Herbário João de Carvalho e Vasconcellos, I.S.A./U.L.

Study Extent

The digitisation project covers all of the LISI collection, whose geographic representativeness includes the Iberian Peninsula (Portugal and Spain), the Azores and Madeira regions. A smaller part of the collection includes specimens from other countries.

Sampling

Specimen sampling follows usual practices for collection, preparation and mounting in herbarium sheets.

Quality Control

The following quality control steps were applied to the preparation of this dataset: (1) Data Quality Control: This dataset follows the best practices recommended by GBIF for specimen data quality (Chapman 2005a, 2005b) and georeferencing (Chapman and Wieczorek, 2006). Data on geography, people’s names (collectors, determiners) and taxonomy were reviewed for consistency and standardization using OpenRefine. Resources used include the GBIF’s Name Parser and Species Matching, and geographic gazetteers like Geonames, Geolocate and OpenStreetmap. (2) Digitisation Quality Control: The following procedures were performed for all images: (a) check the presence of the image Metadata; (b) verification of the presence of the data matrix label with the new catalog number; (c) check if collecting information and determinations tags are always visible in the images; (d) check the image quality (using autofocus whenever necessary; checking the quality every 10 images); (e) verification the correct association of the specimen image to the Specify record.

Method steps

1. Databasing The collection database is managed using Specify 6. The following steps were performed until the current situation: Pre-processing data: data gathered from an Access database was exported to an excel file and imported to OpenRefine. Extensive data revision was performed in the datatable, for consistency checks, standardisation of names, duplicates, namely on the catalog number, outlier identification and correction. When required, paper files and other documents were used to cross-check corrections. Fields verified include taxonomy fields - references include IPNI, Flora Iberica and Brummitt and Powell (1992) for species authorship names. Tools and resources include GBIF’s Species Matching and Names Parser; geographic administrative units - standardised and completed following the oficial administrative limits of Portugal (CAOP 2013) and Spain (BDLJE); dates: format checking people names (collectords, determiners) - homogenisation and consistency checks The corrections and updates were performed in a copy of the original table, but no versioning was made of the individual field changes. Import to Specify: Data was inserted into the Specify database using the import tool Specify Workbench. Data quality checks were performed following this import process. Post-processing of specimens’ data: Along with the specimen digitization (see next step), data was reviewed/confirmed and updated/completed when necessary.
2. Specimen imaging The process of specimen digitization is ongoing. Preparation of specimens: Before taking the image, specimens are checked for conservation condition and cleaned when necessary. New data matrix tags are placed in the herbarium sheet. Image acquisition: Images are taken using a planetary scanner I2S eScan Open System, and LIMB Capture software. Default image resolution is 400 dpi, and converted to TIFF format without compression. The filename is based on the catalog number, using a letter suffix if more than one image was created for the same specimen. Metadata of the image uses a predefined template including the name of the operator and license. A scale ruler and a photography colour scale ColorGauge Nano Target is placed in the image frame before acquisition. Image storage: Images were stored in a storage server and in an external NAS. Later on, imagens were attached to Specify’s record using the attachment tool in the software.
3. Two manuals were prepared to support current and future cataloguing and digitisation activities: Manual de Digitalização (Digitization Manual, in Portuguese) LISI Herbarium Digitization Workflow

Vascular plants

1. Plantae
   common name: Plants rank: kingdom
2. Tracheophyta
   rank: phylum
3. Equisetopsida
   rank: class
4. Gnetopsida
   rank: class
5. Liliopsida
   rank: class
6. Lycopodiopsida
   rank: class
7. Magnoliopsida
   rank: class
8. Pinopsida
   rank: class
9. Polypodiopsida
   rank: class
10. Psilopsida
    rank: class

Iberian Peninsula