Difference between revisions of "Technical documentation of management systems, data processing and publication tools not specialised on collection data"

Revision as of 17:07, 12 January 2017

Technical documentation of management systems, data processing and publication tools 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, processing and publishing of data from more than one data domain: collection and observation data, trait data, taxonomic, taxon reference and checklist data, sequence data, sampling data, survey data as well as scientific data packages as a whole. 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 involved in the GFBio dataflow and part of the portfolios of GFBio data centers.

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	BioCASe Provider Software	DiversityDescriptions (DD)	DiversityProjects (DP)	DiversityTaxonNames (DTN)	EDIT Taxonomic Editor	Metacat	Morph-D-Base
General Information	Installations at GFBio collection data centers/ archives	SGN	DSMZ	BGBM, DSMZ, MfN, SGN, SNSB, ZFMK	SMNS, SNSB, ZFMK	SMNS, SNSB, ZFMK	SMNS, SNSB, ZFMK	BGBM	SGN	ZFMK
	Contact persons	Alexander Schmid and A. Allspach (SGN)	C. Söhngen, A. Podstawka and B. Bunk (Mailcontact of BacDive Team: mailto:contact@bacdive.de)	J. Holetschek (BGBM)	V. Sanz and A. Link (SNSB)	T. Weibulat and D. Triebel (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	Biodiversity Informatics BGBM, Germany	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)	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	collection data, collection management data, observation data	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	scientific project-specific metadata and data package-specific metadata, project settings and identifiers	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 organism groups	all	all	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, Linux, Unix, Mac (any OS that runs Python 2.5, 2.6, 2.7)	MS Windows Server 2008 R2, 2012 R2; (clients from MS Windows XP to MS Windows 10)	MS Windows Server 2008 R2, 2012 R2; (clients from MS Windows XP to MS Windows 10)	MS Windows Server 2008 R2, 2012 R2; (clients from MS Windows XP to MS Windows 10)	Linux, Mac OS, MS Windows	Linux, Mac OS, MS Windows	Linux
	Database system	PostgreSQL	MySQL 5.1	MS SQL Server, MySQL, Access, Oracle, Postgres, 4D, Firebirs, Foxpro, Sybase; Excel, CSV	MS SQL-Server 2014	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	On DB level	MS SQL-Server specific; few DWB specific features and roles added	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	Webbrowser	C# desktop application (rich client) (and Web API for the LIASlight project under construction)	C# desktop application (rich client)	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)	-	not applicable	-	-	-	Visualization of distribution and point maps	PostGIS extension, Geoserver (WMS/WFS)	None
	GUIs for data import	generic import tool; import wizard coming soon	-	-	Import wizard (DELTA, SDD, CSV), matrix wizard, local import (FASTA, FASTQ)	generic import tool (coming soon); CSV	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	EXCEL, CSV	CSV,PDF, via webservice: XML, JSON	ABCD and DwC archive export	Export (DELTA, SDD, CSV, FASTA, FASTQ)	various export tools, export wizard (coming soon)	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	English	default: english (multilingual through translation tables)	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	-	-	not applicable	Yes, DD software download	Yes, DP software download	Yes, DTN software download	Yes	Yes	Yes
	Open source	-	-	Yes	Yes, DWB SVN code repository	Yes, DWB SVN code repository	Yes, DWB SVN code repository	Yes, http://cybertaxonomy.eu/taxeditor/source-repository.html	Yes, (Download source distribution)	Available on request
	Licenses	-	-	Mozilla Public License Version 1.1	GPL v.2	GPL v.2	GPL v.2	Mozilla Public License Version 1.2 (Project License)	GPL	GPL
	Information model online		BacDive model	not applicable	DD data model	DP data model	DTN data model	Common Data Model (CDM) http://cybertaxonomy.eu/cdm/latest/	-	Coming soon
	State of development	ongoing; beta version (search portal) online: https://search.senckenberg.de/aquila-public-search/search, http://www.senckenberg.de/root/index.php?page_id=2868	ongoing	ongoing (latest release version 3.6.3 is http://ww2.biocase.org/svn/bps2/branches/stable )	ongoing (latest stable release see under DWB Software)	ongoing (latest stable release see under DWB Software)	ongoing (latest stable release see under DWB Software)	ongoing (latest stable release Version 4.1.1, http://cybertaxonomy.eu/download/taxeditor/stable/ released 07.12.2016)	Vers. 2.5.1 (released January, 2016)	Ver. 3.3
	Code language, developer platform	Java, JavaServer Faces, PrimeFaces	PHP, Python, JavaScript	Python, JavaScript	C#, .Net Framework, since 2012	C#, .Net Framework, since 2013	C#, .Net Framework, since 2005	Java, Eclipse	Java, JSP	Python
	User manual	-	Online manual	BPS Wiki; Beginners Guide	DD Manual as pdf file under DWB User Manuals	DP Manual as pdf file under DWB User Manuals	DTN Manual as pdf file under DWB User Manuals	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	on demand; User Helpdesk	DWB workshops for users and database administrators; DD included since 2013; User Help Desk	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	interface for ingest of GFBio submission information packages (SIPs) (in planning stage)	-	-	-	-
Interfaces to export data in various schemas and standards	xml according ABCD schema	-	-	Yes	-	+	-	+	-	-
	BioCASe Wrapper Version installed, description of dataflow	BioCASe Wrapper V. 3.6.1, 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	+	-	-	+	in preparation (currently no priority)	-	not planned
	xml according EML schema	-	-	-	-	coming soon	-	in preparation (currently no priority)	yes	not planned
	xml according other schemas	-	+	LIDO; arbitrary xml schemas can be handled	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	+	+	yes (DwC-Archive)	+	+	+ (export wizard)	DarwinCore-Archive (csv incl. metadata), Excel (for taxonomic core data)	-	csv
	Notes	-	-	-	several document generators (html, MediaWiki format) and pipelines for dynamic web publication; 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 since Version 3.11; browser based editor (to improve usability) currently available for occurance data; development ongoing and close related to the overall development of the TaxonomicEditor.	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: January 2017

@@ Line 13: / Line 13: @@
 ! style="width:12%" | [http://bacdive.dsmz.de BacDive]
 ! style="width:12%" | BioCASe Monitor Service
-! style="width:12%" |BioCASe Provider Software
+! style="width:12%" |[http://www.biocase.org/products/provider_software/index.shtml BioCASe Provider Software]
 ! style="width:12%" | [http://diversityworkbench.net/Portal/DiversityDescriptions DiversityDescriptions] (DD)
 ! style="width:12%" | [http://diversityworkbench.net/Portal/DiversityProjects DiversityProjects] (DP)
@@ Line 27: / Line 27: @@
 |DSMZ
 |
-|
+|BGBM, DSMZ, MfN, SGN, SNSB, ZFMK
 |SMNS, SNSB, ZFMK
 |SMNS, SNSB, ZFMK
@@ Line 40: / Line 40: @@
 |C. Söhngen, A. Podstawka and B. Bunk (Mailcontact of BacDive Team: mailto:contact@bacdive.de)
 |
-|
+|J. Holetschek (BGBM)
 |V. Sanz and A. Link (SNSB)
 |T. Weibulat and D. Triebel (SNSB)
@@ Line 53: / Line 53: @@
 |DSMZ IT Services & Bioinformatics Group
 |
-|
+|Biodiversity Informatics BGBM, Germany
 |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)
@@ Line 66: / Line 66: @@
 |scientific collection data, trait data, physiological, morphological and environmental descriptions
 |
-|
+|collection data, collection management data, observation data
 |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
 |scientific project-specific metadata and data package-specific metadata, project settings and identifiers
@@ Line 79: / Line 79: @@
 |Bacteria and Archaea (other groups of microorganisms may be in future releases)
 |
-|
+|all recent and fossil organism groups
 |all
 |all
@@ Line 93: / Line 93: @@
 | Ubuntu 12.04 (Apache)
 |
-|
+|MS Windows, Linux, Unix, Mac (any OS that runs Python 2.5, 2.6, 2.7)
 |MS Windows Server 2008 R2, 2012 R2; (clients from MS Windows XP to MS Windows 10)
 |MS Windows Server 2008 R2, 2012 R2; (clients from MS Windows XP to MS Windows 10)
@@ Line 106: / Line 106: @@
 |MySQL 5.1
 |
-|
+|MS SQL Server, MySQL, Access, Oracle, Postgres, 4D, Firebirs, Foxpro, Sybase; Excel, CSV
 |MS SQL-Server 2014
 |MS SQL-Server 2014
@@ Line 119: / Line 119: @@
 |Read rights global, write individual
 |
-|
+|On DB level
 |MS SQL-Server specific; few DWB specific features and roles added
 |MS SQL-Server specific; few DWB specific features and roles added
@@ Line 132: / Line 132: @@
 |Webapplication, Frontend every common webbrowser
 |
-|
+|Webbrowser
 |C# desktop application (rich client) (and Web API for the LIASlight project under construction)
 |C# desktop application (rich client)
@@ Line 145: / Line 145: @@
 | -
 |
-|
+| not applicable
 | -
 | -
@@ Line 158: / Line 158: @@
 | -
 |
-|
+| -
 |Import wizard (DELTA, SDD, CSV), matrix wizard, local import (FASTA, FASTQ)
 |generic import tool (coming soon); CSV
@@ Line 171: / Line 171: @@
 |CSV,PDF, via webservice: XML, JSON
 |
-|
+| ABCD and DwC archive export
 |Export (DELTA, SDD, CSV, FASTA, FASTQ)
 |various export tools, export wizard (coming soon)
@@ Line 184: / Line 184: @@
 |English
 |
-|
+|English
 |default: english (multilingual through translation tables)
 |default: english (multilingual through translation tables)
@@ Line 197: / Line 197: @@
 | -
 |
-|
+|not applicable
 |Yes, [http://diversityworkbench.net/Portal/DiversityDescriptions DD software download]
 |Yes, [http://diversityworkbench.net/Portal/DiversityProjects DP software download]
@@ Line 210: / Line 210: @@
 | -
 |
-|
+| Yes
 |Yes, [http://svn.snsb.info/repos/DiversityWorkbench/ DWB SVN code repository]
 |Yes, [http://svn.snsb.info/repos/DiversityWorkbench/ DWB SVN code repository]
@@ Line 223: / Line 223: @@
 | -
 |
-|
+|Mozilla Public License Version 1.1
 |GPL v.2
 |GPL v.2
@@ Line 236: / Line 236: @@
 |[http://gfbio.biowikifarm.net/int/media/f/f2/BacDive_web_model.pdf BacDive model]
 |
-|
+|not applicable
 |[http://diversityworkbench.net/Portal/DiversityDescriptions_Information_Models DD data model]
 |[http://diversityworkbench.net/Portal/DiversityProjects_Information_Models DP data model]
@@ Line 249: / Line 249: @@
 |ongoing
 |
-|
+|ongoing (latest release version 3.6.3 is http://ww2.biocase.org/svn/bps2/branches/stable )
 |ongoing (latest stable release see under [http://diversityworkbench.net/Portal/Software DWB Software])
 |ongoing (latest stable release see under [http://diversityworkbench.net/Portal/Software DWB Software])
@@ Line 262: / Line 262: @@
 |PHP, Python, JavaScript
 |
-|
+|Python, JavaScript
 |C#, .Net Framework, since 2012
 |C#, .Net Framework, since 2013
@@ Line 275: / Line 275: @@
 |[http://bacdive.dsmz.de/help/ Online manual]
 |
-|
+|[http://wiki.bgbm.org/bps BPS Wiki]; [http://wiki.bgbm.org/bps/index.php/BeginnersGuide Beginners Guide]
 |DD Manual as pdf file under [http://diversityworkbench.net/Portal/DWB_user_manuals DWB User Manuals]
 |DP Manual as pdf file under [http://diversityworkbench.net/Portal/DWB_user_manuals DWB User Manuals]
@@ Line 288: / Line 288: @@
 |on demand
 |
-|
+|on demand; [http://www.biocase.org/help_desk User Helpdesk]
 |[http://www.snsb.info/Workshops.html DWB workshops] for users and database administrators; DD included since 2013; User Help Desk
 |[http://www.snsb.info/Workshops.html DWB workshops] for users and database administrators; DD included since 2013; User Help Desk
@@ Line 301: / Line 301: @@
 | -
 |
-|
+| -
 | management of resources (multimedia objects) related to items, descriptors and descriptor states
 | interface for ingest of GFBio submission information packages (SIPs) (in planning stage)
@@ Line 315: / Line 315: @@
 | -
 |
-|
+| Yes
 | -
 | +
@@ Line 341: / Line 341: @@
 |under construction
 |
-|
+| +
 | -
 | -
@@ Line 354: / Line 354: @@
 | -
 |
-|
+| -
 | -
 | coming soon
@@ Line 367: / Line 367: @@
 | +
 |
-|
+|LIDO; arbitrary xml schemas can be handled
 |SDD-XML
 | +
@@ Line 380: / Line 380: @@
 | +
 |
-|
+| yes (DwC-Archive)
 | +
 | +
@@ Line 393: / Line 393: @@
 | -
 |
-|
+| -
 |several document generators (html, MediaWiki format) and pipelines for dynamic web publication; local import and export of molecular sequence data in FASTA and FASTQ format, DELTA export for use by [http://www.navikey.net NaviKey] installations; see also [http://diversityworkbench.net/Portal/DWB_network_and_installations:_Real_life_examples DWB network and installations at SNSB]; [http://diversityworkbench.net/Portal/DWB_network DWB network solutions]; see also [http://diversityworkbench.net/Portal/DiversityDescriptions_Implementations DiversityDescriptions Quiz Version]
 | -
@@ Line 405: / Line 405: @@
-Status: May 2016
+Status: January 2017

Difference between revisions of "Technical documentation of management systems, data processing and publication tools not specialised on collection data"

Revision as of 17:07, 12 January 2017

Technical documentation of management systems, data processing and publication tools not specialised on collection data at the GFBio Collection Data Centers, Status May 2016

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