Status of the electronic documentation system in the Herbarium of Agricultural University Plovdiv (SOA)

Transcription

1 Scientific Area G Botanical collections and education in botany 701 Status of the electronic documentation system in the Herbarium of Agricultural University Plovdiv (SOA) Kiril H. Stoyanov Agricultural University of Plovdiv, Department of Botany, 12 Mendeleev St., 4000 Plovdiv, Bulgaria, orobanche@abv.bg; Abstract. SOA herbarium contains more than herbarium sheets. Analysing the existing systems and standards, an electronic herbarium documentation system is created. The used software is described and the capacities of the documentation system are demonstrated. The structure of the database is presented and described according to the data blocks and data management levels. On the basis of the stored information in the data management system, the count of types and total count of records, divided by varied criteria, are presented. Key words: biodiversity collections, botanical software, chorological data, database, documentation, herbarium Introduction The Herbarium of Agricultural University Plovdiv (SOA, according to Index Herbariorum) holds valued specimens. Some of them are collected about one century ago as presented by different authors (Delipavlov & al. 1997). SOA consists of more than specimens of Bulgarian vascular flora, which are collected from various floristic regions. The accessions hold information for the plant diversity in Bulgaria and the Balkan Peninsula. That is why although the physical access to the herbarium materials is limited, very often direct search of information by definite criteria is needed. About exsiccates of vascular plants are stored in boxes and shelves according to the index of "Genera Syphonogamarum ad Systema Englerianum" by De Dalla Torre & Harms (1907). In the database we used the taxonomic system accepted in Flora Reipublicae Popularis Bulgaricae. Software description The program module (dsoa) of the database is compiled in the Botanical Department of Agricultural University (Stoyanov 2003). It requires low system resources Windows 95 on Pentium 100 with 16 MB RAM, 2 MB free disk space and VGA are enough to work with the databases. This program does not require any external software for data management. It allows to create unlimited number of thematic relational databases. The user interface of the program module (Fig. 1) is realised in Bulgarian language. The both data windows offer the both table and form view of the records (Fig. 1 A, C). To reach compatibility with other systems is predicted that dsoa system could export and import tables in CSV (Comma Separated Values) format. They could be processed by any office application. The specimen data can be exported to hypertext or plain text documents too, as well as to any user-defined format or template. For example some data could be exported as a Java-midlet and be read on the field using any mobile device (Fig. 1 F). dsoa could prepare complete report by number of stored records and their relation to users, families, genera, authors and type specimens. The program module is able to display the distribution of selected specimens as UTM map (Fig. 1 E). Database structure and data description The structure of the documentation system is shown in Fig. 1 and Fig. 2. The database is multi-file realised. The user access (Fig. 2, box 1) is realised in 3 levels administrator ("root"), registered users and unregistered users ("guest"). The users have the permis- 90 Proceedings of IV BBC Sofia ' 2006

2 702 Plant, fungal and habitat diversity investigation and conservation Proceedings of IV BBC Sofia ' 2006 Fig. 1. Screenshots of the herbarium management software: A herbarium data form; B additional description data; C bibliographic data form; D geographic gazetteer; E map drawing form; F data exported in Java midlet.

3 Scientific Area G Botanical collections and education in botany 703 Administration Main data block (see Fig. 3 for details) 1. User s account (table) 1.1 User name 1.2 Password Taxonomical position DatabaseN Database2 Database1 4. Family Index (table) 4.1 fam. code text* fam. name text 2. Herbar data (see Fig. 3) 5. Genus index (table) 5.1 fam. code text* genus code text* genus name text 5.4 genus author text 5.5 index* number * de Dalla Torre et Harms ( ) 3. Data from literature (see Fig. 3) Chorological references 6. Species index (table) 6.1 genus code text* spec. code text* spec. name text 6.4 spec. author text 11. Country codes (table) 11.1 country code (ISO) text* country name (Bulgarian) text 11.3 country name (English) text 7. Specimen status (table) 7.1 status code byte description text 12. Geographic gazetteers (table set) 12.1 country code text* gazetteer table set Citation data 8. Specimen authors (table) 8.1 auth. code text* Bulg. name text 8.3 Latin name text 9. Bibliographic references 9.1 signature text author text 9.3 title of article text 9.4 source text 10. Addresses of herbaria (table) 10.1 country code text* herb. code* text address text * acronym from Index Herbariorum 12.2.(11.1) Geographic gazetteer toponym text altitude number floristic region number UTM grid code text*(3-/-9) altitude; longitude text 12.3 map & definitions table set 13. Plant communities 13.1 country code text* plant communities table set (11.2) Plant communities unit code* text unit description text unit members text * Bulgarian communities are stored as mapping units according to Bondev (1991) Fig. 2. Functional chart major structure of the database in SOA herbarium. Numbers in bold show the primary index keys in the tables. Field names in bold show the required fields in any record. Left arrow shows input from related field. Right arrow shows output to related field.

4 704 Plant, fungal and habitat diversity investigation and conservation Proceedings of IV BBC Sofia ' 2006 sion to store data and to lock records. The access of the "guests" is free but without permission to write data. The accepted storage system in the herbarium is used according to the standard of Bisby (1994). The taxonomic description is divided in 3 indexed tables as follow: family (Fig. 2, box 4), genus (Fig. 2, box 5) and species (Fig. 2, box 6). These tables are available in the user interface as menus. The real datum in the fields is the index code from the tables. This division is realised in aim to avoid typing errors which is indispensable if the data are stored manually above and to make the main data file more compact. The field of intraspecific taxa remains manually entered because of the big intraspecific diversity. Three index tables are created to enter citation data. The first one (Fig. 2, box 8) describes the authors of the herbarium sheets spelled in Bulgarian and Latin alphabet. The index code allows viewing the names of the authors with both alphabets. The second index (Fig. 2, box 9) describes the literature sources and allows searching floristic data from the literature. The acronyms from Index Herbariorum (Holmgren & Holmgren 1998) are stored in unlinked file available as a list (Fig. 2, box 10). All the geographic reference data are stored in separate data files according to the country name. The names of the countries are stored in a table as Bulgarian and English names indexed as 3-letter ISO standard codes (Fig. 2, box 11). This international coding is accepted in many herbaria, botanical gardens and genebanks (van Hintum 1995; Walter 1995). The country index is used as a trigger for the other two stacks of tables in this group gazetteers and plant communities (Fig. 2, boxes 12, 13). The first one is physically related to the main data set and consists of toponyms, altitudes, numbers of the floristic regions, UTM (MGRS) grid codes and geographic coordinates. The gazetteer sheet is related to map definition sheet. The alphanumeric codes of the UTM grid sets (50 50 km) from Atlas Florae Europeae Project (2002) and the grid (10 10 km) for Bulgaria (Kozhuharov & al. 1983) are accepted as geographic characterisation. The map of 20 floristic regions which is accepted in Flora Reipublicae Popularis Bulgaricae, vols 3 10 ( ) is used for description of Bulgarian floristic data, as well. The altitude is shown in metres above the sea level. The plant communities in Bulgaria are stored as mapping units according to Bondev (1991). The main data block is realised as a stack of thematic databases. All the databases are built on the basis of two tables data from herbarium sheets (Fig. 2, box 2) and data from publications (Fig. 2, box 3). The user can switch between different thematic databases on the fly. The system keeps in each record from the main block information about the date, the name of last editor and the level of accessibility of the record. The plant accessions (about ) and fungal samples (about 5000) are assigned by their herbarium sheet number. This number is used in the scientific publications describing the specimens. We accept the serial number of herbarium sheet as an unique number or primary key index in database. In this way we answer to the both requirements: searching by serial number and limiting the record/number duplication. The data fields as family, genus, species, status (type specimens), geographic data, authors' names and last editor data are linked to the tables described above (Fig. 3, box 2). The date format is "year-month-day" in case to simplify searching. The fields of the intraspecific taxa, data from the original label and landmark have to be stored manually from the keyboard. Because of the diversity of the data, which supports the herbarium sheets, every record can be linked to external files and additional data fields. The additional data fields are defined in a descriptor list. The external files consist of one text file for the revision notes, one file for additional notes about the specimen and one table of other external files, incl. images. This organisation allows to expand the data structure according to the features of the stored taxa. The stored data is searchable by the content of the main fields and by existence of additional files. The chorological data in the literature are structured in another order. Each floristic record for a taxon contains a list of localities sometimes with citation of herbarium sheets. It means that each record in the database (Fig. 3, box 3) must have included table for the chorology and herbarium sheets (Fig. 3, box 3, 3.9). The other fields are linked as the fields in the herbarium records. The field "signature/page" (Fig. 3, box 3, 3.8) is linked to the bibliographic reference table (Fig. 2, box 9). This organisation of the database allows comparison between data from literature and data from herbarium sheets. It makes possible to create comparative distribution maps of any taxon (Fig. 1 E).

5 Scientific Area G Botanical collections and education in botany 705 The table of users' accounts and the direct manual edition of the main data block (for rescue purposes) are accessible only for the administrator. The registered users are allowed to store data in the all other tables. The data levels are as follow: 1. Index data: families, genera, species, authors, countries, herbaria, bibliography. 2. Geographic gazetteer: storage of the toponym data. 3. Main data: records from separate herbarium sheets and records from publications. 4. Data export to external files as CSV tables, text files, maps and other users' formats. The unregistered users have not permission to change the data except the revision notes. Main data block 2. Herbarium specimen data (table) descriptor list for separate herbarium sheet 2.1 Number of the herbarium specimen text 2.2 Family code text (4 letters) Genus code text (6 letters) Species code text (6 letters) Intraspecific taxon text (free text) 2.6 Status byte Original label data memo 2.8 Country code ISO text (3 letters) Floristic region number decimal number Altitude (m) decimal number UTM grid (from D.) text Plant community text Landmark text 2.14 Collector s name (Leg.) text Author s code (Det.) text Date of collecting YYYY-MM-DD 2.17 Herbarium code Last editor (name, date, time) and user s key text Additional fields (external descriptor list) included table 2.20 External files: Revision notes External files Additional notes images or text 3. Data from literature (table) descriptor list for separate card 3.1 Number of the card text 3.2 Family code text (4 letters) Genus code text (6 letters) Species code text (6 letters) Intraspecific taxon free text 3.6 Status byte 3.7 Original data memo 3.8 Signature/page text Chorology included table 3.9. Chorology Country code text (3 letters) Floristic region decimal number UTM grid text (6-9 letters) Altitude decimal number Date YYYY-MM-DD Description text Herbarium sheets text 2.1 Fig. 3. Functional chart of the main data block (continues from Fig. 2).

6 706 Plant, fungal and habitat diversity investigation and conservation Proceedings of IV BBC Sofia ' 2006 Overview of the herbarium data stored till now The stored data till now contain 7004 records holding information about 75 families, 275 genera and 845 species, collected by 40 authors. The count of stored records divided by families is shown in Table 1. The herbarium contains 210 types (Fig. 4). The stored data cover the 20 floristic regions, mainly from the Rhodopi Mts, Thracian Lowland, Black Sea Coast and Balkan Range (Fig. 5). The territory of Bulgaria is presented by 399 UTM (MGRS) squares km (Fig. 6). The bigger part of the specimens is collected from the lowland's belt (Fig. 7). The most intensive collecting season is between May and July, followed by August and September (Fig. 8). The stored records show that the bigger part of the stored specimens is collected between the 40s and 70s of the 20 th century (Fig. 9). Table 1. Count of the stored herbarium data divided by families. Family Genera Species Countries Floristic regions UTM squares Authors Types Years Sheets Alismataceae Alliaceae Amaranthaceae Anacardiaceae Apiaceae Aquifoliaceae Araceae Araucariaceae Aristolochiaceae Asteraceae Brassicaceae Butomaceae Buxaceae Callitrichaceae Campanulaceae Cannabaceae Caprifoliaceae Caryophyllaceae Celastraceae Cephalotaxaceae Chenopodiaceae Clethraceae Colchicaceae Convallariaceae Crassulaceae Cupressaceae Cyperaceae Dipsacaceae Empetraceae Ephedraceae Ericaceae Euphorbiaceae Fabaceae

7 Scientific Area G Botanical collections and education in botany 707 Table 1. Continuation. Family Genera Species Countries Floristic regions UTM squares Authors Types Years Sheets Fagaceae Hyacinthaceae Hydrocharitaceae Hypericaceae Iridaceae Juncaginaceae Lamiaceae Liliaceae Linaceae Loranthaceae Malvaceae Molluginaceae Monotropaceae Moraceae Najadaceae Nyctaginaceae Orobanchaceae Phytholaccaceae Pinaceae Poaceae Polygalaceae Polygonaceae Portulacaceae Potamogetonaceae Pyrolaceae Ranunculaceae Rosaceae Rubiaceae Santalaceae Scrophulariaceae Sparganiaceae Staphylleaceae Taxaceae Taxodiaceae Thymelaeaceae Typhaceae Ulmaceae Urticaceae Violaceae Vitaceae Zannichelliaceae Zosteraceae

8 708 Plant, fungal and habitat diversity investigation and conservation Proceedings of IV BBC Sofia ' 2006 typus 78 isotypus 46 holotypus 28 lectotypus 53 isolectotypus 4 neotypus 1 isotypus 22% holotypus 13% altitude, m typus 38% neotypus 0% isolectotypus 2% lectotypus 25% count of specimens Fig. 7. Vertical distribution of the stored specimens. Fig. 4. The type specimens in the Herbarium of Agricultural University Plovdiv (SOA) % 18 25% % 19 5% % 14 2% 13 1% 12 1% 11 1% 10 3% 9 0% 8 1% 7 0% 6 2% 5 7% 4 0% 3 1% 20 2% 1 12% 2 3% I II III IV V VI VII VIII IX X XI XII Fig. 8. Count of specimens according to the months Fig. 5. Horizontal distribution (by floristic regions) of the stored specimens. 1, Black Sea Coast, 2, Northeast Bulgaria; 3, Danubian plain; 4, Forebalkan; 5, Balkan Range; 6, Sofia region; 7, Znepole region; 8, Mt Vitosha; 9, West Frontier Mts; 10, Valley of Strouma River; 11, Mt Belasitsa; 12, Mt Slavyanka; 13, Valley of Mesta River; 14, Pirin Mts; 15, Rila Mts; 16, Mt Sredna gora; 17, Rhodopi Mts; 18, Thracian Lowland; 19, Toundzha Hilly Country; 20, Mt Strandzha Fig. 9. Count of specimens according to 20-year periods. Fig. 6. UTM map of the localities the localities with more specimens are darker.

9 Scientific Area G Botanical collections and education in botany 709 References Bisby, F Plant names in botanical databases. Plant Taxonomic Data base Standards No. 3, Hunt Institute for Botanical Documentation, Pitts burgh. TDWG. Bondev, I The vegetation of Bulgaria. Map 1: with explanatory text. "St. Kliment Ohridski" Univ. Press, Sofia. De Dalla Torre, C.G. & Harms, H Genera Syphonogamarum ad Systema Englerianum Conscripta. Lipsiae. Delipavlov, D., Cheshmedzhiev, I. & Kovacheva, D The Herbarium of the Higher Institute of Agriculture in Plovdiv. Phytol. Balcan., 3(1): Holmgren, P. & Holmgren, N Onwards (continuously updated). Index Herbariorum. New York Botanical Garden, USA, Kozhuharov, S., Peev, D. & Nikolov, N Conservation, representation and use of the current chorological information. Fitologiya, 22: (in Bulgarian). Stoyanov, K Documentation System in Herbarium of Agricultural University of Plovdiv, Bulgaria. J. Balkan Ecol., 6(1): van Hintum, T.J.L Standardization in plant genetic resources documentation, III: Country and region codes. In: van Hintum, T.J.L., Jongen, M.W.M. & Hazekamp, T. (eds), Standardization in Plant Genetic Resources Documentation. Report of the 2 nd Technical Meeting of Focal Points for Documentation in East European Genebanks, Pp Centre for Genetic Resources, Wageningen. Walter, K.S Standardization of documentation in botanic gardens. In: van Hintum, T.J.L., Jongen, M.W.M. & Hazekamp, T. (eds), Standardization in Plant Genetic Resources Documentation. Report of the 2 nd Technical Meeting of Focal Points for Documentation in East European Genebanks, Pp Centre for Genetic Resources, Wageningen. 91 Proceedings of IV BBC Sofia ' 2006

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