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Flora Croatica Database Application

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Flora Croatica Database Application Flora Croatica Database Application Krešimir Fertalj 1,Toni Nikoliæ2, Tomo Helman1, Vedran Mornar1, Damir Kalpiæ1 1Chair of Computer Science, Department of Applied Mathematics Faculty of Electrical Engineering and Computing, University of Zagreb Unska 3, HR-10000 Zagreb, CROATIA , 2Department of Botany Faculty of Science, University of Zagreb Maruliæev trg 20/2, HR-10000 Zagreb, CROATIA Abstract: A client-server database application, named CROFlora has been developed to foster the endeavour for the systematic and taxonomic classification of the Croatian flora. The software consists of several modules to encompass the taxonomy, herbarium, literature, horology and ecology. The paper presents the underlying database structure, querying and reporting. Standard reports cover the taxon sheets, taxa checklists, herbarium labels and bibliography labels. Rather complex reports are also available. A connection to the geographical information system (GIS) has made easier the production of distribution maps and has enabled comprehensive spatial analysis. Key-Words: taxonomy, vascular flora, distribution, database application, geographical data, Croatia 1. Introduction text and multimedia data and can be connected to GIS applications. Development of new technologies like databases, multimedia and Internet has had its impact on the CROFlora is a part of broader Croatian Information treatment of botanical data. It gave rise to devising of Service for Biodiversity - Database (CIS-B Database) various approaches regarding the construction of [30], which also contains raw species list for all other research-oriented databases [1],[2],[5],[9],[18],[19]. groups of living organisms in Croatia (Animalia, Lichens, Monera, Mycota, Plantae non vascular and This papers describes Flora Croatica database Protista). In addition to data management, the main application (CROFlora), which enables the storage of purpose of CROFlora is to be used as a tool for flora taxa and specimen oriented data, updating, and data analysis and preparation of the Atlas of the vascular analysing of Croatian vascular flora. CROFlora was flora, as well as Flora Croatica, which need to be developed in collaboration between the Department of produced in the near future. Applied Mathematics, Faculty of Electrical Engineering and Computing and the Department of Botany, Faculty 2. CROFlora Database of Science, both from University of Zagreb, Croatia. 2.1. Taxonomy The first version of CROFlora [25] was developed as a multi-user database handled by a client application and Taxonomically, the database deals with vascular flora, supplemented with web interface. The taxonomic i.e. Pteridophyta and Magnoliophyta divisions. The backbone is newly developed Checklist of Croatian lowest level that can be defined in the database is Flora (CCF), produced by the Department of Botany subspecies. The lower levels, as varieties and forms, are [26],[27],[28]. The data is deriving from taxonomy included only as part of synonyms. CROFlora has the (nomenclature, synonyms, authorisation), horology systematic arrangement according to [8], with minor (distribution based on literature data, herbaria modification. collections, field investigations, oral reports), bibliography, etymology, ecology (ecological indexes) The taxa are classified in nine hierarchical levels etc. The database supports the processing of numerical, (Kingdom to Genus) as presented by the conceptual data sub-model in Fig. 1. 1 Besides the officially recognised levels, the database AuthorOfSpecies AuthorOfName contains aggregates (also known as complex) – a group AuthorOfSubspecies of mostly small species, to facilitate work with difficult groups, as commonly practised [13]. Synonym Kingdom CommonName Subkingdom ConservationStatus Division Species/Subspecies EcologicalIndex Subdivision Class HerbariumSheet Blob Subclass ObservationDetail Order LocalityCitation Object Technique Family Fig. 2 – Species/Subspecies and related data Genus Species/Subspecies The data on the authors of scientific names Aggregate (AuthorOfName) is stored according to [7]. Initially, the Fig. 1 – The model of taxa hierarchy data were obtained in digital form and were imported into CROFlora. The essential data about species or subspecies (Species/Subspecies in Fig. 1 and Fig. 2) comprise the The abbreviated author’s name is used as basis to form values such as species name and subspecies name, place valid names of taxa. Additional information about the of publishing, taxa name abbreviation and free-form authors of scientific names (AuthorOfSpecies, taxa description. The data stored in the database were AuthorOfSubspecies) contains a prefix and a suffix collected from several sources. Nomenclature and (parenthesis, et, non, etc.) that are used to create the full related data that form a basic list of about 12000 taxa, scientific name of taxa. For example, full scientific originate from the database for middle Europe name Vitis vinifera L. ssp. sylvestris (C. C. Gmelin) FLOREIN [4]. This original data contained the taxa list Hegi is automatically created based on the values for of Central European Flora according to [13]. genus: Vitis, species: vinifera, author of species: L., subspecies: sylvestris and authors of subspecies: C. C. As the work on CCF was going on, this original list has Gmelin (prefixed and suffixed by a rounded parenthesis) been successively modified according to new proprietary and Hegi. results [26],[27],[28]. The taxa names were checked out by comparing with Names in Current Use (NCU) [17] Relationship between taxa (Species/Subspecies) and an and with taxa list from digital version of Flora universal set of synonyms (Synonym) carries Europaea Database, which is part of PANDORA information about the type of the synonym (basionym, taxonomic database system at the Royal Botanic Garden exclusive, inclusive, nomen ambygum, nomen nudum, Edinburgh [32],[33]. nomen illegitimum, pro parte and doubtful), information about the author of non-valid name and Information on doubtful data (taxonomically or place of publishing. horologically), as well as on endemic, cultivated and naturalised taxa, are derived from the CCF. Data on The initial data on the vernacular names endangered taxa (ConservationStatus) are following (CommonName) were included in database according to marks according to IUCN Conservation Monitoring [11]. The data entry for common names from several Centre [3]. Besides the standard IUCN marks, there is other sources is currently in progress. also a special mark for taxa protected by the Law for protection of Nature in the Republic of Croatia. The multimedia data (images and video clips) are stored as binary large objects (Blob). The additional data The data on endangered taxa (273) originated from Red describe multimedia contents (Object), such as whole data book [37], and were modified (mostly plant, fruit, leaf, blossom, pollen, etc. The applied supplemented, now more than 400) with data from the method (Technique) can be for instance digital camera new CCF. The complete data set contains information acquiring photography/slide scanning or about the endangered taxa in other European countries. 2 microphotography. Photo documentation is related to the and persons (Author) who collected (Collector), CCF. It was mostly produced by the associates of the determined (Determinator) or re-determined Department of Botany. The production of multimedia is (Redeterminator) the species. The re-determination data still being in progress. (Redetermination) include the re-determination date and the author’s comments. Binding to the DEscription Language for TAxonomy (DELTA) standards [10] is foreseen for future The HerbariumSheet stores all the data necessary for development. the management of herbarium. For the flexibility reasons, the user is allowed to store only the information 2.2. Ecology about the genus and/or the aggregate of the specimen (i.e. temporarily not determined below genus). Ecological data include index parameters (see Fig. 3) according to [12], [14], [15], [16], [20], [21], [22], [23], The information about the type of collected specimen [31], [34], [35] and [36]. (SpecimenType) is codified as holotype, isotype, lectotype, neotype, paratype and sintype. The origin of ELifeForm LWater Phytogeography the specimens (SpecimenOrigin) can be designated as a LDispersion Species/Subspecies EAnatomy deposit, a substitution, a purchase or a gift. DPollination DistribMechanism Collected specimen (HerbariumSpecimen) can be described (SpecimenPart) as fruit (carpological EPhytocenology LContinentality collection), wood, root, seed, leaf, whole plant, etc. ELeafPersistence LLight Predefined modes of preservation (PreservationMode) EStrategy LHumus include dried material, liquid media, silica gel media etc. Author ESalt LTemperature LReaction LNutritient Redeterminator Determinator Collector LHumidity EcologicalIndex KHameroby Redetermination EHumidity KSocioEco Species/Subspecies Collection ENitrogen Pasture EReaction Origin EContinentality LLight Genus HerbariumSheet EHMResistance ETemperature SpecimenOrigin EHumidityDynamic SpecimenType Aggregate Fig. 3 - Model of ecological index parameters according HerbariumSpecimen to several authors SpecimenPart PreservationMode Altogether, thirty ecological parameters for 7300 taxa Fig. 4 - Herbarium sub-model aimed to handle were obtained in digital form from two sources. The information about collections first part of data was obtained on the commercial basis from Verlag Erich Goltz Goltze / Co.
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