible values:

References 64
· References 61
· RIS support 63
· Taxa 35
· Synonyms 39
· Importing 67
· Exporting 68
· Working with tables 24

65 TAXIS 3 Help
· Searching 27
· Sorting 28
· Customizing 28
Printing 25
9.2 Linking to taxa

Each reference can be linked to series of taxa and synonyms.
To link taxon to reference requires these steps:
1. Select reference (or set of references with either Ctrl or Shift)
2. Select taxon in the tree
3. Press "Link taxon" button in the Linking toolbar. This button is disabled if selected taxon is already
linked.
4. (Optional) Enter text comments in the empty field in the list of linked taxa. This info will refer only
to this link.
To link synonyms to reference repeat the same steps except that after selecting taxon select its
synonym from the list and press "Link synonym" button.
Linking toolbar:
9.3 Organizer
Represents a tree that helps group references into arbitrarily created categories.
Use context menu to edit the Organizer's tree:
You con show/hide Organizer using View|Organizer

References 66
9.4 Input form

Input form for the references table.
Navigator at the bottom allows browsing and editing of the records.

67 TAXIS 3 Help
9.5 External file link

External file link allows to link your reference records to real files on your computer.
You can enter the path to the reference file in the column 'File' (if it is not visible use Customize 28 ).
- opens file select dialog.

- if the cell is not empty, runs the file with associated application (e. g. *.pdf files will open in Adobe
Acrobat if it is installed in the system).
9.6 Importing
Imports references form RIS 63 files.
Access this option via Tools|Import references (RIS):
Navigate to the file that is compatible with RIS format. When the file is selected and it has either *.ris or
*.txt (enable "Include *.txt files" option) extension, the contents are shown in the memo:

References 68
9.7 Exporting
Exports references to RIS format 63 text files.
You can select destination folder and the file name for exported references.
Exported file is saved with *.ris extension.
RIS formatted file can be used by other compatible bibliographical applications.
10 Images
All images loaded from files (for taxa 37 , samples 47 , character states 52 , and localities 61 ) are
stored in the image library. Image is actually copied from the source file, so that this file is not needed
any further.

69 TAXIS 3 Help
Here you can add image information (author, data, time, comments, image type, subject view) and
keep track of the image source as every image is assigned unique id number.
All objects linked to a selected image 69 can also be checked from image library.
You can also use image library to preload all the images you intend to use and when assigning the to
the item just select 'Load from library'.
To load large amount of images from selected directory and export large amount of images from
image library use Import/export 71 features
10.1 Images in other sections

Image of selected taxon is displayed in a separate window, which can be hidden or opened (the last
condition and position is saved). Navigation buttons and some additional information is displayed at the
bottom if the image window (author, date, image number in the library)
Use context menu or tool bar button to toggle image window:

Images 70
Use context menu (click right mouse button) to add, and delete taxon image (NOTE: when you delete
a reference to the image, the image itself stays in the image library 68 ):
Load from file - Opens a dialog to select an image file. After you click 'Open' images is added to the
image library. Reference to this image is added to current taxon. If the image is present already in the
library 68 , the warning message pops up and the reference to this image is added to current taxon.

71 TAXIS 3 Help
Load from library - Create a reference to already loaded image.

Delete reference - deletes reference to the image but keeps the image in the library.
The number of images of each taxon is displayed in additional column:
Images can be attached to any taxon. To force the display of images assigned to lower taxa use
following button on the tool bar or in the context menu. Pressed button makes possible to have all the
images of lower taxa (you need to scroll through them using navigation buttons), if not pressed images
are shown only those assigned directly to selected taxon.
For example, if two images are assigned to two species of one genus and one to that genus, the
selection of the genus (with 'Include sub images' button pressed) will result in three images. Only one
image will be seen if select the genus with this button not pressed.
10.2 Import/Export
Use Tools|Export all images to files and Tools|Import images from selected folder:

GIS 72
11 GIS
GIS section of TAXIS is responsible for handling geographic data (supported formats 83 ).
The basic idea behind the implementation of GIS features in TAXIS is to facilitate the work for
researchers dealing simultaneously with biological and geographic data. TAXIS provides a way to link
taxonomic database entities and geographic maps in one application. Creating distribution maps 82 is
possible without leaving TAXIS and using the familiar tools available in other GIS applications.
Samples can be plotted 82 on the map on-the-fly while browsing through specimen data or taxonomic
data plotting all specimen records for selected taxon.
Handling of vector maps is organized in the same way as in popular GIS applications. Vector and
raster files can be loaded as map layers 74 . View properties can be adjusted for each layer and the
whole map view can be saved and opened later.
Built-in full featured editor allows creating and editing of vector layers without leaving TAXIS but in the
same time retaining the compatibility with other GIS applications.
11.1 Working with maps
After you have one or more layers loaded into the view 73 you can do the following:
· Save map view configuration in project file 73 (*.ttkgp)
· Add/delete layers 74
· Create new layers 80

73 TAXIS 3 Help
· Change layer properties 75
· Browse and edit metadata 79
· Edit vector layers 80
· Zoom
· Options|Zoom
puts the map into Zoom mode and you can use the mouse pointer to zoom in (draw a
rectangle from upper left to lower right direction)
· View|Full extent
zooms out to the full extent of the map
· View|Zoom to layer
zooms to the extent of selected layer
· View|Zoom to selected
zooms to the extent of the selected shape
· Select
(Options|Select) Now you can use the mouse pointer to select a shape on the currently
selected layer.
· Scroll
(Options|Scroll) Now you can use the mouse pointer to scroll the map in any direction.
· Create distribution maps 82
This is a tool for linking distribution layers to taxonomic information stored in the database.
· Plot samples 82
Dynamically plot samples into the map view.
11.2 Map views

GIS view in TAXIS has two components: Legend 74 and Map. Legend displays all layers 74 that are
loaded to the map. You can change the appearance of each layer by double-clicking its name (or
Layer|Properties command).
Information about layer collection is stored in .ttkgp Project file. It contains all the information about
each layer and its configuration including thematic mapping and SQL commands.
Use GIS menu items to access functions dealing with map view.
· New project - Creates new map view, which is represented by a text (Project) file with *.ttkgp
(TAXIS GIS) extension. This file contains information about all layers in the view. By default
when you first open TAXIS GIS section it is already represented by the file stored in current

GIS 74
database folder under GIS/prj.ttkgp.

· Open project - opens saved view.
· Save project - saves current view.
· Save project copy - saves a copy of current view.
· Save as image - saves current view to image file (tiff, jpeg). Note the created image file is
georeferenced and can be loaded back to the view as raster.
· Import distribution - imports existing distribution map to selected taxon (read more 82 about
distribution maps)
· View properties - currently only background color for the view.
11.3 Legend
Legend control shows layers 74 loaded into the map view 73 .
Selecting the layer with mouse activates it for further actions (removing, properties, etc. )
Double-clicking the layer name activates Layer Properties 75 dialog.
Layer can be dragged to change its position in the map view in relation to other layers.
11.4 Layers (themes)

Map view 73 displays maps arranged in layers. Each layer is listed in the legend 74 and (in most
cases) represents a file on disk 83 . Read more about layers in Layer properties 75 .
Use Layer menu items to access functions dealing with selected layer's properties.

75 TAXIS 3 Help
· New layer - Loads existing file to the view (vector or raster - select the file type in the Open
dialog).
· Load layer - creates a new vector layer (polygon, polyline, point) and loads it to the map view.
· Remove layer - removes selected layer from the view.
· Properties 75 - activates Layer properties dialog.
· Metadata 79 - shows DBF file content of SHAPE file 83 .
· Export to SHP 79 saves selected vector layer to SHAPE file 83 .
11.4.1 Properties (parameters)

Double-click on the layer's name in the legend 74 opens up a dialog via which you can control the
appearance of the layer in the map.
All of the parameters available in this dialog are stored in the project file 73 and do not affect the actual
data in the layer (e. g. SHP file itself).
You can control all aspects of layers appearance, include labels, charts, rendering, querying (based on
metadata 79 ).

GIS 76

77 TAXIS 3 Help

GIS 78

79 TAXIS 3 Help
11.4.2 Metadata (attributes)

As currently only SHP file format is supported in TAXIS from vector formats the Metadata window
displays the contents of the .dbf file of the selected SHP layer.
You can edit the contents of all fields as well as add new and delete fields.
"Auto select" function automatically highlights the corresponding shape in the map view. In Select
mode when working with map automatically scrolls metadata table to corresponding record.
11.4.3 Export
This command saves a copy of a SHAPE file 83 of selected layer. It is especially useful when working
with dynamically mapped Taxa distributions 82 that are stored in default folders under internal unique
ID names and Sample locations 82 which coordinates are stored in Samples table 44 .

GIS 80
11.5 Editing vector maps

You are able to edit only vector layers.
To start editing:
· Select a vector layer in the legend.
· Enable editing via Edit|Enable editor
Editor bar becomes available:

81 TAXIS 3 Help
· (you are automatically in Select mode now) click on the shape you want to edit
, or
· Select Edit|Add shape and click the area of the map to add a first node of the shape (what kind
of shape is created depends on the type of the layer - polygon, line, or point).
· (now you are automatically switched to "Edit|Vertex edit" mode which allows you to edit nodes).
· you can continue adding nodes to create the kind of shape you want.
· to change the position of the node simply click and drag it to new position.
· to delete a node click on it once.
· in the layer of type Point, single node represents a Point shape itself.
During editing Undo/Redo buttons available.
To enable snapping of the nodes (moved or inserted) to the nodes of the shapes in the same or

GIS 82
different layers select Edit|snap|Snap layer.

This would mean that when the node is moved or inserted it automatically "snaps" to the closest node
of the "snap layer" within "snap margin".
Edit|Save commands allow you to either save/revert individual layers or all layers that have been
edited.
To stop editing click the "Edit|Enable editor" button again.
11.6 Taxa distribution maps

To create a distribution map for a taxon do the following:
· In the GIS section of TAXIS create a desired map view with necessary layers.
· Click "View|Show taxa" which will display the Taxa tree.
· Select the taxon you want to create a distribution map for.
· Click "View|Add taxon layer" . This step actually creates a new SHAPE file which is stored
in [your database folder]\GIS\distributions\[taxon ID].shp (if the distribution has been
already created before, it just loads into the view form the same path).
· Now you can work with this layer just as with any other vector layer.
· You can load as many distribution maps as you like.
In Taxa section of TAXIS, when the GIS view is open, distributions created here will load into the view
automatically as you browse through taxa (read more here 40 ).
11.7 Plotting samples

To plot the samples of selected taxon on the map do the following:
· In the GIS section of TAXIS create a desired map view with necessary layers.

83 TAXIS 3 Help
· Click "View|Show taxa" which will display the Taxa tree.

· Click "View|Show samples" which will display the table of samples for selected taxon and
automatically plot all the samples that have the coordinate record (X_coord and Y_coord
columns in the Samples Section 44 of TAXIS).
· Browsing through taxa will dynamically plot appropriate samples to the map.
Each time the samples are plotted, the temporary shape file is created. You can save the current
Samples layer to another location via "Layer|Export to SHP"
Another useful tool is "View|Coordinate picker" which allows you to record the coordinates to the
selected specimen by just clicking the map at any point on the map. To record the coordinates
manually - refer to Samples GIS 48 .
11.8 Supported formats

Currently these are the file formats supported by TAXIS GIS module:
· ESRI SHAPE file (.shp) for vector format.
· TIFF (georeferenced) for raster format.
12 Tools
main menu: Tools
These tools are available:
Slide show 84 - full screen slide show

Tools 84
Web site 84 - exports database contents to HTML

Labels 85 - design and generate label sample labels from database
Import/Export routines 88 - depends on the current section 34
12.1 Slide show

Runs full screen slide show with selected options.
12.2 Web site

Tools|Create web site command displays the following window where you can customize the look of
the created web site. It uses Cascading Style Sheet (.css) file that you can customize your self, which
is stored in the root folder of created web site (make sure you back up changed css file under another
path, because it can be overwritten next time you export to web).
Fill in the following form and press Export:

85 TAXIS 3 Help
12.3 Designing and printing labels

Tools|Design and print Labels command allows you to visually design labels for samples.
When you click this menu item the Designer window is displayed. By default there is a simple design
already loaded but you can change it and save under the same or another name. You can design
several layouts and save them under different names.
If you haven't had an experience with such reporting tools before it may be very unclear how to handle
it, but once you get used to the concept it will become a very useful tool.
Quick start
As this reporting tool is a third-party product (FastReports Inc) it is provided "as is" and many of its
functions are not discussed here so you may explore at your own risk. I will describe the basic
capabilities needed get used to the idea and start working.

Tools 86
First, click File|Preview to see what the current layout looks like on printed on paper (print preview
window will open).

87 TAXIS 3 Help
How it works
If you look at the designer window you will see that there is only one "label" and when you click preview
- you get as many labels as sample records. The idea is that you design the label ones and then it is
multiplied as many times as there are sample records.
You can click on different parts on the designer page and see that the properties of selected object are
displayed in Object Inspector window (Tools|Toolbars|Object Inspector). You can modify all the
properties of selected object in Object Inspector. By dragging with your mouse, you can change the
position and size of the objects.
Deletion is easy - just select and press Del.
Adding a new object can happen in different ways. You can select some object on the left hand toolbar,
for instance a Memo (first one) and click on the page to place it there. Depending on the type of the
object selected you may get different events when you place it on the page. In this case a window will
be displayed where you can enter the contents of this Memo. To edit the contents later, just double
click the object.
Placing the object on so-called "band" (a gray area under the "label") will repeat its contents for each
label when you click Preview. In this way you can add static text to labels.
To add an object that will contain column values from database specific to each label needs a different
approach. The simple way is to open "Insert data field" window (via Tools|Toolbars menu), which
contains a list of Sample table columns, click the desired field, and drag it the place you want it to be.
Basically, it is the same Memo object that contains a text in a special form so that it is recognized as a
dynamic data field and not as static text (e. g. [Samples."date1"]), but you can add any text outside []
and it will not change from label to label.
The frame of the label is another type of object, which properties you can modify.
If you click the "band" you will see that there is a property called "Columns" and "Column gap"
manipulating which in conjunction with "Height" you can design labels of different sizes
You can save the designed layout via File|Save and File|Save as commands.
To further complicate your life :) - after you have previewed your layout (while in preview) double click
the page and you will see yet another window which allows you to modify each created label

Tools 88
individually. I am not going to explain why would you want to do that, but you will need this for sure.
Taxon and locality (IMPORTANT)
To have an object that dynamically displays the taxon and locality information for each label you need
to place Memo objects (no text contents) and change their property "Name" to "Taxon" and "Locality"
respectively (both are present in the default layout that comes with TAXIS).
12.4 Import/Export
Collection of Import/Export options under Tools menu changes depending on the current section 34 .
Taxa:
Import/Export species list 41
Import/Export all taxa 43
References:
Importing RIS 67
Exporting RIS 68
Images:
Import/Export 71
13 Appendix
13.1 Bio-Tools.Net
Home page:
http://www.Bio-Tools.Net
Registration page:
http://www.bio-tools.net/products/taxis/register.htm
Forum:
http://forum.bio-tools.net/
TAXIS online help:
13.2 Credits
I would like to thank following people for providing data to illustrate this manual:
Tuomo Niemelä
Finnish Museum of Natural History, Botanical Museum
(Polypores of Finland database)
&
Ernest C.J. Seamark

Transvaal Museum, Mammal Department
(African Chiroptera database)

89 TAXIS 3 Help
Index -F-
Formats 83
-A-
about TAXIS 11
-G-
add/delete columns 46 Geographic information system 12, 72
Adding new characters 12, 50 GIS 12, 40, 48, 72, 73, 74, 79, 80, 82, 83
Attributes 79
-B- -I-
Identification 12, 48, 49, 53, 54, 57, 58, 60
Backup 32 Identification builder 48
bars 21 Identification control 54
bugs fixed 4, 5, 6 images 12, 37, 47, 52, 58, 61, 68, 69, 71
building identification 12, 50 import 41, 43, 67, 71, 88
information 11
-C- Input 66
categories 65
Character states 52, 55, 60
-L-
Character tree 49 Labels 48, 85
Characters 48 layers 74
Characters tree 55 legend 74
collapse 24 license 12
Control 54 Link 67
create new database 12, 30 linking references to taxa 65
customizing 24 Localities 60, 61
customizing tables and trees 28
-D- -M-
Main screen 35
Database 12, 29, 30, 31, 32, 33, 34 map layers 74
description 11 map legend 74
design labels 85 Map views 73
Distribution maps 82 Maps 72, 73
menus 21
-E- Metadata 74, 79
Editing 80, 82
Editing taxa 12, 36 -N-
example 12 Navigating tables and trees 29
expand 24
export 41, 43, 68, 71, 74, 79, 84, 88
External file 67

Index 90
Standard 12
-O- start 12
Student 12
Summary 33
open database 29
Supported GIS formats 83
Organization 12
Synonyms 39
Organizer 65
-P- -T-
table 24
page setup 24, 25
Taxa 35, 60, 65, 82
parameters 75
Taxa GIS 40
plotting samples 82
Taxa images 12, 37
print preview 24, 25
Taxa import/export 41, 43
printing 24
Taxa references 38
Printing labels 48
Taxa samples 37
printing tables and trees 25
Taxa synonyms 39
Private 12
TAXIS 12
Professinal 12
taxonomic information 35
Properties 31, 74, 75
taxonomic tree 35
Themes 74
-Q- Tools 83, 84
tree 24, 35
quick start 12 tutorial 12
-R- -U-
Reader 12 Updates 4, 5, 6
References 12, 38, 61, 63, 65, 66, 67, 68 used characters 57
Remaining taxa 57 using 21, 22, 69
RIS 63 Using images in identification 58
-S- -W-
sample labels 85 Web sitre 84
Samples 12, 37, 44, 45, 46, 48, 82 Vector 79
Samples GIS 48 Vector maps 80
Samples images 47 version 12
searching 24 What is TAXIS 11
searching tables and trees 27 What's new in 3.5? 4, 5
Sections 34, 69 View 73
selected state 60 windows 22
Shape files 79, 80 Working 72
Slide show 84 Working with samples table 12, 45
software 11
sorting 24
sorting tables and trees 28

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TAXIS 3.

Part I Whats new in TAXIS 3.5 4

Part III Database 29

© <2004> Evgeniy Meyke, Bio-Tools.Net

Part VI Identification builder 48

Part VII Identification 53

Part VIII Localities 60

© <2004> Evgeniy Meyke, Bio-Tools.Net

Part XII Tools 83

Part XIII Appendix 88

© <2004> Evgeniy Meyke, Bio-Tools.Net

1 Whats new in TAXIS 3.5

© <2004> Evgeniy Meyke, Bio-Tools.Net

· Help files rewritten.

1.1 What's new

© <2004> Evgeniy Meyke, Bio-Tools.Net

· Help files rewritten.

1.2 Bugs fixed

· Taxa: Export/Import of taxa is fixed

Version 3.5 (27 Sep 2004)

· Full screen image preview stretching small images.

1.3 Updates history

© <2004> Evgeniy Meyke, Bio-Tools.Net

© <2004> Evgeniy Meyke, Bio-Tools.Net

© <2004> Evgeniy Meyke, Bio-Tools.Net

© <2004> Evgeniy Meyke, Bio-Tools.Net

TAXIS 2.04 (31 January 2001)

TAXIS 2.03 Beta (14 December 2000)

TAXIS 2.02 Beta (24 October 2000)

© <2004> Evgeniy Meyke, Bio-Tools.Net

· Specimens of selected taxon

It is strongly recommended to go through at least the Introduction topics:

The online copy of this help can be accessed at

Last updated on 31 July 2004

2.1 What is TAXIS?

© <2004> Evgeniy Meyke, Bio-Tools.Net

Please read about TAXIS license and versions here 12 .

2.2 TAXIS licenses and versions

Standard - includes all features except GIS components.

2.3 Quick start

To create a new database use menu item - Database|New

© <2004> Evgeniy Meyke, Bio-Tools.Net

You can insert new taxon by:

© <2004> Evgeniy Meyke, Bio-Tools.Net

To delete taxon press Delete button

Add image to taxa:

Displays images of the selected taxon.

Shows thumbnails of all images loaded for selected taxon.

Add characters and linking to taxa:

© <2004> Evgeniy Meyke, Bio-Tools.Net

© <2004> Evgeniy Meyke, Bio-Tools.Net

For Numeric character the following table appears:

Identification is managed in Identification control 54 window.

© <2004> Evgeniy Meyke, Bio-Tools.Net

Working with Samples table:

Two special column require a bit different handling when editing.

© <2004> Evgeniy Meyke, Bio-Tools.Net

© <2004> Evgeniy Meyke, Bio-Tools.Net

© <2004> Evgeniy Meyke, Bio-Tools.Net

© <2004> Evgeniy Meyke, Bio-Tools.Net

2.4 Using bars and menus

© <2004> Evgeniy Meyke, Bio-Tools.Net

Navigation bar allows