Valorization of Historical Natural History Collections Through Digitization: The Algarium Vatova–Schiffner
Abstract
:1. Introduction
2. Digitization of NHCs
3. Digitization Workflows for Historical NHCs
4. A Case Study: The Algarium of Aristocle Vatova and Victor Schiffner
- pre-digitization planning;
- pre-digitization curation;
- digital imaging;
- metadata transcription;
- geo-referencing;
- publication and dissemination.
4.1. Pre-Digitization Planning
- Will a unique identifier be given to each specimen? Unique Identifiers (UIDs) are particularly relevant, since they allow us to address univocally each specimen in a collection. Normally, they are associated with the specimen as a written alphanumeric string, a barcode, or a QR-code. Meadows et al. [46], Juty et al. [47], Hardisty et al. [48], and Islam S. et al. [49] have covered well the topic of Persistent Identifiers (PIDs) to properly identify digital representations of physical specimens, suggesting the assigning of a unique identifier to every locality and collection date, to properly track specimens. According to Hardisty et al. [48], preferred identifiers for NHCs specimens include CETAF Stable Identifiers [50], International Geo Sample Numbers (IGSNs) [51], GUIDs, Darwin Core Triplets, institution/collection codes, and catalog numbers.
- Will full imaging be performed? The specimens may have been preserved in envelopes, boxes, tubes, or other containers. Especially when envelopes have been used, labels or annotations have often been placed on the external surface of the envelope, while the specimen(s) are not visible unless the envelope is opened. This can be true also for specimen parts, microscopic slides, and other ancillary material linked to a specimen. In such cases, full digital imaging would require the opening of each envelope and the image label(s) and/or annotations being together with the specimen(s), thus achieving a complete digital representation. Alternatively, it is possible to focus on imaging the label(s) alone, greatly speeding up the process, with obvious impact on the duration and the cost of the digitization process.
- Which image resolution, quality of image, and format will be adopted? The International Image Interoperability Framework (IIIF, [52]) provides recommendations for digitizing cultural heritage materials, emphasizing the need for high-resolution images for detailed examination and research. As noted by Nieva de la Hidalga et al. [18], the majority of botanical institutions follow the digitization guidelines of the Global Plants Initiative (GPI) [53], which specifies the elements to include and the resolution for herbarium sheet images. According to Takano et al. [54], images should be usable and suitable for long-term storage. Capturing and preserving high-quality specimen images offers opportunities to take advantage of future improvements in image analysis, Optical Character Recognition (OCR) [55], natural language processing, handwriting analysis, and data-mining technologies [30]. While the minimum resolution for digital images should be set at 300 dpi, a resolution of 600 dpi is recommended, to capture fine details. However, image resolution should be a trade-off between quality and equipment costs, which can be relevant. Given that digital images are not included in the Minimum Information about a Digital Specimen (MIDS) up to level 2 [56,57], a lower resolution can be acceptable in the case of equipment restrictions. A trade-off should also be decided between quality and storage, given that permanent digital storage for images can be quite expensive. While a TIFF format allows for higher quality, it also calls for larger digital storage. On the other hand, JPEG images require far less (approx. 102) storage room, but are of lower quality than other formats. Another option is the adoption of PNG compression. The latter is a lossless compression method, while the JPEG is a lossy one. Thus, the quality of PNG images is intrinsically higher. This, however, comes at the price of a larger file size, even if not comparable with that of TIFF files.
- Which workflow type will be adopted? Nelson et al. [30] described three dominant digitization workflows for natural history collections: (a) data capture with occasional specimen imaging, (b) parallel data and specimen imaging, and (c) imaging of specimens and labels followed by data capture from the images (image-to-data workflow). The latter has multiple advantages. It requires handling the specimens only once (for the digital imaging phase), while the transcription is made from the images. Furthermore, it allows for different operators to work on separate tasks (digital imaging and transcriptions), thus significantly increasing throughput [36]. In general, an image-to-data workflow should always be preferred, since it at least allows for reduction of the times a specimen is handled during the process (ideally down to once) if digital imaging is planned.
- Will all the annotations on a specimen be transcribed? The Minimum Information about a Digital Specimen (MIDS) [56,57] framework provides a structured approach to the digitization of natural history specimens. Each MIDS level provides a certain amount of information, which increases from level 0 to level 3. As an example, MIDS level 1 includes basic metadata, such as taxon name and gathering locality, while higher levels incorporate more detailed information [22]. Labels are the primary source of information about a specimen, especially as far as taxon name, locality, and date of collection are concerned. However, other annotations can be present on the label or elsewhere (on the herbarium sheet, on other labels, etc.). Annotations are not normally the focus of digitization [30], but they can be fundamental to the fitness-for-use of specimens [58]. While transcribing at least MIDS levels 1–2 generates a dataset fit for most uses, all the remaining annotations, which can be quite rich, can be of great interest as well, and may broaden the array of the potential uses of the specimens. However, their extraction may require a large investment, in terms of time and money. Again, a trade-off between costs and results should be achieved.
- Which data scheme will be adopted? The choice on how the data will be organized is closely related to the previous point, i.e., what will be transcribed. As an example, if the transcription focuses on MIDS up to level 3 then the Simple Darwin Core [59] flat structure can be easily adopted for organizing the data in a widely adopted standard format. However, if the transcription results in more complex data structures, with relationships different from 1:1, the Simple Darwin Core flat structure may be more difficult to adopt. For instance, if a specimen undergoes one or more revision event, the relationship between the specimen and the identification events will be 1:many. Thus, a proper representation of the specimen in the digital domain would call for a relational structure, instead of the flat structure of Simple Darwin Core [59]. The Darwin Core Archive overcomes this issue, allowing for 1:many relationships, thanks to the use of extensions, such as Identification History, Measurement or Fact, or Simple Multimedia. These extensions allow for relating one or more events or images to a single observation/specimen. At the same time, the ABCD standard [60], which was specifically designed to represent specimens and their 1:many relationships with events, data, and media, may be more useful in this case. In general, once a decision has been made on the amount and type of data that will be extracted from the specimens, a data model should be selected, taking into account also that data should be made interoperable on digital platforms, such as the Global Biodiversity Information Facility (GBIF) [61]. Since the Darwin Core Archive can accommodate specimens data, and it is the data standard adopted in the GBIF (but not only in the GBIF), its adoption should be preferred.
- Given that one-to-many specimens were present on each sheet, and given the structure of the digital archive of the Museum, which allowed for a single code for each herbarium sheet, it was decided to give to each specimen a UID, which would be made by an alphanumeric string composed by the code of the sheet followed by a sequential number for the specimen (e.g., MSNVE-0001234.1). When the dataset was published in the GBIF, CETAF stable identifiers would be adopted as well.
- During the digital imaging phase, all the envelopes were to be opened, and all the microscopic slides were to be digitized. This would call for a 1:many relationship between the specimens and the images, i.e., for each specimen, one or more images would exist.
- Images of the whole herbarium sheets were to be taken with a planetary scanner, while close-up images of particular morphological features, as well as for some slides, were to be captured, using a full-frame reflex camera. The images were to be stored as JPEG compressed files. The adoption of JPEG compression was due to the necessity of limiting the storage requirements, even in comparison with PNG compressed files, while ensuring an acceptable level of image quality to the viewers. Whenever possible, however, the adoption of higher quality formats is suggested. Image data were to be organized following the terms of the Simple Multimedia extension of the Darwin Core Archive in the version of the dataset that was to be published in the GBIF.
- An image-to-data-(to web) workflow was to be adopted. Specimens were to be digitally imaged, and then stored again, while transcription was to be performed using the digital images.
- Primary data and annotations were to be transcribed. Notes on each specimen about peculiar annotations or interventions were to be reported in the dataset. Annotations in other languages (i.e., German manuscript by V. Schiffner) were to be exposed to the users by means of digital images as extensions of the specimens [14].
- The Darwin Core standard model was to be adopted. In particular, among the Darwin Core terms, the following were to be used: catalogNumber; verbatimIdentification; scientificName; verbatimLocality; locationID; decimalLatitude; decimalLongitude; eventDate; recordedBy; recordedByID; identifiedBy; identifiedByID; identificationRemarks; occurenceRemarks. Furthermore, a non-standard term (Notes) was to be added for reporting annotations of scientific and historical interest that arose during the digitization process. This term was to be organized following the terms of the Measurements or Facts extension of the Darwin Core Archive in the version of the dataset that was to be published in the GBIF.
4.2. Pre-Digitization Curation
4.3. Digital Imaging
4.4. Metadata Transcription
4.5. Geo-Referencing
4.6. Publication and Dissemination
5. Discussion
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
ABCD | Access to Biological Collection Data |
DwC | Darwin Core |
GBIF | Global Biodiversity Information Facility |
MIDS | Minimum Information about a Digital Specimen |
NHC | Natural History Collection |
NHM | Natural History Museums |
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Seggi, L.; Trabucco, R.; Martellos, S. Valorization of Historical Natural History Collections Through Digitization: The Algarium Vatova–Schiffner. Plants 2024, 13, 2901. https://doi.org/10.3390/plants13202901
Seggi L, Trabucco R, Martellos S. Valorization of Historical Natural History Collections Through Digitization: The Algarium Vatova–Schiffner. Plants. 2024; 13(20):2901. https://doi.org/10.3390/plants13202901
Chicago/Turabian StyleSeggi, Linda, Raffaella Trabucco, and Stefano Martellos. 2024. "Valorization of Historical Natural History Collections Through Digitization: The Algarium Vatova–Schiffner" Plants 13, no. 20: 2901. https://doi.org/10.3390/plants13202901
APA StyleSeggi, L., Trabucco, R., & Martellos, S. (2024). Valorization of Historical Natural History Collections Through Digitization: The Algarium Vatova–Schiffner. Plants, 13(20), 2901. https://doi.org/10.3390/plants13202901