The West African Vegetation Database and VegDa 3.0 Marco Schmidt, Anne Mette Lykke, Salifou Traoré Introduction With growing IT infrastructure, initiatives such as the Global Biodiversity Information Facility (GBIF) and a growing demand for biodiversity data, e.g. due to the rise in applications of species distribution modelling, biodiversity databases have been growing rapidly in the recent past. Databases are in a number of ways superior to other more simple forms of data storage, especially when it comes to long‐term data security, data exchange and cross‐linking of different data sources, error prevention and data quality control, reduction of redundancy and management of large quantities of data. The West African Vegetation Database (www.westafricanvegetation.org) has been developed to securely store vegetation data from West Africa and establish a network of data providers and users within the region and beyond. It has been designed for keeping phytosociological and dendrometrical data and is available online and in an offline version that can be synchronized with the online database. This is a guide to both versions. Participants of the 2007 workshop on biodiversity databases at the Senckenberg Research Institute in Frankfurt, where important decisions on the design and development of the West African Vegetation database have been taken after fruitful discussions with the partners. Structure A relational database is basically built on different tables with their respective data fields and relations between these tables. Therefore it is not just two‐dimensional with rows and columns like a spreadsheet, but can, by using queries, easily combine data fields from different tables via the defined relations. Tables are designed to store data that belong together, e.g. locality parameters for a relevé and at the same time they can serve as standard lists (e.g. for dropdown menus) facilitating data entry and avoiding typing mistakes. More important than the thematic congruence however is minimizing redundancy (called ‘normalization’ in the database context) and maximizing performance (in our case e.g. storing the biodiversity indices in a table instead of calculating them every time). Relations of the main tables of the West African Vegetation Database. Tables mentioned in the text are highlighted. All tables mainly serving as standard lists for field parameters, strata, taxon authors, countries, life forms, photosynthetic types etc. are omitted in this overview. Two central tables in the West African Vegetation Database are the Relevés table with sampling site and event information and the Species table with species‐specific information including nomenclature and the link to higher taxa. Equally important are the two Species Data tables linking the species sets to the particular relevés. One of them is for species based relevés including phytosociological data, inventories, etc. and the other one for individual based dendrometrical relevés. User guide West African Vegetation Database The start screen shows a scalable Google Map of West Africa with relevé locations. Different icons show different relevé types (P: phytosociological = with cover values for each species, I: inventory = simple species presence lists, D: dendrometrical = relevés of individual‐based tree measurements). By clicking the icons you can see the name of the relevé and search for it in the database.On the upper right is a link to log‐in, which is necessary to enter data. On the left side is a navigation menu with options to search and enter data that are available after log‐in. The language can be chosen by clicking the flags below the title. The simple search and download menu can be reached via this navigation menu. It allows to look for relevés within a specified range of coordinates or containing text within its name or other fields that matches the text entered in the free text search field. You can follow the link ‘Advanced searches’ for specifying specific field values. If your search criteria matched any relevé records, you will obtain a list of search results. You can browse through this list, have a look at the details of those accessible to you (your own data, public data, or data shared with you) and eventually add selected records or all records to the data clipboard for later download. The clipboard (link below the banner) gives you the possibility to define access options to your relevés (only your own). For each relevé you can define whether it is only accessible to you, shared with other users from the West African Vegetation Database (which you can chose from a list of users) or publicly available. Furthermore you can download your selected data (including shared and public) into comma separated files (matrices for community analyses, occurrence point lists for species distribution modelling or lists of calculated biodiversity indices) or a Google Earth kml file. If you follow the ‘Enter and modify data’ link from the navigation bar on the left you get a summary table of your account, a link to a further summary with whom you are sharing data, download options for your own data as in the data clipboard but also the possibility to download a personalized offline vegetation database in MS Access 2007 (VegDa 3.0) that you can synchronize with the online database. Finally you can chose to enter new data. For entering new data you first need to specify, which type of relevé data you are going to enter, because the data entry forms and available values will be chosen accordingly. The first form contains the event‐ and site‐specific data. After entering these, you can continue with the species set or additional field parameters. If a species name entered is not in the database, you will be directed to an entry form for new species. The database has an extensive list of >70,000 names of African plants, so it is very unlikely to have species unknown to the database. Please make sure that you are not entering misspelled species as new ones and control the spelling with the African flowering plants database (http://www.ville‐
ge.ch/musinfo/bd/cjb/africa/) or a standard flora of your country. The respective form in the offline database offers some more information (see below). User guide VegDa 3.0 From the online database you can download a personalized version of the offline database VegDa 3.0 (navigate to “Enter and modify data” then chose “Download personalized initial database”). Working offline is of advantage when internet connections are bad, but also offers you more possibilities through full access to the database structure. The database is in Access 2007 format and to work properly, you might need to allow it to use VBA code and macros (for security reasons this is by default often disabled in recent Windows versions). The initial database does not contain any of your online records, but all forms and tables and all available lists of taxa, field parameters, countries, etc. To fill it with your online data, you need to synchronize with the online database. A button from the start form leads you to the synchronization form where you need to enter the password of your online account. Synchronization may take a long time depending on your data holdings. The Start form appears automatically upon opening the database, contains a short summary of the contents and gives you the options to navigate to summary tables, relevés, species or export or synchronization forms. You can also select the language or find all records of a specific species. The summary tables for phytosociological and dendrometrical indices not only give a convenient overview of biodiversity indices (with an export option into excel) but are also a way to browse through the relevés with the option to enter the relevés form via the “Details” button. The relevé form contains all data on the relevé site and the event and also in two subforms the lists of species (with stratum and values) and field parameters. When entering data you need to specify the method before entering species data, because the design of the species subform changes accordingly. If you are entering several relevés from the same researcher and location you might find it useful to set default values with the button in the upper right corner that are set for all subsequent relevé records. If your coordinates are in degrees, minutes and/or seconds you can convert them into decimal degrees with the coordinate calculator. The species form allows you to enter information about new taxon names (species and infraspecific taxa) and it also produces a list of all records of the species within the database. It allows field names to be used (mark the “provisional name” box) and to document synonymies via the “Accepted name” field. [Again: be sure not to enter misspellings as new names!] The export form can be used to export data into a matrix of species and relevés. The design can be changed by applying filters to the respective query design. Any further changes in the query design are discouraged if you are not an experienced Access user. The form “Replace species names” is meant for cases in which field names can be replaced throughout the whole database by the real names. Use it very carefully since changes are irreversible. Since VegDa 3.0’s structure is fully accessible to the user, it is possible to design queries for specific research questions based on the data stored in the database. Update queries may be used to import data from imported or linked text files or Excel tables into the relevant tables of the database. This requires some experience in MS Access (see “Further reading” for online tutorials). An alternative way to import data is by copy‐and‐pasting them (e.g. from Excel) into the respective tables (Use exactly the same fields=columns!). Essential for both approaches is the use of the same standard entries as in the import files. The workflow for the import of data by copy‐and‐pasting could be as follows: 1. Copy a few lines from the tables Releves_tbl, Species_Data_tbl, Species_Data_dendro_tbl and Parameter_Data_tbl into separate spreadsheets as templates. 2. Arrange your data in the respective columns. The ID columns can be left empty (whatever there is will be replaced by automated numbers). The entries for “Modified offline” should be set “TRUE”/”VRAI” in the working language of your Access version, because otherwise they will not be synchronized during your next synchronization. Delete the example lines that you copied from Access. 3. If your species data is in a matrix format (relevés x taxa) you need to rearrange it into the columnar format of the Species_Data_tbl. This can be done by hand, but you can also get a VBA routine for this transformation from [email protected]. 4. Copy the data including all columns (but without the column headers) from your spreadsheet. Mark the last line for new records in the respective Access table and paste. Do this for the Releves_tbl before the other tables and click the “refresh all”‐button, because you’ll need the relevé names as standard entries for the other tables. 5. Check for import errors after each table import. These are usually caused by typos (very frequent in species names), rarely by new species, etc. not known to the database. Be sure to correct typos and if there really are new species, you’ll need to add them to the Species_tbl and “refresh” before trying to import those records again. Other biodiversity databases The West African Vegetation Database is a regional approach to store vegetation data. On the global level there are many more vegetation databases (http://www.givd.info/) and even more collection databases with some ready‐made software solutions, e.g. BRAHMS (http://dps.plants.ox.ac.uk/bol/) and Specify (http://specifysoftware.org/). Some collection databases with West African records include those of Aarhus (http://herb42.bio.au.dk/aau_herb/search_form.php), Frankfurt (http://sesam.senckenberg.de/), Wageningen (http://www.nationaalherbarium.nl/virtual/home.htm) and Paris (http://coldb.mnhn.fr/Consultation?catalogue=1). Many of these databases are also contributing to the Global Biodiversity Information Facility (http://www.gbif.org/) a network of primary biodiversity data providers including both collection and observation data. Using spreadsheets for data storage Even though there are numerous advantages of relational databases, in some cases it is sufficient to use spreadsheets and they are a common way of storing data, especially when the data structure is simple. Spreadsheets are similar to single tables in a relational database and designing good spreadsheets is consequently also very similar to table design. A few simple rules can make good spreadsheets: 1. Different tables should be on different spreadsheets. Related spreadsheets should be in a common file and given a meaningful name. 2. There should not be any empty rows or columns dividing a table. 3. Comments should never be in the data cells themselves, but in an extra column. 4. In most cases single (‘atomic’) information categories should have separate columns, because filtering and sorting options are much more powerful then. [e.g. use separate columns for latitude and longitude instead of one single column ‘coordinates’] 5. Use the same data format throughout a field [e.g. don’t mix UTM and lat/long in the same fields]. Further reading / resources African Plants Database (version 3.3.4). Conservatoire et Jardin botaniques de la Villle de Genève
and South African National Biodiversity Institute, Pretoria.
<http://www.ville-ge.ch/musinfo/bd/cjb/africa/>.
Chapman AD (2005) Principles of Data Quality, version 1.0. Kopenhagen, Global Biodiversity
Information Facility. http://www.gbif.org/orc/?doc_id=1229
Chapman AD (2005) Principles and Methods of Data Cleaning – Primary Species and SpeciesOccurrence Data, version 1.0. Kopenhagen, Global Biodiversity Information Facility.
http://www.gbif.org/orc/?doc_id=1262
Janßen T, Schmidt M, Dressler S, Hahn-Hadjali K, Hien M, Konaté S, Lykke AM, Mahamane A,
Sambou B, Sinsin B, Thiombiano A, Wittig R, Zizka G (2011) Addressing data property rights
concerns and providing incentives for collaborative data pooling: the West African Vegetation
Database approach. Journal of Vegetation Science 22: 614-620.
Morris, PJ (2005) Relational database design and implementation for biodiversity informatics.
PhyloInformatics 7: 1-66. http://systbio.org/files/phyloinformatics/7.pdf
Schmidt M, Janßen T, Dressler S, Hahn K, Hien M, Konaté S, Lykke AM, Mahamane A, Sambou B,
Sinsin B, Thiombiano A, Wittig R, Zizka G (2011) The West African Vegetation Database.
Biodiversity and Ecology 4: xx-yy. (in print).
Taxonomic Nomenclature Checker - GRIN http://pgrdoc.bioversity.cgiar.org/taxcheck/grin/index.html.
[Useful tool to check correct spelling, but taxon sets for West Africa incomplete]
Selected online tutorials for MS Access 2007
http://www.dealing-with-data.net/create-access-query.html
http://www.ms-access2007.com/tutorials/index.html
http://www.jcu.edu.au/old_library/Training/6‐Access 2007 Tutorial/Access 2007 Tutorial.pdf