Five major types of biological data have been defined in GFBio and are recognised by the Data Centers in NFDI4Biodiversity. They are used for the "Service Description" of the individual Data Centers as well as in the context of the Technical Documentations of processing tools.
Types of biological data:
Type 1: Biodiversity and Occurrence data
These are the data from the classical collection and alpha-diversity research domain, i.e. digital objects with taxon name(s), georeferences, e.g. locality, date and often referenced resources as multimedia objects. We distinguish between:
- Type 1a: Collection Data (with reference to physical object)
- Type 1b: Observation Data (without reference to physical object)
Used standards:
- ABCD (Access to Biological Collection Data) and extensions
- DwC (Darwin Core) and extensions
- DC (Dublin Core) as included in ABCD and DwC for basic bibliographic information
Used identifiers:
- primary identifier: biological (digital) object (digital specimen or observation)
- main secondary information: geo-information and time, related (multimedia) resources
Example packages:
- Curators Herbarium B (2020). Digital specimen images at the Herbarium Berolinense. [Dataset]. Version: <2020-10-07>. Data Publisher: Botanic Garden and Botanical Museum Berlin. https://data.bgbm.org/dataset/gfbio/0001/. [Please cite individual specimens with their stable ID, for images add the image ID.] (digital specimens), also accessible via GFBio VAT
- Schott, H. (2018). IBF Monitoring of Orthoptera, University of Regensburg. [Dataset]. Version: 20181205. Data Publisher: Staatliche Naturwissenschaftliche Sammlungen Bayerns – SNSB IT Center, München. http://www.diversitymobile.net/wiki/IBForthopteracoll_About. (digital observations), also accessible via GFBio VAT
- Rakotoarison, A.; Scherz, M. D., Bletz, M. C.; Razafindraibe, J. H.; Glaw, F. & Vences, M. (2019). Media and additional measurements belonging to the description of Cophyla fortuna (Microhylidae, Cophylinae). [Dataset]. Version: 1.0. Data Publisher: Zoological Research Museum Koenig - Leibniz Institute for Animal Biodiversity. https://doi.org/10.20363/media-cophyla-fortuna-1.0. (digital specimens), also accessible via GFBio VAT
Notes
The time investment for individual scientific data curation to be done by data providers and GFBio data managers before and during data transformation is varying.
Type 2: Taxon Data
These are taxon-related data (e.g. in a catalogue, checklist or so-called red list).
Used standards:
- ABCD (Access to Biological Collection Data) and extensions
- DwC (Darwin Core) and extensions
- DC (Dublin Core) as included in ABCD and DwC for basic bibliographic information
Used identifiers:
- primary identifier: class name (taxon), e.g., as defined by the nomenclatural rules of the three International Codes of Biological Nomenclature
- main secondary information: taxonomic classifications and concepts, synonymy, vernacular names, geo- and conservation status information etc.
Example packages:
- Taxon list of vascular plants from Bavaria, Germany compiled in the context of the BFL project, also accessible via GFBio terminology service and as taxon backbone in GFBio portal
- Taxon list of animals with German names (worldwide) compiled at the SMNS, also accessible via GFBio terminology service and as taxon backbone in GFBio portal
Notes
The time investment for individual scientific data curation to be done by data providers and GFBio data managers before and during data transformation is varying.
Type 3: Environmental Biological and Ecological Data
These are environmental biological and ecological study data including functional and phylogenetic trait data and other kind of analysis data.
Used standards:
- EML (Ecological Metadata Language)
- DELTA (Description Language for Taxonomy, for trait data)
- SDD (Structured Descriptive Data, for trait data)
- GML (Geography Markup Language) and ISO 19139 metadata
Used identifiers:
- primary identifier: biological class concept (e.g., OTU or OFU)
- main secondary information: trait and environmental (analysis, measurement, transformation, translocation) information
- primary identifier: environmental and ecological study item and event
- main secondary information: biological and ecological information, measurements and description of the environment
Example packages:
- SDD example with EML for basic bibliographic information
- see DOI: 10.25897/5/nhc7-0d72 and DOI: 10.25897/5/tyc9-k378 (SNSB data publication pipeline under construction)
- EML example with CSV table data structured according the EAV data model
- Ferger, Stefan; Schleuning, Matthias; Hemp, Andreas; Howell, Kim; Böhning-Gaese, Katrin (2018): Various investigations to analyze the effects on species richness of birds during the KiLi (Kilimanjaro) Project. PANGAEA, https://doi.org/10.1594/PANGAEA.896128
- see DOI: 10.25897/5/j2cs-q186 and DOI: 10.25897/5/kk8s-7a12 (SNSB data publication pipeline under construction)
Notes
The time investment for individual scientific data curation before and during data transformation of (matrix) data into a highly structured and standard schema-compliant format at data item level might be high. Thus, the data management process has to be agreed between data provider and GFBio data curator before starting (see DMPs).
Type 4: Non-Molecular Analysis Data
These are non-molecular analysis data (data sets and/or data packages) in its original data file format (often RAW format).
Used standards
- EML (Ecological Metadata Language) for basic bibliographic information
- DC (with Pansimple XSD) for basic bibliographic information
Used identifiers:
- primary identifier: as provided by data producer
- main secondary information: as provided by data producer
Example packages:
- coming soon
Notes
This type of data is accepted, as far as well documented and with a core set of standard-compliant metadata and appropriate for long-term archiving.
The time investment for individual scientific data curation to be done by data providers and GFBio data managers before and during data transformation might be limited.
Type 5: Molecular Sequence Data
These are molecular sequence data including MIxS-compliant metadata.
Used standards:
- MixS (Minimum Information about any (X) Sequence)
Used identifiers:
- primary identifier: molecular sample accession
- main secondary information: geo-information and time
Example package:
Notes
The time investment for individual scientific data curation to be done by data providers and GFBio data managers before and during data transformation might be limited.
Additional Information
For more details see also
