Technical documentation of multimedia data management systems

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Technical documentation of multimedia data 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 portal (www.gfbio.org) and decentralised infrastructure – they will 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.

Multimedia objects and other digital assets in binary format (like PDF documents, MS Excel files and MS PowerPoint presentations) are managed and archived as part of the regular tasks of the collection data centers. Import and export of files, conversion of file formats, as well as searching within, managing and archiving the files (including their versioning) is carried out by the different systems in place. In general, the multimedia software is integrated in the particular in-house system environment and file storage methods to fulfill the requirements of the collection community by enrichment of digital assets with museum and archive relevant meta information. All GFBio collection data center use at least one solution to manage multimedia objects, as shown in the table below. The deployed software spans a wide range from picture editing, image processing and storage solutions (e.g. Canto Cumulus, FSI-System, Thumps) to more complex environments providing a deeper spectrum of functionalities. Some of the systems in place are very flexible to add any kind of structural, descriptive and administrative metadata (rights and technical metadata included). For types of metadata see Anonymous 2004. The descriptive metadata might be domain-specific and hierarchically structured, e. g. in DWB and MorphDBase.

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


Biowikifarm Multimedia Canto Cumulus DWB Multimedia EasyDB FSI Image Viewer and FSI Server MorphDBase Zoomify
General Information Homepage with Description http://species-id.net/openmedia/Main_Page (for files with open license)
http://species-id.net/specialmedia/Main_Page (for non openly-licensed files. e.g. Institution Logos)
Canto Diversity Workbench, multimedia metadata and file URI management is done as part of seven DWB database components; check also SNSB standards for file processing programmfabrik FSI Server software to display and manage 250MB single source images on user demands in different resolutions, for zooming (on the fly; without pre-processing).It produces all the right variations including color profiles and formats in real-time. This concept is known as "single source dynamic imaging". Login to BGBM mediastorage possible upon request MorphDBase Zoomify
Installations at GFBio collection data centers/ archives MfN MfN SNSB, SMNS (ZFMK does instead use MorphDBase) MfN BGBM (DSMZ uses BGBM installation; see below) ZFMK SGN
Contact persons G. Hagedorn (MfN) F. Glöckler (MfN) D. Triebel, W. Reichert (SNSB) F. Glöckler (MfN) D. Röpert, M. Gleisberg (BGBM) P. Grobe (ZFMK) A. Schmid, L. Menner (SGN)
Developer group, country Wikimedia Foundation, USA Canto, Germany DWB Software, Germany programmfabrik, Germany NeptuneLabs GmbH, Germany Team at ZFMK and Uni Bonn, Germany Santa Cruz, California
Still images yes yes yes yes yes yes yes
Video yes no yes yes yes yes no
Audio yes no yes yes no yes no
3D models no[1] no no yes yes yes no
2D vector graphics yes no yes yes no yes no
Documents partially[1] possible, but unused yes yes yes yes no
Exemplary published multimedia file URIs Polygonum aviculare ssp. aviculare http://coll.mfn-berlin.de/img/MFN_MIN_1977_0386__Achat_a.jpg (no public access to Cumulus, but MfN uses the web service internally for delivering the images to http://coll.mfn-berlin.de/img/{filename}) SNSB single image: http://pictures.snsb.info/BSMvplantscoll/web/M-0184/M-0184687_20120423_113805.jpg; SNSB stack of images: http://www.gbif.org/occurrence/1099846642; SNSB single audio: http://media.snsb.info/IBForthopteracoll/web/ID-4468/ID-446810_20121210_102417.wav; SMNS single image: http://www.gbols.smns-bw.org/images/Philodromus_dispar_SMNS-1174_01.jpg; SMNS-Morphyll single image: http://pictures.snsb.info/Morphyllcoll/web/GDKE/GDKE_PB2006-50/GDKE_PB2006-5000-LS.jpg - BGBM single image: http://herbarium.bgbm.org/object/B100209588 ;BGBM stack of images: http://herbarium.bgbm.org/object/B100190491;BacDive/DSMZ single image: Chondromyces crocatus Cm c2 Cm_c2_M3197_S2265.tif BacDive/DSMZ stack of images: The BacDive entry for Chondromyces crocatus Cm c2 contains a stack of images associated to this bacterial strain. The images are presented via the FSI Viewer (Correct code is generated by the FSI Server at the time of image selection and just needs to be embedded into the html page). Single image: www.morphdbase.de/?Z_FREDIE_20140702-M-2978.1
Stack of images: www.morphdbase.de/?E_Tilic_20150220-M-24.1
MorphDBase links to a website with all the information avaliable for this multimedia entry. This allows publication of image stacks or interlinked media entries. However, a direkt link to the image file is possible: www.morphdbase.de/StorageMedia/images/Z_FREDIE/2014/05/Z_FREDIE_20140702-M-2978.1.jpg
SGN single image:
http://webapp.senckenberg.de/zoomify/index.html?image=bilder/aq-media/bestikri/images_tiled/2/GLM-46928_Rosa%20canina.zif&params=zMeasureVisible%3D1%26zUnits%3Dmm%26zPixelsPerUnit%3D23.6&conversationContext=1

SGN single image:
https://webapp.senckenberg.de//zoomify/index.html?image=bilder/aq-media/bestikri/images_tiled/2/FR-0120112.zif&params=zMeasureVisible%3D1%26zUnits%3Dmm%26zPixelsPerUnit%3D23.6&conversationContext=5

Geolocation support (Gazetteer, coordinates, GIS shapes) no[1] - yes yes yes no no
Taxonomic support (no, partial, internal, linked) no not natively, but possible linked (DiversityCollection) possible no (combined taxonomic and mulitmedia info available in metadata of images in JACQ internal, linked no
Morphological/anatomical ontology support no not natively, but possible linked (DiversityDescriptions) possible no in development (DFG project) no
Link to specimen management system no - yes yes yes yes (internal) yes (internal)
Trait data support (no, partial, internal, linked) no - yes possible no no no
Software and Database System Server Operating System Linux MS Windows Server 2008 R2 MS Windows Server 2008 R2, 2012 R2, 2016 (clients from MS Windows XP to MS Windows 10) Linux (Windows possible) MS Windows Server 2012 R2 (Linux possible) Linux Linux (Mac and Windows possible)
Based on (DBMS) MariaDB/MySQL 5.5 proprietary, but mirroring to MySQL MS SQL-Server 2008 R2 to MS SQL-Server 2016 or MS SQL-Server Express MariaDB/MySQL 5.5 MySQL 5.5 MySQL 5.5 PostgreSQL
User rights management Biowikifarm+LDAP LDAP-connection to institution-wide Active directory own local authorization or LDAP own own LDAP
Client (Windows, Mac, Android, Web-based) web browser desktop client + web-based (limited functionality) Windows Desktop + Mobile web browser web-based webbrowser webbrowser
Software is Open Access (freely available) yes no yes no no yes no
Software is Open Source yes no yes yes no yes no
Software License (commercial, open source) GNU GPL 2 commercial GNU Public License commercial, fallback to opensource should company become insolvent commercial GNU Public License commercial
Information model documented online yes no, because generic yes no no yes no
State of development ongoing commercially ongoing ongoing commercially ongoing commercially ongoing ongoing commercially ongoing
Code language, developer platform PHP web client and gallery: Java, JSPX C#, .NET PHP Java, JSPX, Flash Python web client, HTML5 and JS, Flash Player (v9 or newer)
User manual online, open available from vendor client help file + online online, open availabe from vendor publication, online available from vendor
Training on demand on demand workshops on demand on demand on demand support by Zoomify
Interfaces to export data and identifiable multimedia file URIs in various schemas and standards XML export (which schemas) Mediawiki XML page export, structured data from templates through TemplateParameterIndex Export extension Cumulus XML ABCD, GPI/JSTOR ABCD,GPI/JSTOR - - -
txt, CSV export no CSV,TSV,TXT CSV,TSV CSV,JSON CSV,TXT - -
Additional information Roadmap status within GFBio data center (legacy, to be replaced, uncertain, primary) primary uncertain primary potentially primary primary primary uncertain
Important services and features not mentioned above API for Bots -- krpano Viewer installation used for several projects; example Product URI: http://zoomview.snsb.info/BSMlichenscoll/M-0025/M-0025264_20120511_125425.html -- Graphical interface for users to manage their own image repositories; wizards for publishing images in different use cases - Feature overview, Useful measurement tool
General Notes main file repository for all of the biowikifarm wikis -- multimedia management included in DiversityCollection, DiversityDescriptions, DiversityMobile, DiversitySamplingPlots and other DWB applications main 3D repository of MfN; to be expanded into other capacities. Main data model will be conformal with University of Göttingen BGBM uses, amongst others, ThumpsPlus for picture editing (see link for additional infos); DSMZ provides multimedia data (tiff files) of the Myxobacterial data set via the FSI Server of the BGBM - customers

Status: July 2018

  1. 1.0 1.1 1.2 many file types can be uploaded and stored, but only for the major file types preview/player support exists

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