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dataflow:general_dataflow [2021/03/22 14:14] – birgit | dataflow:general_dataflow [2023/04/03 11:20] (current) – [Publication of Data] pgrobe | ||
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- | ====== Dataflow for Preservation of Digital Information at ZFMK Biodiversity Data Center | + | ====== Dataflow for Preservation of Digital Information at LIB Biodiversity Data Center ====== |
- | ===== Data pipeline of research data and corresponding metadata using ZFMK in-house-management systems (DWB, Morph·D·Base, | + | ===== Data pipeline of research data and corresponding metadata using LIB in-house-management systems (DWB, Morph·D·Base, |
- | The [[https:// | + | The [[https:// |
- | The workflow for submission, archiving and publication of data at ZFMK-BDC | + | The workflow for submission, archiving and publication of data follows the standard for a __O__pen __A__rchival __I__nformation __S__ystem ([[https:// |
- | The different modules from Diversity Workbench for specimen occurrence data, literature, taxonomies, and others are used at ZFMK for data and metadata import, metadata enrichment and data quality control (see [[https:// | + | The different modules from Diversity Workbench for specimen occurrence data, literature, taxonomies, and others are used at LIB for data and metadata import, metadata enrichment and data quality control (see [[https:// |
The workflow with these central components is illustrated in figure 1 and described in the text below. | The workflow with these central components is illustrated in figure 1 and described in the text below. | ||
- | **Figure 1: The ZFMK-BDC Data Workflow.** | + | **Figure 1: The LIB Biodiversity Data Center Data-Flow.** |
- | + | ||
- | {{: | + | |
+ | {{ : | ||
; ABCD : Access to Biological Collections Data schema | ; ABCD : Access to Biological Collections Data schema | ||
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; DIP : Dissemination Information Package | ; DIP : Dissemination Information Package | ||
; VAT : Visualizing and Analysing Tool | ; VAT : Visualizing and Analysing Tool | ||
- | |||
==== Submission and Ingestion of Data ==== | ==== Submission and Ingestion of Data ==== | ||
- | Data providers submit their original research data and corresponding metadata via the [[https:// | + | Data providers submit their original research data and corresponding metadata via the [[https:// |
For multimedia data is [[https:// | For multimedia data is [[https:// | ||
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==== Curation of data and metadata ==== | ==== Curation of data and metadata ==== | ||
- | Different types of data require different types of management systems for curation. At ZFMK we use for curation of the following data types specialized software suits: | + | Different types of data require different types of management systems for curation. At LIB we use for curation of the following data types specialized software suits: |
; Occurence data : All specimen related data are integrated in [[http:// | ; Occurence data : All specimen related data are integrated in [[http:// | ||
- | At dataset level there are also stored | + | Metadata |
; Morphological data : The online web-repository [[https:// | ; Morphological data : The online web-repository [[https:// | ||
- | ; Multimedia : The Digital Asset Management System [[https:// | + | ; Multimedia : The Digital Asset Management System [[https:// |
- | ; Metadata : Metadata describing data and associated multimedia are either stored together with the data entries (unit level) or handled in different management modules of DiversityWorkbench, | + | ; Metadata : Metadata describing data and associated multimedia are either stored together with the data entries (unit level) or handled in different management modules of DiversityWorkbench, |
| | ||
- | **Sensible data**: Each of the specialized systems listed above allows to withhold or blur data for publication. This can be the complete entry or part of an entry, e.g. information about the exact sampling location of a specimen. All sensible data are handled according to our [[: | + | **Sensible data**: Each of the specialized systems listed above allows to withhold or blur data for publication. This can be the complete entry or part of an entry, e.g. information about the exact sampling location of a specimen. All sensible data are handled according to our [[: |
=== Enrichment and Annotation of Data and Metadata === | === Enrichment and Annotation of Data and Metadata === | ||
- | The data and metadata submitted to ZFMK-BDC | + | The data and metadata submitted to the LIB Biodiversity Data Center |
- | As far as part of GFBio consensus documents they will be published. | ||
**Identifiers: | **Identifiers: | ||
- | **Licenses: | + | **Licenses: |
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==== Publication of Data ==== | ==== Publication of Data ==== | ||
- | All data uploaded, curated, and archived in the management systems of ZFMK-BDC | + | All data uploaded, curated, and archived in the management systems of LIB Biodiversity Data Center |
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Datasets containing occurrence data are published by creating a snapshot from the data and metadata in DiversityWorkbench for one dataset. This is done with the external helper tool, available from: [[ | Datasets containing occurrence data are published by creating a snapshot from the data and metadata in DiversityWorkbench for one dataset. This is done with the external helper tool, available from: [[ | ||
- | https:// | + | https:// |
- | Datasets stored and curated in [[https:// | + | Datasets stored and curated in [[https:// |
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For each published major version of an occurrence dataset a DOI is assigned. Datasets in Morph·D·Base or easyDB receive a DOI on demand. | For each published major version of an occurrence dataset a DOI is assigned. Datasets in Morph·D·Base or easyDB receive a DOI on demand. | ||
- | The ZFMK is registered at [[https:// | + | The LIB is registered at [[https:// |
== Citation == | == Citation == | ||
- | Published datasets are citable using direct URLs to the DIP or via the DOIs. Based on the data provider' | + | Published datasets are citable using direct URLs to the DIP or via the DOIs. Based on the data provider' |
- | Example: '' | + | Example: '' |
- | ==== ZFMK-BDC archiving system | + | ==== Archiving |
- | Archival Information Packages (AIPs according to OAIS) are created from all data and metadata submitted and curated within the ZFMK in-house-management systems. | + | Archival Information Packages (AIPs according to OAIS) are created from all data and metadata submitted and curated within the LIB in-house-management systems. |
; GitLab : In GitLab are all submitted files - as they are - archived. Furthermore the used import schemes for DiversityWorkbench are archived here. | ; GitLab : In GitLab are all submitted files - as they are - archived. Furthermore the used import schemes for DiversityWorkbench are archived here. | ||
- | ; DWB : Occurences | + | ; DWB : Occurence |
- | ; ZFMK Intranet Filesystem : Backups stored | + | ; LIB Intranet Filesystem : Backups stored |
- | ; easyDB : Multimedia files and versioned ABCD packages are stored in easyDB, which has its own backup in the ZFMK Tape Library. | + | ; easyDB : Multimedia files and versioned ABCD packages are stored in easyDB, which has its own backup in the LIB tape library. |
- | ; ZFMK Tape Library : The generated AIPs are archived in the ZFMK Tape Library. These tapes are stored with two identical copies at two different locations in the ZFMK. | + | ; LIB Tape Library : The generated AIPs are archived in the LIB tape library. These tapes are stored with two identical copies at two different locations in the LIB. |
- | ; Morph·D·Base : The data in MDB is regularly backed up. This backup is available as a redundant copy separate from the running production system. The backup is copied to a file server located in the ZFMK IT department, whereas the running system is housed within the data center of the University of Bonn. | + | ; Morph·D·Base : The data in MDB is regularly backed up. This backup is available as a redundant copy separate from the running production system. The backup is copied to a file server located in the LIB IT department, whereas the running system is housed within the data center of the University of Bonn. |
- | For detailed information about backups and recovery see [[: | + | For detailed information about backups and recovery see [[: |
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==== Access to data via different portals ==== | ==== Access to data via different portals ==== | ||
- | Indexed and faceted data are available in public portals such as GBIF, Europeana and GFBio, which are operated by national or international consortia. Specialized web portals for access to the data are developed and provided by the ZFMK-BDC. These include the [[https:// | + | Indexed and faceted data are available in public portals such as GBIF, Europeana and GFBio, which are operated by national or international consortia. Specialized web portals for access to the data are developed and provided by the LIB Data Center. These include the [[https:// |
The published data are provided with a recommended citation, license and DOI (see above). | The published data are provided with a recommended citation, license and DOI (see above). | ||
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=== Access to published data (unit level) === | === Access to published data (unit level) === | ||
- | ; GFBio and VAT : GFBio has developed a web portal that provides search functionalities for datasets and data. Data are annotated by GFBio' | + | ; GFBio, VAT, and LAND : GFBio has developed a web portal that provides search functionalities for biodiversity related |
; Europeana : The multimedia data are accessible via [[https:// | ; Europeana : The multimedia data are accessible via [[https:// | ||
- | ; Digital Collection Catalogue : All data based on physical vouchers within the natural history collections of ZFMK are accessible via the [[https:// | + | ; Digital Collection Catalogue : All data based on physical vouchers within the natural history collections of LIB are accessible via the [[https:// |
; Morph·D·Base : The online web-repository for morphological data provides public access to specimen, taxon, literature and multimedia data. All data are directly accessible in [[https:// | ; Morph·D·Base : The online web-repository for morphological data provides public access to specimen, taxon, literature and multimedia data. All data are directly accessible in [[https:// | ||
- | ; easyDB : the Digital Asset Management System at ZFMK provides access to the digital assets (i.e. multimedia, documents, zip archives) stored in easyDB. They are published from within the software via [[https:// | + | ; easyDB : the Digital Asset Management System at LIB provides access to the digital assets (i.e. multimedia, documents, zip archives) stored in easyDB. They are published from within the software via [[https:// |
- | ; id.zfmk.de : the API to all occurrence data are accessible by humans and machines in html, json, oder rdf format using https:// | + | ; id.LIB.de : the API to all occurrence data are accessible by humans and machines in html, json, oder rdf format using [[https:// |
=== Access to original and raw data (dataset level) === | === Access to original and raw data (dataset level) === | ||
- | We provide landing pages and direct download links to the datasets from within search results of the [[https:// | + | We provide landing pages and direct download links to the datasets from within search results of the [[https:// |