The OBIS Data Entry Toolkit is a Java application written as a custom data entry client for the Indo-Pacific Mollusk project. With a valid username and password it can be used to enter and edit data, without, it can be used to browse and search the database.
java -jar bltools.jar
Linux
double click on the icon you created in Xwindows, or from the command line
cd to the directory containing bltools.jar and type /usr/java/jre1.3.1/bin/java
-jar bltools.jar
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The first screen in the toolkit application is the login dialog. Enter your login information here. Most data entry users will enter the following parameters: Driver: ODBC Driver, ODBC Driver Name: IndoPacific, username, and password. If you are using the jTDS jdbc driver, select JDBC Driver and use the following: JDBC Driver class:net.sourceforge.jtds.jdbc.Driver JDBC Driver url: jdbc:jtds:sqlserver and use the ipaddress and database name shown on the image to the right. |
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Press ok. The program switches to the main menu. (The program does not log you in to the server until you select an option from the main menu).
The obis toolkit (since version 1.5) can also be run in a read only form. At the login prompt, select Access Mode: Public Access, read only. You can also specify the details for the connection you wish to use to the database. Browsing, searching, and viewing details options of the database are all enabled, but changes to the database are not possible in this mode.
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The main menu has four options. The Action menu allows you to exit the program or reenter your password if a login attempt fails. The Admin menu allows you to see who else is logged on to the database, and allows you to free blocked up processes in the database. The Admin menu privilegeds priviliged users to edit the hierarchichal distributionion region heirarchy. Most work proceeds through the Data menu. The data menu allows you to enter new references, browse and search for taxonomic names, and enter new taxonomic names. The help menu shows the version of the program and has some help on data entry. Screen shots shown here have been taken on Linux, Mac OS X, and Windows workstations. Exact appearance will vary depending on your desktop settings. |
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If you access the database in public access mode, some menu options will not be available. |
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The Admin Menu is for administrative tasks. View Proceses allows you to see the list of current users on the server, and to remove blocking processes (occasionally two users will similtaneously be trying edit the same record in a manner that the SQL Server is unable to resolve - resulting in both users locking each other out). Edit distribution regions allows users who have been granted rights by the database administrator to edit the distribution region heirarchy. |
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Data Menu. For normal access to the database, both for data entry and for searches. |
There are two points of entry for adding new names into a database:the text based add new taxa option on the /main/data entry menu, and tree browser based editing in the browse a family option of the /main/data entry menu.
Browse a Family - (actually browse a portion of the taxonomic heirarchy starting at any point, families are good starting points for most tasks). Selecting this option will bring up a dialog asking for the name of a family. Enter the name of the family (or genus) for the taxon you are working on and press ok. If the taxon name you enter isn't found, a list of possibly similar names will be returned.
If the taxon name you entered is present in the database, that portion of the taxonomic heirarchy will be loaded and displayed as a tree in the taxon tree browser window. You can search within this portion of the tree by entering a name in the search field and pressing go (this search will only cover the portion of the tree within the taxon name you entered). The search will highlight all matching names within the current portion of the tree, or if no matches are found, will close the display of the tree and only show the name you entered. If you are entering taxa using the main menu/add new taxa option and want to keep this window open to browse a the same time, you can press the refresh button to reload the tree from the database to reflect any recent changes you have made in other windows. The taxon tree display is similar to the taxon tree browser in BioLink. Taxon names are shown in bold, followed by their rank, available names are in plain text folowed by "[Available]", literature names are in italics followed by [Literature]. The exact appearance of the icon in front of the name will depend on your system, but clicking on the icon will expand or close portions of the tree. The taxon name you entered (i.e. the family name) will be displayed at the top of the tree and cannot be edited from here.
You can work with taxa and with names using the heirarchy by right clicking on an entry to bring up a popup menu. The content of the menu will depend on whether you have selected a taxon name or an available or literature name. The popup menu for all names shows the name you clicked on at the top followed by the options show details and metadata. Show details will open the taxon details screen for the current taxon (if you select current details for a literature or available name, the taxon details screen for the parent taxon name will open, and the name you selected will be shown on the available or literature name part of the taxon details screen, to add more information about the desired available literature or available name you can then double click on that name in the taxon details screen).
You can reach the screens to enter a new taxon either from the main menu (main menu/data/enter new taxa) or from the taxon tree (main menu/data/browse a family, select a taxon, right click and select add child from the pop up menu). The first screen for entering a new taxon allows you select a default reference and the parent of the taxon you are adding. The default reference field allows you to enter or select the reference code for the reference you are currently getting information from. This reference code is placed as the default in all fields that indicate information that we usualy gather from secondary sources. The buttons next to the parent taxon name field allow you to select the parent of the taxon you wish to edit or add. That is, if you wish to work on the speciesMurex (Murex) scolopax, you will need to select the subgenus Murex (Murex) as its immediate parent (parent in this context meaning next higher enclosing taxon). To clarify with an example:Murex is the parent of Murex (Murex) and Murex (Murex) scolopax is a child of Murex (Murex).
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To enter more information about an existing taxon, select the parent and double click on the desired child. The taxon details screen for the taxon you wish to edit will appear.
To add a new taxon, select the parent of that taxon (the genus or subgenus for a species, the species for a sub species, the family or sub family for a genus). Once you have selected the parent taxon, and can see that the taxon you wish to add is not included in its current list of children, press the add child button. This brings up the add child dialog.
To enter a new taxon in the new child dialog, type the new epithet into the New Epithet box, and press the tab key. The epithet of the new subgenus Chicoreus (Siratus) is Siratus. Pressing the tab key will run a search to find all names in the database that might match the name you entered (the search is very broad and should turn up lots of possibly similar names). This search will tell you if the name that you wish to add as a taxon is currently present in the database as a taxon placed somewhere else in the tree (as in a different subgenus), or if it has been entered allready in the synonyomy of another taxon (as an available or literature name). Should the epithet you wish to enter turn up a match with an existing name, you will have to evaluate whether the information you have in front of you is more recent than the information used to create the entry found in the search. If no matches turn up, or if you have resolved any issues with them, you can press one of the buttons at the bottom of the dialog to add the new name as a taxon. The buttons will list the valid choices for new children of the currently selected parent (e.g Species groups and species for a Subgenus). Pressing the New species button will create a new species using the new epithet you provided and take you to the taxon details screen for your new taxon.
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Add multiple distributions. Selecting the ABRS regions or OBIS regions tabs lists the most commonly picked distribution regions within those those two sets.
Add multiple distributions. Selecting the all regions tab displays a tree containing the entire distribution heirarchy. Double click on a distribution region to add it to the distribution of the currently selected taxon. The name of the region you chose will appear at the top of the screen, and you can add page, and qualifier information for that distribution and check off whether it is an introduced, uncertain, or throughout region distribution.
The reference you enter or pick at the top of the dialog is the source for all of the distribution regions you add through this form at one time, and will be tied to all the regions you have added to the list on the form when you exit the form. To add distributions from multiple sources, open this dialog once for each source, or use the add a single distribution dialog.
Adding a single distribution. Generally, use add multiple distributions instead by picking data/add distributions from the menu. Three buttons: Save/Close, Add, and Cancel need some explanation. The same three buttons are also used on the dialogs for adding individual keywords and common names. Save/Close saves the information you are currently displaying and closes the dialog. Add saves the information you are currently displaying and prepares the dialog to add a new distribution. Using add you can add multiple distributions from one reference without closing the dialog. The add multiple distributions dialog should usually be used instead of this one. Cancel closes the dialog without saving the information currently displayed. To add two distributions, you could bring up the dialog, enter the first distribution, press add, enter the second distribution and press save/close.
Adding an available name
Adding a literature name
You can reach the references either by pressing a reference picker button 
on any form that has reference fields, or from the main menu (data/references. The reference search screen allows you to search for (and if needed pick) references based using the author, year, and reference code. Use * as a wild card. For most searches, entering the first few letters of the author's name and a wild card will suffice.
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Select a reference in the list of search results by clicking on it. The full reference will appear in the box above the search results. |
Double click on reference to pick, or right click on reference for popup menu.
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The reference popup menu options will vary depending on the rights you have been granted. Most users will only be able to view, add, and edit references.
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Search and pick journals by pressing the delta button next to the journal title field.
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This dialog allows you to enter any valid sql select query for the database and
returns a result set. The query must be in the form of an sql select statement
without the word select. The default query is select count(*) from
tblBiota, expressed in the dialog as count(*) from tblBiota. Use
the sql wild cards % and _ in like queries, use single quotes to enclose strings.
count(*) from tblBiota where bitAvailableName = -1 and chrElemType = 'SP'count(*) from tblBiota where bitLiteratureName = 0 and bitAvailableName = 0 and
(chrElemType = 'SP' or chrElemType = 'SSP')vchrFullName from tblBiota where vchrEpithet='alba'BioLink, and thus the IndoPacific Mollusk project, uses some non-standard terminology to describe the storage of biological and nomenclatoral information in the database.