Technical Documentations
Technical documentation of collection management systems at the GFBio collection archives
Technical documentation of collection management systems at the GFBio Collection Data Centers
Technical documentation of collection management systems at the GFBio Collection Data Centers, Status 2014
One of the goals of GFBio is to strengthen the data centers at the Natural History Collections and Culture Collections in Germany and improve their infrastructure to manage, archive and publish biodiversity research data on the long run. As a consequence - latest after the realisation of the GFBio platform and federal infrastructure - they should be able (a) to mobilise their own data resources for research purposes and (b) to provide their technical infrastructure for managing, archiving and publishing biodiversity research data including multimedia data.
In this context, knowledge on the existing database structures, particularily concerning the collection management systems being housed at the respective GFBio collection archives is of highest priority. To be able to fulfill all GFBio requirements, systems need to be technically extended and adopted by developer groups in Germany, for instance, by establishing more and most different interfaces for the dynamic import and export, transfer and provision of data. Only in this way, data- and workflows can be professionalised in the GFBio context.
The collection management systems documented below have to develop data exchange mechanisms for internal communication as well as for archiving and publishing data in the GFBio context. New architectures of workflows with regard to the common management of metadata and multimedia data, analysis data from experiments, data streams, methods applied and the linkage of identifier systems are needed for delivering well-structured open data for GFBio and the national (and international) research community.
Further Wiki pages with technical documentations will follow, e. g., including information on the multimedia data repositories and archiving systems in use by the GFBio collection data centers/ archives.
General Information
Software and Database System
Interfaces to export data in various schemas and standards
| Database system, Homepage | Diversity Collection (DC) | DSMZ-DB | JACQ/ Virtual Herbarium | SeSam | Specify | SysTax |
|---|---|---|---|---|---|---|
| Installations at GFBio collection archives | SMNS, SNSB, ZFMK | DSMZ | BGBM | SGN | MfN | - |
| Contact persons | T. Weibulat (SNSB), A. Jandl (SMNS), P. Grobe (ZFMK) | C. Söhngen and D. Gleim | D. Röpert and D. Fichtmüller | L. Menner and A. Allspach | F. Glöckner | J. Hoppe, Herbarium ULM, Botanical Gardens |
| Developer group, country | SNSB IT Center Germany (together with MfN and UBT as far as the whole DWB platform is concerned) | Leibniz Institute DSMZ GmbH, Germany | NHM Vienna, Austria and BGBM Berlin, Germany | Senckenberg IT Services; Team Application Development | originally: Biodiversity Institute University of Kansas, USA; currently: joint developments within the international DINA-Specify consortium | Institut für Systematische Botanik und Ökologie, Universität Ulm, Germany |
| Data domains | Collection data, collection management data, observation data | Collection data, collection management data | Collection data, collection management data | Collection data, collection management data, observation data | Collection data, collection management data | Collection data & collection management data for collections and botanic gardens, observation data, multimedia data incl. sound file archive |
| Organismic data | all recent and fossil organisms groups | bacteria, fungi, cell lines, plant viruses | all recent and fossil organisms groups | all recent and fossil organisms groups; geological data | all recent and fossil organisms groups | all organism groups |
| Operating System Server | MS Windows Server 2008 R2, 2012 R2; (clients from MS Windows XP to MS Windows 8) | MySQL Backend, MS Access Frontend | any server with PHP support | MS Windows Server 2003; MS IIS | MySQL, Java desktop application & web API | SysTax 4: Client/server architecture, ORACLE 8i. SysTax 5: PostgreSQL 9.1 |
| Database system | MS SQL-Server 2012 | MySQL | MySQL | MS SQL-Server 2003 | MySQL | PostgreSQL 9.1 |
| User rights management | MS SQL-Server specific; few DWB specific features and roles added | MySQL-Server Specific | Role based user management within the software | Granular user rights assignment | ? | ? |
| Client | C# desktop application (rich client) (and web API for the GBOL project) | MS Access frontend | web API (any browser) | Webapplication, Frontend every common webbrowser | Java desktop application and web API | web API (any browser) |
| GIS functionalities | GIS-Editor | - | GeoLocate via WebService, Export: KLM | - | plugins: GeoLocate, GoogleEarth | Google maps |
| GUIs for data import | Import-Wizard, txt, CSV, xml in various schemes, xml/xslt, shapes in ESRI-Format | Individual import/export txt, CSV, XLS, MySQL | Import-Wizard for txt, CSV | Import wizard | Specify Workbench: CSV,xls, image files | no GUI; import from txt, cvs, xml or SysTax-GBIF format files |
| GUIs for data export/ reports | txt, CSV, xml in various schemes, xml/xslt, shapes in ESRI-Format | Exports/Reports via Access frontend (CSV, XLS, XML) | txt, CSV, XML | csv; GUI selectable fields | reports from customizable templates, graphics from statistics | no GUI; export into txt, cvs, xml or SysTax-GBIF format files |
| GUI language | default: english (multilingual through translation tables) | english | default: english (multilingual translation via Google Translate possible) | german, english | default: english (multilingual through translation files) | english, german |
| Open access | DC software download | - | yes | - | Software download | intended |
| Open source | DWB SVN code repository, DiversityMobile GitHub repository | - | git repository at SourceForge | - | SVN at Sourceforge | bitbucket repository |
| Licenses | GPL v.2 | - | GPL v.2 | - | GNU General Public License 2 (GPL2) | - |
| Information model online | DC data model | Data model | Data model | Data model | Data model | SysTax 4 |
| State of development | ongoing | ongoing | ongoing | ongoing; new version soon | ongoing | redesign SysTax 4 -> 5; ongoing |
| Code language, developer platform | C#, .Net Framework, since 2002 | SQL, MS Access | PHP, Yii Framework | ASP, VBScript | Java | SysTax 4 (1989 - 2013): ORACLE-Developer; SysTax 5 : PHP, Symfony framework |
| User manual | DC Manual as pdf file under DWB Wiki | Documentation | Documentation | SysTax 4 | ||
| Training | DWB workshops for users and database administrators since 2007; User Help Desk | on demand | on demand | on demand | For workshops and video tutorial contact: Andrew Charles Bentley | on demand |
| Notes | DC is one of the 13 moduls of the Diversity Workbench (DWB) platform; taxonomies, scientific terms, agents, projects, references, resources, descriptions, sampling plots are managed in stand-alone applications linked by DWB interfaces; smartphone app DiversityMobile; user help desk; feedback system for DWB user, annotation system for external user; DWB technical documentation and DWB user support for installation | Ticket System | central database system for biodiversity data suitable for collaborative revision work on taxa, thus avoiding problems of data integration from different local database installations | |||
| xml according ABCD schema | ABCD 2.0 (natively), ABCD 2.0 (using BioCASe V.3.5) | ABCD 2.0 (using BioCASe V.3.5) | ABCD 2.0 | ABCD 2.0 | ABCD 2.0 - (natively), ABCD 2.0 (using BioCASe) | ABCD 2.0 |
| BioCASe Wrapper Version installed, description of dataflow | V. 3.5, underlying db: DWB PostgreSQL cache database with information from several distributed DWB databases (DC, DP, DTN) | V. 3.5, underlying db: MySQL cache DB with information from the Catalogue of the DSMZ culture collection | not part of the software package, but BioCASe Provider Software can be installed next to it. | BioCASe Wrapper V. 3.5, underlying db: My-SQL view | BioCASe Provider Software 3.5; connections to different database management systems: MySQL, PostgreSQL, MSSQL, MS Access | ? |
| xml according DarwinCore schema | + (using BioCASe V.3.5) | not yet mapped, planned via BioCASe V.3.5 | + | + | - | + |
| xml according EML schema | - | - | - | - | - | - |
| xml according other schemas | GPI schema | - | GPI schema | - | - | |
| txt, CSV export | + | custom exports on request of collaboration partners (+) | + | + | Excel export | + |
| Notes | DWB network solutions; DiversityDescriptions xml export acc. SDD schema | Mapped fields listed via BioCASe wrapper response on DSMZ_prokarya | We added a JSON export for internal purposes |
