Technical documentation of multimedia data management systems
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 | Digilib | EasyDB | FSI Image Viewer and FSI Server | MorphDBase | Teamnotes | 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 | Server software to display 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". | 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 | Teamnotes software to manage all images on user demands. Connect images with BGBM internal information systems (e.g. JACQ, BoGART, DNA-Bank). Login to pictures.bgbm.org possible upon request | Zoomify |
| Installations at GFBio collection data centers/ archives | MfN | MfN, deprecated | SNSB, SMNS (ZFMK does instead use MorphDBase) | BGBM | MfN, ZFMK (media.zfmk.de) | (BGBM; DSMZ uses BGBM installation; see below) | ZFMK | BGBM (pictures.bgbm.org ) | SGN | |
| Contact persons | F. Glöckler (MfN) | F. Glöckler (MfN) | D. Triebel, W. Reichert (SNSB) | D. Röpert, M. Gleisberg (BGBM) | F. Glöckler (MfN)
P. Grobe (ZFMK) |
D. Röpert, M. Gleisberg (BGBM) | P. Grobe (ZFMK) | D. Röpert, M. Gleisberg (BGBM) | L. Menner (SGN) | |
| Developer group, country | Wikimedia Foundation, USA | Canto, Germany | DWB Software, Germany | digilib community | programmfabrik, Germany | NeptuneLabs GmbH, Germany | Team at ZFMK and Uni Bonn, Germany | teamnext GmbH, Germany | Santa Cruz, California | |
| Still images | yes | yes | yes | yes | yes | yes | yes | yes | yes | |
| Video | yes | no | yes | yes | yes | yes | yes | yes | no | |
| Audio | yes | no | yes | no | yes | no | yes | no | no | |
| 3D models | no[1] | no | no | yes | yes | yes | yes | yes | no | |
| 2D vector graphics | yes | no | yes | yes | yes | no | yes | yes | no | |
| Documents | partially[1] | possible, but unused | yes | yes | 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 | Example digilib image api:
BGBM stack of images: https://herbarium.bgbm.org/object/B100190491
Example mirador viewer: https://iiif.jacq.org/b/?manifest=http://herbarium.bgbm.org/object/B100844095/manifest.json |
GFBio Archive:https://media.zfmk.de/detail/120015
Collection object image: https://media.zfmk.de/detail/139822 --------------------- |
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 |
https://pictures.bgbm.org/ | SGN single image: http://webapp.senckenberg.de/zoomify/index.html?image=bilder/aq-media/bestikri/images_tiled/2/GLM-46928_Rosa%20canina.zif¶ms=zMeasureVisible%3D1%26zUnits%3Dmm%26zPixelsPerUnit%3D23.6&conversationContext=1 | |
| Geolocation support (Gazetteer, coordinates, GIS shapes) | no[1] | not natively, but possible | yes | yes | yes | yes | no | yes | no | |
| Taxonomic support (no, partial, internal, linked) | no | not natively, but possible | linked (DiversityCollection) | yes, linked to JACQ | possible | no (combined taxonomic and mulitmedia info available in metadata of images in JACQ | internal, linked | yes, linked to JACQ | no | |
| Morphological/anatomical ontology support | no | not natively, but possible | linked (DiversityDescriptions) | no | possible | no | in development (DFG project) | no | no | |
| Link to specimen management system | no | yes | yes | yes | yes | yes | yes (internal) | yes | yes (internal) | |
| Trait data support (no, partial, internal, linked) | no | no | yes | no | possible | no | no | no | no | |
| Software and Database System | Server Operating System | Linux | MS Windows Server 2008 R2 | MS Windows Server 2012 R2, 2016 (clients from MS Windows XP to MS Windows 10) | Linux Docker | Linux (Windows possible) | MS Windows Server 2012 R2 (Linux possible) | Linux | Linux | Linux (Mac and Windows possible) |
| Based on (DBMS) | MariaDB/MySQL 5.5 | proprietary, but mirroring to MySQL | MS SQL-Server 2012 to MS SQL-Server 2016 or MS SQL-Server Express | - | MySQL 5.7+, PopstgresSQL | MySQL 5.5 | MySQL 5.5 | MS SQL | PostgreSQL | |
| User rights management | Biowikifarm+LDAP | LDAP-connection to institution-wide Active directory | own | LDAP | local authorization or LDAP | own | own | own + LDAP | LDAP | |
| Client (Windows, Mac, Android, Web-based) | web browser | desktop client + web-based (limited functionality) | Windows Desktop + Mobile | web-based | web browser/API | web-based | webbrowser | web-based | webbrowser | |
| Software is Open Access (freely available) | yes | no | yes | yes | no, but open-source extensions | no | yes | no | no | |
| Software is Open Source | yes | no | yes | yes | yes | no | yes | no | no | |
| Software License (commercial, open source) | GNU GPL 2 | commercial | GNU Public License | GNU General Lesser Public License (LGPL) version 3.0 | commercial, fallback to opensource should company become insolvent | commercial | GNU Public License | commercial | commercial | |
| Information model documented online | yes | no, because generic | yes | yes | no, because individually extensible | no | yes | no | no | |
| State of development | ongoing | commercially ongoing | ongoing | ongoing | commercially ongoing and open-source community plugins | commercially ongoing | ongoing | commercially ongoing | commercially ongoing | |
| Code language, developer platform | PHP | web client and gallery: Java, JSPX | C#, .NET | Java | PHP | Java, JSPX, Flash | Python | C# | web client, HTML5 and JS, Flash Player (v9 or newer) | |
| User manual | online, open | available from vendor | client help file + online | online | online | availabe from vendor | publication, online | available from vendor | available from vendor | |
| Training | on demand | on demand | workshops | on website | on demand | 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 | - | easyDB XML, JSON Schema | - | - | - | - |
| txt, CSV export | no | CSV,TSV,TXT | CSV,TSV | JSON | CSV, JSON | CSV,TXT | - | CSV, TXT, JsonLD , JSON | - | |
| Additional information | Roadmap status within GFBio data center (legacy, to be replaced, uncertain, primary) | primary | to be replaced | primary | primary image delivery (frontend) | ZFMK: potentially primary,
MfN: primary |
to be replaced | primary | primary (backend) | uncertain |
| Important services and features not mentioned above | API for Bots | automated data import and metadata (EXIF) synchronization | krpano Viewer installation used for several projects; example Product URI: http://zoomview.snsb.info/BSMlichenscoll/M-0025/M-0025264_20120511_125425.html | By using diglib as an iiif compatible image server it is possible to use any iiif compliant viewer (https://github.com/IIIF/awesome-iiif#image-viewers). Currently BGBM uses the Mirador viewer. |
API, manageable workflows | Graphical interface for users to manage their own image repositories; wizards for publishing images in different use cases | - | Graphical interface for users to manage their own image repositories. | 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.
Main repository at ZFMK for all multimedia/byte streaming data (e.g. images, movies, genetic sequence files, PDS, zips) |
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: March 2020
- ↑ 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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