Technical documentation of collection management systems at the GFBio Collection Data Centers

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Technical documentation of collection management systems at the GFBio Collection Data Centers

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.

Furthermore, the GFBio collection data centers documented their installations of management systems not specialised on collection data, multimedia data management systems, long-term archiving solutions and of GFBio related IT services, tools and databases at the data centers.

Database system, Homepage DiversityCollection (DC) DSMZ-DB JACQ/ Virtual Herbarium SeSam Specify
General Information Installations at GFBio collection data centers/ archives SMNS, SNSB, ZFMK DSMZ BGBM SGN MfN
Contact persons T. Weibulat (SNSB), J.C. Monje (SMNS), P. Grobe (ZFMK) L. Reimer and C. Ebeling D. Röpert and D. Fichtmüller L. Menner and A. Allspach F. Glöckler
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
Data domains Collection data, collection management data, occurrence and observation data Collection data, collection management data Collection data, collection management data Collection data, collection management data, observation data Collection data, collection management data
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
Software and Database System Server Operating System MS Windows Server 2012 R2, 2016; (clients from MS Windows 7 to MS Windows 10) MySQL Backend, MS Access Frontend any server with PHP support MS Windows Server 2003; MS IIS MySQL, Java desktop application & web API
Database system MS SQL-Server 2012 to MS SQL-Server 2016 or MS SQL-Server Express MySQL MySQL MS SQL-Server 2005 MySQL
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 Granular user rights assignment based on roles in the software, but each user is added as MySQL users
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
GIS functionalities GIS-Editor - GeoLocate via WebService, Export: KLM - plugins: GeoLocate, GoogleEarth
GUIs for data import Import-Wizards, 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
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
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)
Open access DC software download - yes - Software download
Open source DWB SVN code repository, DiversityMobile GitHub repository - git repository at SourceForge - SVN at Sourceforge
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
State of development ongoing ongoing ongoing ongoing ongoing
Code language, developer platform C#, .Net Framework, since 2002 SQL, MS Access PHP, Yii Framework ASP, VBScript Java
User manual DC Manual as pdf file under DWB Wiki User manual DSMZ DB Documentation SeSam Manual Documentation
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
Notes DC is one of the 13 modules of the Diversity Workbench (DWB) platform; taxonomies, scientific terms, vocabularies, gazetteers, agents, projects, references, descriptions, sampling plots are managed in stand-alone applications linked by DWB interfaces; resources are managed together with domain metadata; 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
Interfaces to export data in various schemas and standards xml according ABCD schema ABCD 2.0 (natively), ABCD 2.0 and ABCD 2.1 (using BioCASe V.3.6, V.3.7 or V. 3.8) ABCD 2.0 (using BioCASe V.3.8) ABCD 2.0 ABCD 2.06 ABCD 2.0 - (natively), ABCD 2.0 (using BioCASe)
BioCASe Wrapper Version installed, description of dataflow V. 3.6, V. 3.7, V. 3.8 underlying db: DWB PostgreSQL cache databases with information from several distributed DWB databases (DC, DP, DTN) V. 3.8, 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. 3.6.1 BioCASe Provider Software 3.5; connections to different database management systems: MySQL, PostgreSQL, MSSQL, MS Access
xml according DarwinCore schema + (using BioCASe V. 3.7, V. 3.8) not yet mapped + + -
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 and installations at SNSB, DWB network solutions; application also appropriate for species monitoring projects and geoscience collections (fossils, minerals and rocks) Mapped fields listed via BioCASe wrapper response on DSMZ_prokarya We added a JSON export for internal purposes

Status: October 2021

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