Technical documentation of management systems, data processing and publication tools not specialised on collection data
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Revision as of 15:48, 7 June 2016 by Dagmar Triebel (Talk | contribs)
Technical documentation of management systems not specialised on collection data at the GFBio Collection Data Centers, Status May 2016
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.
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, taxon reference and checklist data, sequence data, sampling data and survey 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, multimedia data management systems and of long-term archiving solutions.
| Database system, Homepage | AQUiLA | BacDive | DiversityDescriptions (DD) | DiversityTaxonNames (DTN) | EDIT Taxonomic Editor | Metacat | Morph-D-Base | |
|---|---|---|---|---|---|---|---|---|
| General Information | Installations at GFBio collection data centers/ archives | SGN | DSMZ | SMNS, SNSB, ZFMK | SMNS, SNSB, ZFMK | BGBM | SGN | ZFMK |
| Contact persons | L. Menner and A. Allspach (SGN) | C. Söhngen, A. Podstawka and B. Bunk (Mailcontact of BacDive Team: mailto:contact@bacdive.de) | V. Sanz and A. Link (SNSB) | J. Monje (SMNS), D. Triebel (SNSB) and P. Grobe (ZFMK) | A. Müller and K. Luther (BGBM) | E.-M. Gerstner and C. Weiland (SGN) | L. Vogt (Uni Bonn) and P. Grobe (ZFMK) | |
| 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) | 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) | Knowledge Network for Biocomplexity (KNB), U.S.A. | Biodiversity Informatics ZFMK | |
| Data domains | collection data, collection management data, observation data | scientific collection data, trait data, physiological, morphological and environmental descriptions | triple-structured scientific data, e. g. any kind of descriptive or trait data, attribute data, molecular sequence data, sampling data; matrix data import; interactive key functions | taxonomic data, taxon reference and checklist data | collection data, taxonomic data (core functionality), molecular data, descriptive data, identification keys | scientific data packages, data sets and data tables, particularly from ecology and environmental science | morphological descriptions, taxonomic data, character matrices; current project: ontology based descriptions | |
| 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 | all recent and fossil organisms groups (potentially) | all | all | |
| Software and Database System | Server Operating System | Ubuntu, Apache Tomcat, Mapserver | Ubuntu 12.04 (Apache) | MS Windows Server 2008 R2, 2012 R2; (clients from MS Windows XP to MS Windows 8) | MS Windows Server 2008 R2, 2012 R2; (clients from MS Windows XP to MS Windows 8) | Linux, Mac OS, MS Windows | Linux, Mac OS, MS Windows | Linux |
| Database system | PostgreSQL | MySQL 5.1 | MS SQL-Server 2014 | MS SQL-Server 2014 | MySQL, PostgreSQL, H2, SQL Server | PostgreSQL (or another SQL92-compliant RDBMS like Oracle) | MySQL, ZOPE ODB | |
| User rights management | Granular user rights assignment | Read rights global, write individual | MS SQL-Server specific; few DWB specific features and roles added | 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) | Metacat supports internal password file authentication or the use of LDAP as an external authentication mechanism; multiple access right control (specification of rwx rights to single persons, user groups, etc.) in combination with Morpho, a Java-based import wizard for EML which interfaces with the KNB Metacat server | Group based user rights. Entries can be shared read-only or writable within groups. Released entries readable by the public | |
| 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) | C# desktop application (rich client) | desktop application (rich-client), browser based client (for less complex operations, in development) | Browser based client | Browser based client | |
| GIS functionalities | PostGIS extension, Mapserver (WMS/WFS) | - | - | - | Visualization of distribution and point maps | PostGIS extension, Geoserver (WMS/WFS) | None | |
| GUIs for data import | Import wizard | - | Import wizard (DELTA, SDD, CSV), matrix wizard, local import (FASTA, FASTQ) | generic import tool, import wizard; CSV | Currently very simple (but more complex UIs planned) | Webform or Morpho | direct into the database, bulk upload of images possible | |
| GUIs for data export/ reports | csv; GUI selectable fields | CSV,PDF, via webservice: XML, JSON | Export (DELTA, SDD, CSV, FASTA, FASTQ) | various export tools (e. g. for hierarchy, for accepted names etc.), export wizard; CSV | Currently very simple (but more complex UIs planned) | Export format: EML, Download via Webform or Morpho | CSV, RDf (in development) | |
| GUI language | german, english | English | default: english (multilingual through translation tables) | default: english (multilingual through translation tables) | English and German (Easy to extend for other languages) | English | English | |
| Open access | - | - | DD software download | DTN software download | Yes | Yes | Yes | |
| Open source | - | - | DWB SVN code repository | DWB SVN code repository | Yes http://cybertaxonomy.eu/taxeditor/source-repository.html | Yes (Download source distribution) | Available on request | |
| Licenses | + | + | GPL v.2 | GPL v.2 | Mozilla Public License Version 1.2 (Project License) | GPL | GPL | |
| Information model online | not available yet | BacDive model | DD data model | DTN data model | Common Data Model (CDM) http://cybertaxonomy.eu/cdm/latest/ | - | Coming soon | |
| State of development | Beta Version online (intern) | ongoing | ongoing | ongoing | ongoing (latest stable release Version 4.0, http://cybertaxonomy.eu/download/taxeditor/stable/ released 03.05.2016) | Vers. 2.5.1 (released January, 2016) | Ver. 3.3 | |
| Code language, developer platform | Java, JavaServer Faces, PrimeFaces | PHP, Python, JavaScript | C#, .Net Framework, since 2012 | C#, .Net Framework, since 2005 | Java, Eclipse | Java, JSP | Python | |
| User manual | not available yet | Online manual | DD Manual as pdf file under DWB Wiki | DTN Manual as pdf file under DWB Wiki | Integrated into the help system of the software. Online available only older versions. Update is planned. | Online manual (Metacat Administration Guide) | -- | |
| Training | on demand | on demand | DWB workshops for users and database administrators; DD included since 2013; User Help Desk | DWB workshops for users and database administrators; User Help Desk | on demand; Testversion of EDIT Demo-DB with nightly reset, usable with current EDIT version; Handout-EDIT-Platform-Workshop | - | Workshops, individuals on demand | |
| Notes | - | - | management of resources (multimedia objects) related to items, descriptors and descriptor states | - | - | - | - | |
| Interfaces to export data in various schemas and standards | xml according ABCD schema | ABCD 2.0 | - | - | - | yes | - | - |
| 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 | planned | coming soon | |
| 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) | yes | not planned | |
| xml according other schemas | - | + | SDD-XML | + | 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 | Transformations from EML to Dublin Core performed by Metacat OAI-PMH produce simple Dublin Core (DC). | DC; RDF in development | |
| txt, CSV export | + | + | + | + (export wizard) | DarwinCore-Archive (csv incl. metadata), Excel (for taxonomic core data) | - | csv | |
| Notes | - | - | several document generators (html, MediaWiki format), local import and export of molecular sequence data in FASTA and FASTQ format, DELTA export for use by NaviKey installations; see also DWB network and installations at SNSB; DWB network solutions; see also DiversityDescriptions Quiz Version | DTN managed open data (taxon reference lists and checklists) are in the DWB cloud at SNSB IT Center and available through DTN REST Web Service; documentation under http://services.snsb.info/DTNtaxonlists/rest/v0.1/static/api-doc.html | Remote editor included in Version 3.11; browser based editor (to improve usability) currently prototype, development ongoing, release scheduled for 2016 | The establishment of a Metacat repository does not mean that the database system automatically has a connection to DataOne. SGN will manage and archive the GFBio compliant EML-structured xml-files completely independently (though membership to DataOne might be considered.) | -- |
Status: May 2016
