The LIB Biodiversity Data Center is one of the seven GFBio Collection Data Centers that are part and form the backbone of the GFBio Submission, Repository and Archiving Infrastructure. The data archiving and publication at LIB includes the management systems Diversity Workbench as well as the online platform Morph·D·Base, and digital asset management system easydb. Management tools and archiving processes as done at the Datacenter are described under Technical Documentations. This includes services for documentation, processing and archiving of the provided original data and metadata sets (source data; SIP). Data producers are welcome to use Spreadsheet templates as provided under Templates for data submission. The workflow for submission, archiving and publication of data follows the standard for a Open Archival Information System (OAIS - Open archival information system and Reference Model for an Open Archival Information System (pdf)). This ISO standard basically distinguished between different information packages for submission (SIP), archiving (AIP), and dissemination (DIP). For an overview of ISO standards for digital archives see ISO Standards for Digital Archives.
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 Tools & Workbenches for Data Management at GFBio).
The workflow with these central components is illustrated in figure 1 and described in the text below.
Figure 1: The LIB Biodiversity Data Center Data-Flow.
Data providers submit their original research data and corresponding metadata via the GFBio Submission System to our datacenter or contact it directly using the Email: datacenter@leibniz-lib.de. Completeness of the data and metadata are checked and missing data are requested from the data provider. A Submission Information Package (SIP according to OAIS) is build by several steps, including corrections, back-answers, cleansing, and refinement of the original data. Changes on the data are tracked in the GitLab revision control system at LIB, following a standard procedure as documented in Data flow for Original Data. Correspondence with data providers are stored and documented in our ticketing system. All relevant information is stored and archived on tape.
For multimedia data is Morph·D·Base used, where a user account is provided and the user can transfer his data directly. All available metadata are stored for each record.
Each SIP is imported into the management systems and prepared for dissemination by transforming the original research data and corresponding metadata to meet domain specific requirements as well as requirements data exchange, such as standards like ABCD.
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:
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 Data Policy: Data provision for upload. For personal data the GDPR as described in the LIB Privacy Policy applies.
The data and metadata submitted to the LIB Biodiversity Data Center can be enriched and annotated within the management systems listed above. This is done manually by one of the LIB data curators in close cooperation with the data provider or by domain experts with access to the management systems.
Identifiers: Identifiers are used to provide unambiguous identification of information, e.g. unique identifiers for person names such as ORCID or to interlink information with one another. Identifiers can be added to the (meta-)data by using controlled classifications (i.e. whether the identifier is a sequence information, a person identifier, or a crossref for literature, etc.) and URLs.
Licenses: Different licenses can be applied to the submitted data. They are part of the metadata on unit or dataset level. All metadata stored and published by the Dtacenter receive the Creative Common CC0 waiver. The most frequently used license for specimen related data and multimedia is the CC BY-SA 4.0. An overview about all available CC licenses are here.
All data uploaded, curated, and archived in the management systems of LIB Biodiversity Data Center can be published. Publishing of datasets are negotiated with the data provider. Aspects to consider are sensible data for withhold (see above), or publishing restrictions caused by third parties.
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: LIB GitLab: VCAT-Transfer. All data are mapped using the BioCASe Provider Software to the ABCD 2.1 Standard. A Dissemination Information Package (DIP according to OAIS) is created and stored as zip-archive in the digital asset management system easydb at LIB. Each DIP is versioned and the version is identified by a date suffix and its version number consisting of a major version and a minor version (e.g. 2.1). Major changes, such as the addition of further data, increment the major version. Minor changes, e.g. correction of typing errors or changes in the metadata are reflected in an increment of the minor version.
Datasets stored and curated in Morph·D·Base or easyDB are published from within the software.
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 LIB is registered at ZB MED and can therefore create a DOI at DataCite DOI Fabrica. The DOI is added to the corresponding version of the information package and is also part of the citation of the data set (see below).
Published datasets are citable using direct URLs to the DIP or via the DOIs. Based on the data provider's input the citation of the dataset will be prepared by the LIB data curator adjusting the input (submission metadata) to be conform with the GFBio citation pattern. The citation is finalized in close collaboration with the data provider. For details see General part of GFBio publication of type 1 data via BioCASe data pipelines
Example: ZFMK Coleoptera Working Group (2023). ZFMK Coleoptera Oberthuer collection. [Dataset]. Version: 2.0. Data Publisher: LIB Biodiversity Datacenter. https://doi.org/10.20363/ZFMK-Coll.Oberthuer-2023-02
Archival Information Packages (AIPs according to OAIS) are created from all data and metadata submitted and curated within the LIB in-house-management systems.
For detailed information about backups and recovery see Preservation Plan.
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 LIB digital collection catalogue, the portal of the German Barcode of Life project (GBOL), or interfaces to the data, which also provide APIs for machine readable formats and access to the data using CETAF stable identifiers (id.zfmk.de, or id.zmh-coll.de).
The published data are provided with a recommended citation, license and DOI (see above).
We provide landing pages and direct download links to the datasets from within search results of the GFBio web portal, our GitLab installation at gitlab..leibniz-lib.de (login required), the digital asset management system easydb (see above), and the BioCASe Provider Software (BPS) and local query tool of BPS as operated at LIB.