Technical documentation of management systems, data processing and publication tools not specialised on collection data
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Revision as of 19:43, 11 February 2015 by Falko Glöckler (Talk | contribs) (→Technical documentation of management systems not specialised on collection data at the GFBio Collection Data Centers, Status 2014)
Technical documentation of management systems not specialised on collection data at the GFBio Collection Data Centers, Status 2014
The tools and systems below are set up for management of data from more than one data domain: collection and observation data, trait data, taxonomic data, molecular data, sampling data and interview data. Some are browser-based applications with own online portal, others are usable as desk top stand-alone applications or are part of a client-server network. All are eventually involved in the GFBio dataflow.
In parallel, the GFBio collection data centers documented their installations of collection management systems. Additional 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.
| Database system, Homepage | AQUiLA | BacDive | DiversityDescriptions (DD) | EDIT Taxonomic Editor | Morph-D-Base | Canto Cumulus | Anymals & plants | Offene Naturführer | |
|---|---|---|---|---|---|---|---|---|---|
| General Information | Installations at GFBio collection data centers/ archives | SGN | DSMZ | SMNS, SNSB, ZFMK | BGBM | ZFMK | MfN | (MfN) | MfN |
| Contact persons | L. Menner and A. Allspach | C. Söhngen, A. Podstawka and B. Bunk (Mailcontact of BacDive Team: mailto:contact@bacdive.de) | V. Sanz and A. Link (SNSB) | A. Müller and K. Luther (BGBM) | L. Vogt (Uni Bonn), P. Grobe (ZFMK) | N.N. (G. Hagedorn, J. Hoffmann, F. Glöckler) | F. Glöckler (MfN), D. Zitterbart (AWI), T. Uher (Uni Erlangen) | G. Hagedorn | |
| Developer group, country | Senckenberg IT Services; Team Application Development | DSMZ IT Services & Bioinformatics Group | SNSB IT Center Germany (together with MfN and UBT as far as the whole DWB platform is concerned) | BGBM (and Naturalis,NL implementing the Validation Framework) | Biodiversity Informatics ZFMK | Canto, Germany | T. Uher (Uni Erlangen), Germany | ... | |
| Data domains | Collection data, collection management data, observation data | Scientific collection data, trait data, physiological, morphological and environmental descriptions | Triple-structured data, e. g. any kind of descriptive or trait data; interactive key functions; molecular data; with the next releases in 2015 sampling data and interview data | collection data, taxonomic data (core functionality), molecular data, descriptive data, identification keys | morphological descriptions, taxonomic data, character matrices. current project: ontology based descriptions | digital assets (multi media) | observation data | taxonomic data, identification keys | |
| Organismic data | all recent and fossil organisms groups; geological data | Bacteria and Archaea (other groups of microorganisms may be in future releases) | all recent and fossil organisms groups; diversity data | all recent and fossil organisms groups (potentially) | all | - | animals and plants | potentially all | |
| Software and Database System | Operating System Server | Ubuntu, Apache Tomcat, Mapserver | Ubuntu 12.04 (Apache) | MS Windows Server 2008 R2, 2012 R2; (clients from MS Windows XP to MS Windows 8) | Linux, Mac OS, MS Windows | Linux | MS Windows Server 2008 R2 | Linux | Linux |
| Database system | PostgreSQL | MySQL 5.1 | MS SQL-Server 2014 | MySQL, PostgreSQL, H2, SQL Server | MySQL, ZOPE ODB | proprietary, but mirroring to MySQL | MySQL, PostgreSQL | MySQL | |
| User rights management | Granular user rights assignment | Read rights global, write individual | MS SQL-Server specific; few DWB specific features and roles added | Roles can be assigned to users according to taxonomic groups and data types (e.g. distribution data only). Project admins have rights to edit all types of data. The underlying software library allows very granular user rights assignment (not yet implemented in the user interface) | Group based user rights. Entries can be shared read-only or writable within groups. Released entries readable by the public | LDAP-connection to institution-wide Active directory | online registration | online registration confirmed by admin | |
| Client | Webapplication, Frontend every common webbrowser | Webapplication, Frontend every common webbrowser | C# desktop application (rich client) (and Web API for the LIASlight project under construction) | desktop application (rich-client), browser based client (for less complex operations, in development) | Browser based client | desktop client, web-based client and web-based gallery | mobile application and website | mobile application and website | |
| GIS functionalities | PostGIS extension, Mapserver (WMS/WFS) | - | - | Visualization of distribution and point maps | None | - | geoserver, PostGIS | - | |
| GUIs for data import | Import wizard | - | Import wizard (DELTA, SDD, CSV) | Currently very simple (but more complex UIs planned) | direct into the database, bulk upload of images possible | included in the desktop client | - | provided by Mediawiki | |
| GUIs for data export/ reports | csv; GUI selectable fields | CSV,PDF, via webservice: XML, JSON | Export (DELTA, SDD, CSV) | Currently very simple (but more complex UIs planned) | CSV, RDf (in development) | CSV, XML | CSV, XML | ... | |
| GUI language | german, english | English | default: english (multilingual through translation tables) | English and German (Easy to extend for other languages) | English | German, English, several others | English, German, Portuguese, Bahasa | German, English, several others (provided by Mediawiki) | |
| Open access | - | - | DD software download | Yes | Yes | - | Yes | Yes | |
| Open source | - | - | DWB SVN code repository | Yes http://cybertaxonomy.eu/taxeditor/source-repository.html | Available on request | No | on request | Yes | |
| Licenses | + | + | GPL v.2 | Mozilla Public License Version 1.2 (Project License) | GPL | - | CC BY-SA 3.0 German license | CC BY-SA 3.0 | |
| Information model online | not available yet | BacDive model | DD data model | Common Data Model (CDM) http://cybertaxonomy.eu/cdm/latest/ | Coming soon | no, because generic | not yet | ... | |
| State of development | Beta Version online (intern) | ongoing | ongoing | ongoing (latest stable release Version3.4, http://cybertaxonomy.eu/download/taxeditor/stable/ released 16.12.2014) | Ver. 3.3 | commercially ongoing | ongoing | ... | |
| Code language, developer platform | Java, JavaFaces, PrimeFaces | PHP, Python, JavaScript | C#, .Net Framework, since 2012 | Java, Eclipse | Python | web client and gallery: Java, JSPX | website: Python, app: Java | PHP | |
| User manual | not available yet | Online manual | DD Manual as pdf file under DWB Wiki | Integrated into the help system of the software. Online available only older versions. Update is planned. | -- | available from vendor | included in app/website as tooltips | ... | |
| Training | on demand | on demand | DWB workshops for users and database administrators; DD included since 2013; User Help Desk | on demand | Workshops, individuals on demand | on demand | on demand | on demand | |
| Notes | - | - | - | - | -- | ||||
| Interfaces to export data in various schemas and standards | xml according ABCD schema | ABCD 2.0 | - | - | yes | DC | - | ABCD 2.06 | - |
| BioCASe Wrapper Version installed, description of dataflow | BioCASe Wrapper V. 3.5, underlying db: PostgreSQL view | BioCASe Wrapper V. 3.5, BacDive export under construction | - | possible on demand | coming soon | - | BioCASe Wrapper V. 3.5 | - | |
| xml according DarwinCore schema | under construction | under construction | - | in preparation (currently no priority) | not planned | - | - | - | |
| xml according EML schema | under construction | - | - | in preparation (currently no priority) | not planned | - | - | - | |
| xml according other schemas | - | + | SDD | CDM-XML. Most data are available through WebServices, most of them as XML or JSON. Documentation available at http://cybertaxonomy.eu/cdmlib/rest-api.html | RDF in development | Cumulus XML | Anymals XML | ... | |
| txt, CSV export | + | + | + | DarwinCore-Archive (csv incl. Metadata), Excel (for taxonomic core data) | csv | CSV,TSV,TXT | CSV | ... | |
| Notes | - | - | DWB network and installations at SNSB; DWB network solutions; DELTA export for use by NaviKey installations | Remote editor and browser based editor (to improve usability) will be available in 2015 | -- |
Status: December 2014
