Quickstart

This quick start manual is for all users who would like to have a short overview of the basic information and applications of the LEDA Traitbase.

The LEDA Traitbase: An open internet database of life-history traits of the Northwest European flora

The LEDA Traitbase (LEDA: Life history traits of the Northwest European Flora - a database) can be used as a data source for fundamental research on plant biodiversity and coexistence, macro-ecological patterns and plant functional responses. A selection of the 3000 priority vascular plant species was made according to the species frequencies in the core countries i.e. UK, The Netherlands and Germany, disregarding alpine species and extremely rare species.

The database consists of a relational database linking species with 26 plant traits and reference information about data source, location, habitat and trait measurement protocol on three core sets of traits: (i) persistence (vegetative) traits such as leaf, stem and clonal growth characteristics; (ii) regeneration traits such as seed production, seed longevity and (iii) dispersal traits such as seed weight, dispersal vectors, floating capacity and vertical terminal velocity of propagules.

The trait data were derived from several databases (see Kleyer et al., 2008 for details) and from literature. Data identified as missing in the literature were obtained following strict collecting and measuring standards are described in Knevel et al. (2005).

Information about the organisation of the LEDA Traitbase (e.g. traits in LEDA, geographical range Traitbase, taxonomic core) can be found under the Organisation button on the left site menu:

The submenu under the Usage button guides you further towards the data standards used for collecting and measuring the data (see also Knevel et al. 2005), Data structure and aggregation as well as tutorials to show some potential applications of the LEDA Traitbase:

Who can use the database?

LEDA is a useful and important source of information for all who are interested in plant traits and their relevance to the conservation and sustainable use of biodiversity in changing European landscapes. For instance, the LEDA Traitbase will facilitate retrieval of the data by researchers, land use managers, nature conservation managers, and landscape planners, to name a few.

The database holds a wealth of information for all who are interested in plants species; from a single species to large species pools. The LEDA Traitbase will be therefore useful in the functional analysis of plant species-environment relations and the prediction of plant biodiversity change in EU on a habitat, landscape or region scale.

How do you extract data from the database?

The web address www.leda-traitbase.org brings you to the homepage of the LEDA Traitbase. There are several ways to be able to get the data from the database: 1). Query the database on a plant trait level using (WebQuery tool), or 2). Query the database on a species level (Species fact sheet). Using the WebQuery tool you can query the whole database or your own selected species list that you can upload to the database. The Species fact sheet gives a trait overview of one species (see further below for details. The application "Species Fact Sheet" can be used without the need to login to the database, but to be able to query the database you have to register first. Registration is just a formality and can be done by clicking on the "Register now!" on the righthand site of the screen and fill in your details:

How to register. Registration is a formailty so your details and email address are know, i.e. to be able to send query results to you.

After registration you receive a confirmation email and you are ready to login with your choosen username and password. After login you are able to use all applications. To start your query of the database you can either use the Species factsheets or Queries under the dropdownmenu under the Applications button:

The welcome page of the LEDA Traitbase after login, with left the menu to navigate through the website. Under the Aplications button you can find the Species factsheet and the web query tool (Queries).

NOTE: Whenever browsing through the webpage and want to go back, it is advised to use the "leda (see Fig. 2) link" in menu at the top of the page to go back to the home page. Please keep in mind that the usage of the browser's back-button can confuses this webapplication. Please use the built-in navigation functions instead.

Species factsheet

If you would like to have an overview of a species and its traits, the species factsheet is the fastest way to get that information. The factsheet will give 1 aggregated or mean value per trait for that species. When you click on the Species factsheets button (under LEDA Traitbase/Applications) you can choose on the welcome page if you would like to use Search or Species list to obtain the species information. With these methods you can search for a species covered by the LEDA Traitbase. However, before you start a search you need to select a species list in which you would like to search for a species (see fig. 3) as species might have different names in different countries.

For the Search method you have to enter a search condition, which can be either a species name or part of a species name (not case sensitive), for instance "quer" for Quercus robur (see fig. 4). After you click search an alphabetical list of matching species names is displayed as result of each successful search operation. Choose your species from the list and the Species fact sheet will be displayed.

When using the Species list method, clicking on the first letter of the species will give you a list of species beginning with that letter and you can choose subsequently from that list (fig. 4). To get more detailed species information (in German!) or a picture of the species, there is a link to FloraWeb at the bottom of the species fact sheet.

Figure 3. On the species factsheet start page (top) you can choose if you would prefer to fill in your own Search conditions (middle) or find your species in an alphabetical list using Specieslist (bottom). For both methods the first thing to do is to select the species list in which you would look for your species. The most important list is the SBS species list of standardised European names from SynBioSys (see http://www.synbiosys.alterra.nl/eu/). Other lists included are: STUK Great Brittian; NO Norway; BE Belgium; SCAN Scandinavia; D Germany; ECN_EU Central Europe; P Poland; NL Netherlands. The other species lists are of less important as far as the names are concerned.

Figure 4. The result for a search using the Search method (top left) and using the Specieslist method (top right), for the species factsheet of Quercus robur. Note: The search string is not case sensitive. It may be any substring of a species name, e.g. "Quercus robur" can be found by entering "quer", "cus" or "robur".

WebQuery tool

To obtain more detailed trait information; the WebQuery Tool is the method to use. For this method you need to be registered and login. When you click on Queries (under LEDA Traitbase/Applications) you can choose to query the whole list of species contained in LEDA (go straight to the query by clicking on the Query Composition tab). Alternatively, you could choose to upload your own species list (click Species Selection tab):

When you click on Species Selection to upload your own species list, make sure that the file should be a text file (.txt file extension) and each row should contain a single species name or genus name Please note that there should be no lines and no trailing blanks following the species names in the file as this will break down the upload. Step 1 is to upload your species list and click the Add LEDA species from file button. This make take a few minutes, so please be patient. In step 2 you can select a few species from your file or decide to keep the whole list. Select your species and click the Add to species election button:

After selection of the species, the move to the Currently selected species part of the page and you can carry by clicking on the Continue to query composition:

After clicking on the Continue to query composition button you come to the query building phase. When you logout of LEDA, the database will remember your selected species for the next time you want to use the database, as is the case with the last selected trait and attributes.

At the start page of the query composition you can choose to show or hide the instructions to help you through the query:

To start a query, you first select a single trait from the dropdown menu (i.e. Terminal velocity), click add trait and after that you will be able to select the trait attributes you want. You can use the default button which gives you a standard list of attributes, or select your own attributes from the dropdown menu and click the add attribute button to select the attribute. Please note that you select one attribute at a time, but multiple attributes can be selected as a whole:

Please refer to the online help (click help button in the main menu at the top of the page) for the distinction between aggregated attributes (indicated with "(aggr)") and non-aggregated attributes or go to Usage/DATA STRUCTURE. If you need aggregated attributes please select only "SBS name", "SBS number" and the respective aggregated attributes. If you need raw data records, do not select the aggregated attributes (will give an error message anyway). Aggregated attributes are not available for all traits. Whenever possible, use the raw data, do your own quality check and selection of the data and then perform your own aggregation.

After you choose the trait and its attributes, you can (if you prefer) modify the order (step 2) of presentation of the data, for instance, you can move a certain attribute (e.g. SBS name) to the first column. In step 3 you can modify your query results further by selecting "null values allowed" to allow cells without content to appear in query results:

The 4th step in the query composition is to decide upon your data quality and data type. Here you can select the data to be used in queries and aggregations. The preaggregated data records are either calculated from single measurements or originate from literature and databases. High quality data indicate data that were error-checked several times. Low quality data were not checked for errors.

In the final phase (step 5) the query will be submitted by clicking on the execute query button. Alternatively you can clear the query and start a new one:

After the query has been executed, the Results screen appears. It is possible to save the query (click save query button) or to send the query results to your email address (click on the CSV file button). The query results will be send to your email address as a comma separated file (CSV file) which can be opened with the excel program. When you want to perform another query or change the attributes of the query, please return to the WebQuery tool by clicking on the back to query button. Please do not use the back button of your web browser as this can confuse the webapplication and might cause the loss of your query set up:

When you click on the save query button on the Result page, you get the screen where you can name your query and save it. At a later stage you can find the saved queries under the Predefined & Saved Queries tab and execute, change or delete the saved query:

Where do I get useful background information regarding content and organisation of the LEDA Traitbase?

To receive more information regarding (i) the traits covered by LEDA, (ii) LEDA's geographical range, and (iii) the taxonomic reference lists, please refer to the menue LEDA Traitbase/Organisation. Use either Trait Overview, or Geographical Range and Taxonomy.

Where do I find background information to use the LEDA Traitbase?

The LEDA Traitbase web pages provide information regarding usage of the Traitbase. See LEDA Traitbase/Usage. Select either Data standards, Data structure, Modes of aggregation or Tutorials.

Data standards provide the LEDA Collecting and Measuring Standards for each trait in the database as pdf files. They describe how traits were collected and measured, and their functional relevance

Data structure describes the differences between the "Raw data level", e.g. a trait value of a species from a single referenced study, and the "Aggregated data level", e.g. the mean seed weight of a certain species calculated from all available studies in the Traitbase. Please note that the data can originate from different sources of different quality. The aggregation might mix different data qualities. We recommend to always use the raw data level in addition to the aggregation.

Tutorials comprise case studies that used traits for prediction of successions in land use systems and other interesting fields of applied vegetation science.

Acknowledgements

The LEDA Traitbase project was funded by the European Commission through the 5th framework under the EESD programme, project number EVR1-CT-2002-40022.

More (detailed) information can be found in:

Kleyer, M., Bekker, R.M., Knevel, I.C., Bakker, J.P, Thompson, K., Sonnenschein, M., Poschlod, P., Van Groenendael, J.M., Klimes, L., Klimesova, J., Klotz, S., Rusch, G.M., Hermy, M., Adriaens, D., Boedeltje, G., Bossuyt, B., Dannemann, A., Endels, P., Götzenberger, L., Hodgson, J.G., Jackel, A-K., Kühn, I., Kunzmann, D., Ozinga, W.A., Römermann, C., Stadler, M., Schlegelmilch, J., Steendam, H.J., Tackenberg, O., Wilmann, B., Cornelissen, J.H.C., Eriksson, O., Garnier, E., Peco, B. (2008) The LEDA Traitbase: A database of life-history traits of Northwest European flora. Journal of Ecology, 96, 1266-1274.

Knevel, I.C., Bekker, R.M, Kunzmann, D., Stadler, M. & Thompson, K. (2005) The LEDA Traitbase collecting and measuring standards of life-history traits of the NW European flora. Published by the University of Groningen, Groningen, The Netherlands. Available online at: http://www.LEDA-Traitbase.org.