Herbário João de Carvalho e Vasconcellos, I.S.A./U.L.
Citation
Arsénio P, Cunha A R, Paes P, Vasconcelos T, Figueira R (2021). Herbário João de Carvalho e Vasconcellos, I.S.A./U.L.. Instituto Superior de Agronomia / Universidade de Lisboa. Occurrence dataset https://doi.org/10.15468/olfpjv accessed via GBIF.org on 2024-09-01.Description
The Herbarium João de Carvalho e Vasconcellos (LISI) is a centenary Herbarium, founded in 1917, in the Instituto Superior de Agronomia (ISA), School of Agriculture, of the University of Lisbon (ULisboa). The LISI Herbarium houses more than 80.000 pressed and dried specimens, including 48 type specimens. It holds one of the largest collections of spontaneous vascular plants for mainland Portugal and Azores. The herbarium is in active growth, with about 900 new accessions per year, and is among the reference collections for the Flora Iberica project.Sampling Description
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
- 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.
- 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.
- Two manuals were prepared to support current and future cataloguing and digitisation activities: Manual de Digitalização (Digitization Manual, in Portuguese) LISI Herbarium Digitization Workflow
Additional info
Home page of the collection: https://www.isa.ulisboa.pt/drat/herbario/apresentacaoTaxonomic Coverages
Vascular plants
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Plantaecommon name: Plants rank: kingdom
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Tracheophytarank: phylum
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Equisetopsidarank: class
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Gnetopsidarank: class
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Liliopsidarank: class
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Lycopodiopsidarank: class
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Magnoliopsidarank: class
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Pinopsidarank: class
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Polypodiopsidarank: class
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Psilopsidarank: class
Geographic Coverages
Iberian Peninsula
Bibliographic Citations
- Chapman AD (2005) Principles of Data Quality. Global Biodiversity Information Facility - https://doi.org/10.15468/doc.jrgg-a190
- Chapman, A. D. 2005. Principles and Methods of Data Cleaning: Primary Species and Species-Occurrence Data, version 1.0. Report for the Global Biodiversity Information Facility, Copenhagen. Available online at http://www.gbif.org/document/80528. -
- Chapman AD & J Wieczorek, eds. (2006) Guide to Best Practices for Georeferencing. Copenhagen: GBIF Secretariat - https://doi.org/10.15468/doc-2zpf-zf42
- BRUMMITT, R. K. and POWELL, C. E. (editors) (1992). Authors of plant names. A list of authors of scientific names of plants, with recommended standard form of their names including abbreviations. Royal Botanic Gardens, Kew -
- CAOP 2013 - Carta Administrativa Oficial de Portugal, Direção Geral do Território. -
- Divisiones Administrativas de España (BDLJE) -
Contacts
Pedro Arséniooriginator
position: Curator
Instituto Superior de Agronomia, Universidade de Lisboa
Herbário, Tapada da Ajuda
Lisboa
1349-017 Lisboa
PT
email: arseniop@isa.ulisboa.pt
userId: http://orcid.org/0000-0003-3860-9789
Ana Raquel Cunha
originator
position: Research Fellow - PORBIOTA project
Instituto Superior de Agronomia, Universidade de Lisboa
Herbário, Tapada da Ajuda
Lisboa
1349-017 Lisboa
Lisboa
PT
email: arcunha@isa.ulisboa.pt
userId: http://orcid.org/0000-0002-0536-1628
Paula Paes
originator
position: Técnica de Herbário
Instituto Superior de Agronomia, Universidade de Lisboa
Herbário, Tapada da Ajuda
Lisboa
1349-017 Lisboa
Lisboa
PT
email: appaes@isa.ulisboa.pt
Teresa Vasconcelos
originator
position: Técnica Superior
Instituto Superior de Agronomia, Universidade de Lisboa
Herbário, Tapada da Ajuda
Lisboa
PT
Rui Figueira
originator
position: Researcher
Instituto Superior de Agronomia, Universidade de Lisboa
Herbário, Tapada da Ajuda
Lisboa
1349-017
PT
Telephone: (+351) 213653165
email: ruifigueira@isa.ulisboa.pt
userId: http://orcid.org/0000-0002-8351-4028
Pedro Arsénio
metadata author
position: Curator
Instituto Superior de Agronomia, Universidade de Lisboa
Herbário, Tapada da Ajuda
Lisboa
1349-017 Lisboa
PT
email: arseniop@isa.ulisboa.pt
userId: http://orcid.org/0000-0003-3860-9789
Ana Raquel Cunha
metadata author
position: Research Fellow - PORBIOTA project
Instituto Superior de Agronomia, Universidade de Lisboa
Herbário, Tapada da Ajuda
Lisboa
1349-017 Lisboa
Lisboa
PT
email: arcunha@isa.ulisboa.pt
userId: http://orcid.org/0000-0002-0536-1628
Rui Figueira
metadata author
position: Researcher
Instituto Superior de Agronomia, Universidade de Lisboa
Herbário, Tapada da Ajuda
Lisboa
1349-017 Lisboa
PT
Telephone: (+351) 213653165
email: ruifigueira@isa.ulisboa.pt
userId: http://orcid.org/0000-0002-8351-4028
Pedro Arsénio
administrative point of contact
position: Curator
Instituto Superior de Agronomia, Universidade de Lisboa
Herbário, Tapada da Ajuda
Lisboa
1349-017 Lisboa
PT
email: arseniop@isa.ulisboa.pt
userId: http://orcid.org/0000-0003-3860-9789