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Herbarium specimen image of Knema laurina Warb., part of the collection of Naturalis Biodiversity Center

Part of a training dataset of scanned herbarium specimens. The data paper and a summary landing page will be published on Zenodo as it gets published. Content of this deposition: - A JSON-LD datafile listing the label data associated with this herbarium specimen. The Darwin and Dublin Core data standards are used for most values. - A JPEG image file of the scanned herbarium sheet.

Herbarium specimen image of Ficus saxophila Blume, part of the collection of Naturalis Biodiversity Center

Herbarium specimen image of Garcinia nervosa Miq., part of the collection of Naturalis Biodiversity Center

Herbarium specimen image of Dissochaeta monticola Blume, part of the collection of Naturalis Biodiversity Center

Herbarium specimen image of Euphorbiaceae, part of the collection of Naturalis Biodiversity Center

Herbarium specimen image of Ludwigia adscendens subsp. adscendens, part of the collection of Naturalis Biodiversity Center

Herbarium specimen image of Dioscorea anguina Roxb., part of the collection of Naturalis Biodiversity Center

Herbarium specimen image of Elephantopus scaber L., part of the collection of Naturalis Biodiversity Center

Herbarium specimen image of Scirpus maritimus L., part of the collection of Naturalis Biodiversity Center

opencc-by-4.0Jan 2019View details →

Large-scale and fine-grained phenological stage annotation of herbarium specimens datasets

This upload is constituted of four datasets of specimens from American herbaria covering different levels of information precision and different floras - from temperate to equatorial. Three of these datasets consist of selected specimens from herbaria located in different geographic and environmental regions. Each specimen of these three datasets was annotated with the following fields: family, genus, species name, fertile / non-fertile, presence / absence of flower(s), presence / absence of fruit(s). The resulting dataset was composed of 163,233 herbarium specimens belonging to 7,782 species, 1,906 genera, and 236 families. Specimens were annotated as “fertile” if any reproductive structures were present, such as sporangia (ferns), cones (gymnosperms), flowers, or fruits (angiosperms). Non-fertile specimens were those that lacked any reproductive structures. The fourth dataset consists of 20,371 herbarium specimens from 11 genera in the sunflower family (Asteraceae). The main difference in this dataset is that it is annotated with fine-grained phenophase scores rather than presence/absence attributes (see description below). Each of these datasets is described below: <ul> <li> NEVP: this dataset of New England vascular plant (NEVP) specimens was produced by members of the Consortium of Northeastern Herbaria. The dataset comprises 42,658 digitized specimens that belong to 1,375 species and come from several North American institutions. Most of the specimens in this dataset are from the north-temperate region of the northeastern United States. </li> <li> FSU: this dataset was produced by the Florida State University's Robert K. Godfrey Herbarium (FSU), a collection that focuses on northern Florida and the U.S. Southeast Coastal Plain, one of North America's biodiversity hotspots. This dataset contains 54,263 digitized herbarium specimen records that belong to 3,870 species, making it the taxonomically richest dataset in this study. Most species in this dataset grow under subtropical or warm temperate conditions in the southeastern region of the United States. </li> <li> CAY: this dataset comes from the IRD’s Herbarium of French Guiana (CAY). CAY is dedicated to the Guayana Shield flora, with a strong focus on tropical tree species. This dataset is composed of 66,312 herbarium specimens that belong to 3,024 species. All digitized specimens of this herbarium are accessible online. Most specimens were collected in the tropical rainforests of French Guiana, with the remaining specimens coming mostly from Suriname and Guyana. </li> <li> PHENO: this dataset includes 20,371 herbarium specimens of 139 species in the Asteraceae produced in a study of phenological trends in the U.S. Southeast Coastal Plain. The dataset is composed of specimen records from 57 herbaria. Each recorded specimen was annotated for quartile percentages (0, 25, 50, 75, or 100%) of (i) closed buds, (ii) buds transformed into flowers, and (iii) fruits. According to the distribution of these three categories for each specimen, a phenophase code was computed. </li> </ul>   Datasets format These datasets are grouped in 3 tasks: <ol> <li>fertility detection</li> <li>flowers and/or fruit detection</li> <li>phenophase classification</li> </ol> The first 2 tasks are carried on the first 3 previous datasets and thus are based on the same set of images, unlike the third task which has its own disjoint set of images. This is why the dataset is presented into two separated files, one for each set of images. Fertility detection & flower/fruit detection These tasks are contained into the herbarium_fertility_annotations.zip archive. It consists of 3 files: <ul> <li>metadata.csv: general information about all the herbarium specimens for these tasks <ul> <li>id: specimen identifier</li> <li>collection: which of NEVP, FSU or CAY does the specimen come from</li> <li>herbarium: institution of origin of the specimen, especially for NEVP collection</li> <li>clade, family, genus, species: classification of the specimen</li> <li>URL: URL of the scan</li> </ul> </li> <li>fertility_task.csv: specific information regarding the fertility detection task <ul> <li>id: specimen identifier</li> <li>is_fertile: True if the specimen has an expression of fertility, False otherwise</li> <li>train_test_set: which subset does the specimen belong to; possible values are: train, random_test, species_test and herbarium_test</li> </ul> </li> <li>flower_fruit_task.csv: specific information regarding the flower/fruit detection task <ul> <li>id: specimen identifier, note that in this case not all the specimen described in metadata.csv are included in this task</li> <li>has_flower: True if the specimen has at least one flower, False otherwise</li> <li>has_fruit: True if the specimen has at least one fruit, False otherwise</li> <li>train_test_set: which subset does the specimen belong to; possible values are: train, random_test, species_test and herbarium_test</li> </ul> </li> </ul> Phenophase classification These tasks are contained into the herbarium_asteraceae_phenophase_annotations.zip archive. It consists of a single file: <ul> <li>annotations.csv: <ul> <li>id: specimen identifier</li> <li>URL: URL of the scan</li> <li>genus: genus of the specimen</li> <li>phenophase: integer from 1 to 9 describing the phenophase of the specimen</li> <li>train_test_set: which subset does the specimen belong to; possible values are: train and test</li> </ul> </li> </ul>   Additional ressources More information can be found in the related paper: Lorieul, T., K. D. Pearson, E. R. Ellwood, H. Goëau, J.-F. Molino, P. W.  Sweeney, J. M. Yost, J. Sachs, E. Mata-Montero, G. Nelson, P. S. Soltis, P. Bonnet, and A. Joly. 2019. Toward a large-scale and deep phenological stage annotation of  herbarium specimens: Case studies from temperate, tropical, and equatorial floras. Applications in Plant Sciences 7(3): e1233. For an example of usage of these datasets as well as a baseline, see: <a href="http://doi.org/10.5281/zenodo.2549996">http://doi.org/10.5281/zenodo.2549996</a>

opencc-by-4.0Dec 2014View details →

Figure 1 in Evidence of an Undescribed, Extinct Philodoria Species (Lepidoptera: Gracillariidae) from Hawaiian Hesperomannia Herbarium Specimens

Figure 1. Philodoria pupal tents on the adaxial surface of Hesperomannia arborescens leaves from Lanai (BISH1022034).

opencc-by-4.0Aug 2024View details →

Associated metadata of the 21 resequenced herbarium tomato specimens

Overview and metadata of the 21 resequenced herbarium specimens obtained from the Herbaria Basel, Basel, and the United Herbaria of the University of Zurich and the ETH Zurich (United Herbaria Z+ZT).

opencc-by-4.0Aug 2024View details →

Sequencing results of the 21 resequenced herbarium tomato specimens

Sequencing results of the 21 herbarium tomato specimens resequenced on an Illumina NovaSeq 600 platform.

Linked collectors and determiners for: Flora Sumatra: Digitizing and data basing specimens of the Sumatran Flora deposited at Herbarium Universitas Andalas (ANDA)-Part 2.

Natural history specimen data linked to collectors and determiners held within, "Flora Sumatra: Digitizing and data basing specimens of the Sumatran Flora deposited at Herbarium Universitas Andalas (ANDA)-Part 2". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/39e85504-1ebe-4671-be65-19ccdc1d7c7d">https://bionomia.net/dataset/39e85504-1ebe-4671-be65-19ccdc1d7c7d</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/39e85504-1ebe-4671-be65-19ccdc1d7c7d">https://gbif.org/dataset/39e85504-1ebe-4671-be65-19ccdc1d7c7d</a>. Formatted as a Frictionless Data package.

Linked collectors and determiners for: Visual Plants (144.41.33.158) - Herbarium specimens from "LOJA" Ecuador.

Natural history specimen data linked to collectors and determiners held within, "Visual Plants (144.41.33.158) - Herbarium specimens from "LOJA" Ecuador". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/863cbacc-f762-11e1-a439-00145eb45e9a">https://bionomia.net/dataset/863cbacc-f762-11e1-a439-00145eb45e9a</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/863cbacc-f762-11e1-a439-00145eb45e9a">https://gbif.org/dataset/863cbacc-f762-11e1-a439-00145eb45e9a</a>. Formatted as a Frictionless Data package.

Linked collectors and determiners for: Visual Plants (144.41.33.158) - Herbarium specimen from "BIEL", Germany.

Natural history specimen data linked to collectors and determiners held within, "Visual Plants (144.41.33.158) - Herbarium specimen from "BIEL", Germany". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/863ba0d8-f762-11e1-a439-00145eb45e9a">https://bionomia.net/dataset/863ba0d8-f762-11e1-a439-00145eb45e9a</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/863ba0d8-f762-11e1-a439-00145eb45e9a">https://gbif.org/dataset/863ba0d8-f762-11e1-a439-00145eb45e9a</a>. Formatted as a Frictionless Data package.

Linked collectors and determiners for: Herbarium specimens of Limoges university (LIMO).

Natural history specimen data linked to collectors and determiners held within, "Herbarium specimens of Limoges university (LIMO)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/fc976aa9-e137-446a-bad6-0999331fcd58">https://bionomia.net/dataset/fc976aa9-e137-446a-bad6-0999331fcd58</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/fc976aa9-e137-446a-bad6-0999331fcd58">https://gbif.org/dataset/fc976aa9-e137-446a-bad6-0999331fcd58</a>. Formatted as a Frictionless Data package.

Linked collectors and determiners for: Some Plant Specimens from PE Herbarium in China from 1900 to 1950.

Natural history specimen data linked to collectors and determiners held within, "Some Plant Specimens from PE Herbarium in China from 1900 to 1950". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/f9336171-e9a9-4147-b9f6-2d6c133afffd">https://bionomia.net/dataset/f9336171-e9a9-4147-b9f6-2d6c133afffd</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/f9336171-e9a9-4147-b9f6-2d6c133afffd">https://gbif.org/dataset/f9336171-e9a9-4147-b9f6-2d6c133afffd</a>. Formatted as a Frictionless Data package.

Linked collectors and determiners for: Database on reference specimens for medicinal plants of the Meliaceae family, conserved at the CNARP herbarium.

Natural history specimen data linked to collectors and determiners held within, "Database on reference specimens for medicinal plants of the Meliaceae family, conserved at the CNARP herbarium". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/f0ad347c-dfaf-4326-9bb3-5e25f9b45514">https://bionomia.net/dataset/f0ad347c-dfaf-4326-9bb3-5e25f9b45514</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/f0ad347c-dfaf-4326-9bb3-5e25f9b45514">https://gbif.org/dataset/f0ad347c-dfaf-4326-9bb3-5e25f9b45514</a>. Formatted as a Frictionless Data package.

Linked collectors and determiners for: Herbarium specimens of Jardins botaniques and Conservatoire Botanique of Nancy (NCY).

Natural history specimen data linked to collectors and determiners held within, "Herbarium specimens of Jardins botaniques and Conservatoire Botanique of Nancy (NCY)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/e553568e-2317-4592-8638-92e5ac93b40c">https://bionomia.net/dataset/e553568e-2317-4592-8638-92e5ac93b40c</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/e553568e-2317-4592-8638-92e5ac93b40c">https://gbif.org/dataset/e553568e-2317-4592-8638-92e5ac93b40c</a>. Formatted as a Frictionless Data package.