Technical documentation of GFBio related IT services, tools and databases at the data centers

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GFBio related IT services, tools and databases at the data centers

The software documented in table 1 is not essentially part of the GFBio IT infrastructure and portfolios of the GFBio data centers, but developped by biodiversity informatics groups there. The applications and services are installed as useful tools for processing, curating and publishing collection and research data. They are freely available and might be of interest for producers of research data in DFG projects as well as for emerging new GFBio data centers. Beside technical information, the scope and usability of the software is explained.

Four additional commercial tools with installations and contact persons at the collection data centers are mentioned in table 2.

In parallel, the GFBio collection data centers documented their installations of collection management systems, management systems not specialised on collection data, multimedia data management systems and of long-term archiving solutions.


Table 1

Software application, Homepage AnnoSys Biowikifarm Diversity GIS Editor DiversityImageInspector DiversityMobile GBIF Webservice Reverse Georeferencing Client NaviKey
General Information Installations at GFBio collection data centers/ archives BGBM MfN SMNS, SNSB, ZFMK SNSB SNSB SGN SNSB
Contact persons Lutz Suhrbier and Walter Berendsohn (BGBM) Gregor Hagedorn (MfN) Wolfgang Reichert (SNSB) Wolfgang Reichert (SNSB) Tanja Weibulat (SNSB) Thomas Hörnschemeyer, Alex Schmid (SGN) Dieter Neubacher (SNSB)
Developer group, country Biodiversity Informatics BGBM, Germany BGBM, MfN, SNSB, ISPI (Germany); James Macklin (CA); PLAZI (CH); Plantnet, Telabotanica (FR) SNSB IT Center, Germany (together with MfN and UBT as far as the whole DWB platform is concerned) SNSB IT Center, Germany (together with MfN and UBT as far as the whole DWB platform is concerned) SNSB IT Center, Germany (together with MfN and UBT as far as the whole DWB platform is concerned) IT Developer group at Senckenberg Museum of Natural History, Germany Universität Bayreuth, SNSB IT Center, Germany
About a generic annotation system for biodiversity data A jointly managed system to combining biodiversity related wikis from projects around the world a web service for reverse georeferencing. It allows the assignment of areas, lines and points (e.g. administrative areas, sea and river names etc.) to known geo-coordinates. a generic tool for querying descriptive data and building interactive identification keys
Notes (e.g., potential user spectrum) A list of all biodiversity portals integrating AnnoSys can be found under Portals integrating AnnoSys. Test cases available in AnnoSys Sandbox Two biowikifarm-wikis are maintained by GFBio: the GFBio Internal Wiki and the GFBio Public Wiki (contact person; D. Fichtmüller, BGBM) researchers with plot-based survey and sampling data gained in the field; show cases under http://wiki.bayernflora.de/web/Diversity_GIS_Editor researchers with sampling data gained in the field researchers working in the field The developed architecture accelerates the digitization procedure of historical museum collections and helps with the quality check. NaviKey is (a) a tool for online providing the contents of DELTA files, (b) a stand-alone application for accessing DELTA files; a list of portals using NaviKey as online tool for interactive identification is found under http://www.navikey.net/webprojects.html
Software and Database System Server Operating System Debian Linux 7 Debian Linux 7 - - MS Windows Server 2008 R2, 2012 R2 Linux (a) any web server; (b) Java runtime environment (JRE)
Database system Virtuoso 7, SQLite, Apache Jena TDB MS SQL 5.5 MS SQL-Server Compact PostgreSQL with PostGIS extension (a) -; (b) -
User rights management Role based rights management focusing on annotated record Mediawiki Users (shared authentication, separate authorization) + LDAP - - MS SQL-Server specific; few DWB specific features and roles added -
Client Web Browser Web Browser C# WPF desktop application (rich client) C# WPF desktop application (rich client) Windows Phone App The webservice reverse-georeferencing serves as an interface between a requesting system (client) and the database containg the geoobject repository. (a) Webbrowser (Java applet providing the contents of DELTA-structured files); (b) a stand-alone Java application for accessing DELTA-structured files
GIS functionalities - - Creation and handling of geo-referenced maps (several Google and OSM layers) and geographic objects (Points, Linestrings, Polygons...) in WGS84 coordinates system, GPS support - Handling of geo-referenced maps, GPS support Web Map Server -
Interfaces for data import Via connected Biodiversity Data Portals (see Notes above) and by submitting a URL to a valid record or BioCASe provider coordinates via REST API calls Standard Mediawiki API, Mediawiki XML Batch Import ArcView shape import including attributes, CSV shape import wizard, GPX and text file shape import - Data records from SQL databases (including taxonomic lists), topographic maps - -
Interfaces for data export/ reports LOD conform access to stable identifiers for annotations and annotated records Standard Mediawiki API, Mediawiki XML Batch Export, TemplateParameterIndex Export Extension ArcView shape export including attributes, CSV shape export, text file shape export CSV table export Data records for SQL databases, multimedia files HTML, XML, WADL -
GUI language English, German(extensible for other languages) English, German, French active, > 150 available (user-selectable) English, German, Spanish (Easy to extend for other languages) English English German English (per default); see notes on language versions for LIAS light below
Open access Yes Yes Yes, DGE software download Yes, DII software download Yes, Windows Phone Store Yes Yes, NaviKey software download
Open source Yes, AnnoSys Project Zipfile Yes Yes, DWB SVN code repository Yes, DWB SVN code repository Yes, DiversityMobile GitHub Yes Yes, NaviKey SVN code repository
Licenses see Terms of Use GPL v.2 GPL v.2 GPL v.2 GPL v.2 GPL v.2
Information model online - Yes, https://www.mediawiki.org - DiversityMobile Information Models http://webservice.senckenberg.de:8080/reverse-georeferencing-client/ -
State of development Continuous delivery. AnnoSys2 in development Continuous delivery; https://www.mediawiki.org/wiki/Version_lifecycle ongoing (latest stable release see under DWB Software) ongoing (latest stable release see under DWB Software) ongoing (latest stable release see under DWB Software) Release version (occasional updates) ongoing
Code language, developer platform Java, Eclipse RAP PHP C#, .Net Framework, since 2010 C#, .Net Framework, since 2016 C#, .Net Framework, since 2010 Web map server: UMN Mapserver, Geoserver, WebGIS Client: Mapbender 3, OpenLayers, JavaEE, JSP, Primefaces, Tomcat7 Java Development Kit (JDK)
User manual AnnoSys User Guide https://www.mediawiki.org/wiki/Manual:Contents DGE Manual as pdf file under DWB User Manuals DII Manual as pdf file under DWB User Manuals DM Manual as pdf file under DWB User Manuals On page manual -
Training Workshops on demand - DWB workshops for users and database administrators; DGE included since 2010; User Help Desk DWB workshops for users and database administrators; DII included since 2016; User Help Desk DWB workshops for users and database administrators; DM included since 2010; User Help Desk - -
Notes - - - NaviKey might be well used together with DiversityDescriptions (DD) installations; DD has DELTA import/ export functions; the NaviKey applet is, e.g., installed for LIAS light (interactive identification of lichens in hitherto 20 languages)
Interfaces to import data in various schemas and standards xml according ABCD schema - Submitting a URL to a valid record or BioCASe provider coordinates via REST API calls - - - -
xml according DarwinCore schema - Submitting a URL to a valid record via REST API calls - - - -
xml according EML schema - - - - -
xml according other schemas - see above - - - - -
RDF, LOD schema - possible through extensions - - - - -
txt, CSV import - possible through extensions + (import of shapes) - - - -
Notes - - DELTA files (TDWG standard)
Interfaces to export data in various schemas and standards xml according ABCD schema Only for annotated records - - - - - -
xml according DarwinCore schema Only for annotated records - - - - - -
xml according EML schema - - - - - - -
xml according other schemas Annotations in RDF/XML Open Annotation format (tbd) see above - - - -
RDF, LOD schema - possible through extensions - - - - -
txt, CSV export - possible through extensions + (export of shapes) + (export of data tables for DWB import wizards) - - -
Notes Most relevant Annotation Metadata available in simple JSON format (intended to be displayed in connected biodiversity data portals). - DELTA files (TDWG standard)



Table 2

Database system, Homepage Geneious Software suite IMDAS-Pro MapForce Recorder 6D
General Information Installations at GFBio collection data centers/ archives SMNS, SNSB, ZFMK SMNS BGBM SMNS
Contact persons at data centers Juan Carlos Monje (SMNS) Angela Jandl Dominik Röpert, Maren Gleisberg (BGBM) Arno Wörz
Developer group, country Biomatters Limited, New Zealand Joanneum Research, Graz Altova GmbH, Wien Dorset Software, GB: Jan Van Breda, German Version: Thomas Schneider on behalf of BfN
About a suite of molecular biology and NGS analysis tools; for data exchange formats see http://assets.geneious.com/manual/8.0/GeneiousManualse15.html an inventory database system for collections (any kind of objects, e. g. artefacts, models and nature science specimens) a graphical data mapping, conversion, and integration tool that maps data between any combination of XML, database, EDI, XBRL, flat file, Excel, JSON, and/or Web service a tool for floristic and faunistic mapping
External Links http://www.geneious.com http://culture.joanneum.at/imdas/?portfolio=imdas-pro https://www.altova.com/mapforce http://www.recorder-d.de/
Notes new major version released every year (around March) in use at the SMNS since 1998, completely replaced by the Diversity Workbench at the end of 2017 30days trial version available; regularly updated in use at the SMNS since 2010 for the floristic mapping of Baden-Württemberg

Status: July 2018


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