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

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.

Identification

Alternate Identifier: 10.15468/olfpjv

Alternate Identifier: https://ipt.isa.ulisboa.pt/ipt_isa/resource?r=herbario_lisi

Alternate Identifier: 835ac57e-f762-11e1-a439-00145eb45e9a

Alternate Identifier: 253

Publication Date: 2021-01-11

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

Abstract: 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.

Dataset Language: PORTUGUESE

Dataset Creator: Instituto Superior de Agronomia, Universidade de Lisboa - Pedro Arsénio (Curator )

Herbário, Tapada da Ajuda , Lisboa , 1349-017 Lisboa , PORTUGAL

Dataset Creator: Instituto Superior de Agronomia, Universidade de Lisboa - Ana Raquel Cunha (Research Fellow - PORBIOTA project )

Herbário, Tapada da Ajuda , Lisboa , Lisboa , 1349-017 Lisboa , PORTUGAL

Dataset Creator: Instituto Superior de Agronomia, Universidade de Lisboa - Paula Paes (Técnica de Herbário )

Herbário, Tapada da Ajuda , Lisboa , Lisboa , 1349-017 Lisboa , PORTUGAL

Dataset Creator: Instituto Superior de Agronomia, Universidade de Lisboa - Teresa Vasconcelos (Técnica Superior )

Herbário, Tapada da Ajuda , Lisboa , PORTUGAL

Dataset Creator: Instituto Superior de Agronomia, Universidade de Lisboa - Rui Figueira (Researcher )

Herbário, Tapada da Ajuda , Lisboa , 1349-017 , PORTUGAL

Metadata Provider: Instituto Superior de Agronomia, Universidade de Lisboa - Pedro Arsénio (Curator )

Herbário, Tapada da Ajuda , Lisboa , 1349-017 Lisboa , PORTUGAL

Metadata Provider: Instituto Superior de Agronomia, Universidade de Lisboa - Ana Raquel Cunha (Research Fellow - PORBIOTA project )

Herbário, Tapada da Ajuda , Lisboa , Lisboa , 1349-017 Lisboa , PORTUGAL

Metadata Provider: Instituto Superior de Agronomia, Universidade de Lisboa - Rui Figueira (Researcher )

Herbário, Tapada da Ajuda , Lisboa , 1349-017 Lisboa , PORTUGAL

Dataset Contact: Instituto Superior de Agronomia, Universidade de Lisboa - Pedro Arsénio (Curator )

Herbário, Tapada da Ajuda , Lisboa , 1349-017 Lisboa , PORTUGAL

Keywords (GBIF Dataset Type Vocabulary: http://rs.gbif.org/vocabulary/gbif/dataset_type.xml )

Occurrence

Keywords (GBIF Dataset Subtype Vocabulary: http://rs.gbif.org/vocabulary/gbif/dataset_subtype.xml )

Specimen

Keywords (GBIF Dataset Type Vocabulary: http://rs.gbif.org/vocabulary/gbif/dataset_type_2015-07-10.xml )

Occurrence

Keywords (NA )

herbarium
Espanha
Vascular plants
Portugal
Spain

Geographic Coverage

Geographic Description: Iberian Peninsula

Bounding Box

West Bounding Coordinate: -10.283

East Bounding Coordinate: 3.428

North Bounding Coordinate: 43.929

South Bounding Coordinate: 35.996

Temporal Coverage

Range of Dates

Begin Date

1857

End Date

2019

Taxonomic Coverage

General Taxonomic Coverage: Vascular plants

Taxonomic Classification

Taxonomic Rank Name: Kingdom

Taxonomic Rank Value: Plantae

Common Name: Plants

Taxonomic Classification

Taxonomic Rank Name: Phylum

Taxonomic Rank Value: Tracheophyta

Taxonomic Classification

Taxonomic Rank Name: Class

Taxonomic Rank Value: Equisetopsida

Taxonomic Classification

Taxonomic Rank Name: Class

Taxonomic Rank Value: Gnetopsida

Taxonomic Classification

Taxonomic Rank Name: Class

Taxonomic Rank Value: Liliopsida

Taxonomic Classification

Taxonomic Rank Name: Class

Taxonomic Rank Value: Lycopodiopsida

Taxonomic Classification

Taxonomic Rank Name: Class

Taxonomic Rank Value: Magnoliopsida

Taxonomic Classification

Taxonomic Rank Name: Class

Taxonomic Rank Value: Pinopsida

Taxonomic Classification

Taxonomic Rank Name: Class

Taxonomic Rank Value: Polypodiopsida

Taxonomic Classification

Taxonomic Rank Name: Class

Taxonomic Rank Value: Psilopsida

License Information

Intellectual Rights

This work is licensed under a

Creative Commons Attribution (CC-BY) 4.0 License

Projects

• Project

Title: Digital cataloguing and imaging of the Herbarium João de Carvalho e Vasconcellos (LISI)

Personnel

Individual Name

Given Name: Pedro

Surname: Arsénio

User ID: 0000-0003-3860-9789

Role: CURATOR

Personnel

Individual Name

Given Name: Rui

Surname: Figueira

User ID: 0000-0002-8351-4028

Role: PROGRAMMER

Personnel

Individual Name

Given Name: Ana Raquel

Surname: Cunha

User ID: 0000-0002-0536-1628

Role: PROCESSOR

Abstract

This project is an initiative by the Instituto Superior de Agronomia of the Universidade de Lisboa to promote the specimen digital cataloguing and imaging of the herbarium. The project has been carried out in several phases, using different sources of funding. Currently, the following operations are being carried out:

- assignment of new catalog numbers and barcodes

- data review for consistency checks, completeness and updates

- digitization of specimens

Funding

This project was supported by several funding initiatives including:

project PORBIOTA – Portuguese E- Infrastructure for Information and Research on Biodiversity – 22127, with reference PINFRA/22127/2016 POCI-01-0145-FEDER-022127, supported by national funds by FCT / MCTES and co-supported by Fundo Europeu de Desenvolvimento Regional (FEDER) throughout COMPETE 2020 – Programa Operacional Competitividade e Internacionalização (POCI-01-0145-FEDER-022127).

Study Area Description

Descriptor

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

Design Description

Description

Two main activities were carried out in the project:

- Digital cataloguing of the herbarium specimens. This activity was performed in different phases and projects. Finally, during the PORBIOTA project, the database was reviewed and imported to Specify 6.

- Digitization of herbarium specimens: This ongoing activity will provide the digitisation of the full herbarium collection. Digitisation is performed with a planetary scanner I2S eScan Open System.

Methods

• Method

Method Step

Description

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.

Method Step

Description

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.

Method Step

Description

Two manuals were prepared to support current and future cataloguing and digitisation activities:

Manual de Digitalização (Digitization Manual, in Portuguese)

LISI Herbarium Digitization Workflow

Sampling

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

qualityControl

Description

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.

Not available