Science Home ... Virtual Herbarium ... User Guide
Acknowledgements
Showcase of Amazonian Specimens
The C. V. Starr Virtual Herbarium
Guide for Use of the Website
Introduction
Initiating a Search
The Search Results Page
The Specimen Details Page
The Taxonomy Details Page
The Bibliography Details Page
The Person Details Page
Introduction: What is the C. V. Starr Virtual Herbarium?
This is the name given to the Garden's database of herbarium specimen data and to the World Wide Web portal to that data. It is named in honor of Cornelius Vander Starr, founder of The Starr Foundation, which has provided several major grants toward endowment and operating support for this important initiative.
For most of The New York Botanical Garden Herbarium’s history, the only way to know what specimens it contained was to look at the specimens themselves. To make the content of the herbarium more accessible, The Garden embarked in 1995 upon the monumental task of creating an electronic catalog of the herbarium. For an explanation of the information contained on an herbarium specimen, please consult An Herbarium Specimen Explained. Today the catalog contains approximately 750,000 specimen entries, as well as high-quality digital images and other multimedia (e.g., documents and links to external web sites). The catalog is updated daily.
Associated with the Virtual Herbarium specimen database are two other databases: Index Herbariorum, which is a directory of the world’s 3000+ herbaria, and the Index to American Botanical Literature, which is a bibliography of references to articles published since 1995 about plants and fungi in North and South America, Central America and the West Indies.
Initiating a Search
The user has the option to search all the Virtual Herbarium data at one time, or to search subsets of it. The subsets, which are usually the equivalent to specific cataloging projects, may be based on the nature of the specimen (e.g., type specimens) taxonomy (e.g., bryophytes, fungi, lichens, vascular plants), or geography (e.g., Intermountain Flora, Flora of Eastern Brazil, Navassa Island). The catalogs are not mutually exclusive – for example specimens in the Costa Rican Fungi catalog are also included in the Neotropical Flora and Mycota catalog.
The catalogs differ in size and breadth, and also in level of completeness. The web page entitled A Summary of Databasing Projects indicates the size and stage of completeness of all Virtual Herbarium Cataloging Projects.
Which Search Option to Use?
Quick Search. The Quick Search option is similar to a “Google” box. A search term or collection of search terms can be entered without punctuation; word order does not matter. The Quick Search box can be used to search for specimens by plant name (division, family, genus, species, or subspecific name) or part of a name (e.g., genus, species epithet), author name, collector name, collector number, barcode number, or kind of type status. Note that geography-based searches (e.g., specimens from Brazil) will not work with the Quick search box; use the Detailed Search option for such searches.
Detailed Search. The Detailed Search option will allow geography-based queries, and also will allow a more structured query on a variety of fields than is possible with the Quick Search. For example, if a user wishes to find all fungi collected in North Dakota by John Smith in 1988, this option will allow such a search.
Checklists. The lists are arranged by family, and within a family, by genus and then by species. The names are hyperlinked, and clicking on the link initiates a search of all records with that name.
Search Tips
Searches in the Virtual Herbarium are word-based by default. The fastest searches are made by using whole words as the criteria.
Wildcard characters can be used to find partial words, but search times will be significantly longer. Use an asterisk (*) as a substitute for any number of characters in a word. (Example: "South*" in the Province/State field will return specimen records from "South Dakota," "South Carolina," etc.). Use an exclamation mark before a word to specifically exclude that word from the search. (Example: "Panicum" in the Genus field and "!diffusum" in the Species field will return all records of Panicum except Panicum diffusum.) Use quotation marks to search for exact phrases. Words not enclosed by quotation marks will be used to search for records with all of the words, but not necessarily in the order typed.
The Scientific Name field can be used to search by the genus, species, infraspecies, and author abbreviations of a name. For example, the search term "viridis" finds specimens of Rauvolfia viridis, Amaranthus viridis, etc. The term "Ekman" finds specimen records of numerous taxa described by Erik Ekman.
The author abbreviations are those used in Harvard University Herbaria's Index of Botanists.
The Search Results Page
When a search is launched, matching records are sought, and if found, these are displayed in a tabular format:
In the Search Results form, the data displayed are a subset of the information captured for all specimens. The data included are:
Image thumbnail: If the specimen has an image associated with it, a thumbnail, or small version of this image, will appear in the first column of the Search Results table.
Taxon: The Taxon column includes the genus, species and author of the determination under which the specimen is filed (previous determinations can be viewed by examining the Specimen Details for this record).
Collector: The Collector column includes the name and number of the primary collector, plus members of the collection team that participated in the collection event. The Collector column also includes the date of collection. For older specimens, some of these data are missing.
Location: The Location column contains all of the geopolitical data provided with the specimen, from largest unit to smallest: Country, State or Department, County, Municipio, city or town, and precise locality. For older specimens, many of these data are missing.
Type Status: The Type Status column indicates what, if any, type status has been designated for this specimen.
ID: This is the barcode number assigned to the specimen.
Check box: Use the checkboxes above to view the Specimen Details Page for multiple records at once. If results span several pages, you may use the navigation links above to make selections from different pages before pushing the "view checked" button below. The "clear all" button will deselect all records from all pages. Users must have javascript and session cookies enabled in your browser to use the Select Multiple form.
Data Download
Users have the option to download Search Results on a page-by-page basis, or, for up to 1000 results, to download all results at one time. In the download, the data are delimited by commas, and are easily imported to Microsoft Excel or other spreadsheet programs. Data downloads larger that 1000 records, or download requests that include information beyond that included in the Search Results table, are available by special request. Such requests should be submitted via email to the NYBG Bioinformatics Managers
The Specimen Details Page
It is possible to view more information about a specimen than is shown on the Search Results page. Users may look at a single record by clicking on the name or on the image thumbnail for a row in the Search Results table. To view the Specimen Details of multiple records on a single screen, users should check the boxes of these records (last column of the Search Results table). If results span several pages, you may use the navigation links above to make selections from different pages before pushing the "view checked" button below. The "clear all" button will deselect all records from all pages. Users must have javascript and session cookies enabled in your browser to use the Select Multiple form.
The Specimen Details page gives all the information that is included on the specimen label, supplemented sometimes by interpretive notes added by the cataloger, and multimedia attachments that relate to the specimen.
Filed as: The name of the family and the binomial and authority for the name under which this specimen is currently filed in the New York Botanical Garden herbarium.
All Determinations: All the different binomials and authorities that have been applied to this specimen by those scientists who have annotated it. Each name listed is hyperlinked to the taxonomy record for that name (see the description of the Taxonomy Details page below).
Location: All the geographical information available about the collection locality, arranged hierarchically: Country, State/Department, County/Municipio, City or town(if applicable), specific locality, geocoordinates(if available).
Maps: If the specimen has been georeferenced, the Maps section will appear; users can choose to see a map of all specimens of this species that have been georeferenced (View Map of this Taxon)or a map with only this specimen on it (View Map of this Specimen ).
Collector: The name of the collector (rendered in the format: First initial. Middle initial. Last name) and collection number, followed by the date. The collector's name is hyperlinked to the database record for that individual (see the description of the Person Detail page).
Description: Any information given on the specimen label about the organism as it appeared in the living condition.
Habitat: Any information given on the specimen label that describes the habitat of the collection, or the environmental conditions or vegetation immediately surrounding that habitat.
Other:
NY Specimen ID: This is the number on the barcode attached to the specimen. Because accession numbers were never used at the New York Botanical Garden, the barcode is often the only unique identifier for a specimen. When requesting a particular specimen on loan it is helpful to cite the barcode ID number.
Taxonomy Notes: Any comments on the identification or nomenclature noted on annotation labels, or by the cataloger.
Specimen Notes: Any comments by the cataloger about the specimen that either do not fit into any specific database field, or that are editorial or explanatory in nature.
Incorporated Herbaria: If the specimen was obtained as part of an herbarium that was wholly or partially incorporated into the New York Botanical Garden Herbarium, the name of that original herbarium is noted here.
Associated Multimedia Attachments
Below the transcription of the specimen label data users will find the multimedia attachments for this specimen, if any exist. There are three types of multimedia attachments: images, documents (e.g., Microsoft Word documents, .pdf files), and links to other websites.
Images: Approximately 100,000 specimen records are accompanied by images of the specimens; these include all of the vascular plant types, and most of the types of mushrooms and related fungi; other projects include some images as well. The images that appear on the Specimens Detail page are thumbnail images. Clicking on the image will reveal the full size image of the specimen. In addition to specimen images, there may be images of the plant in the living condition; micrographs derived from some part of the specimen, or images of notes, drawings, field book entries or correspondence relating to the specimen.
Documents: Microsoft WORD files or .pdf files can be attached to a specimen record; these are often reprints of articles that refer to the specimen, to the locality where it was collected, or to the project for which it was collected.
Website links: Links are included to web sites that provide additional information about the specimen, about the locality where it was collected, or about the project for which it was collected. For example, if the specimen has been sampled for DNA and the resulting sequences submitted to GenBank, a link to that sequence might be provided.
The Taxonomy Details Page
Users reach the Taxonomy Details page by clicking on the highlighted taxonomic name from the Specimen Details page.
The information displayed on the Taxonomy Details page always includes the name of the plant (binomial plus authority). This page also shows the following information, if it has been entered in the database: primary citation a bibliographic reference to the original place of publication for the species. The title of the article, if given, is hyperlinked to the bibliographic record for that publication (see Bibliography Details page). If other names have been designated as synonyms of the name, these will be listed as synonyms. A description of the species, or information relating to the nomenclatural status of the species may be included under "Description."
Associated Multimedia Attachments
Below the transcribed taxonomic information, users will find the multimedia attachments for the name, if any have been entered. There are three types of multimedia attachments: images, documents, and links to other websites.
Images: These may be images of the species or its parts, or those relating to its uses, pollination or dispersal, symbioses, or scanned text pertaining to the species. The images that appear on the Specimens Detail page are thumbnail images. Clicking on the image will reveal the full size image of the specimen.
Documents: Scanned text, Microsoft WORD files or .pdf files can be attached to a taxonomy record; these will be published or unpublished accounts of the species obtained from contributing staff members, students or collaborators, online repositories, or the archives of the LuEsther T. Mertz Library of the New York Botanical Garden.
Website links: Links are provided to sites that provide additional taxonomic, ecological, ethnobotanical, or evolutionary information about the species. For example, if the species has been sampled for DNA and sequences submitted to GenBank, a link to that sequence might be provided.
The Bibliography Details Page
The Bibliography Details page is accessed through the Taxonomy Details page in the Virtual Herbarium. There are actually two levels of detail If the bibliographic reference gives the title of the article as well as the title of the publication (e.g., journal article or book) then there will be bibliographic details for both the article and the publication.
The information displayed includes the name of the Author, which is hyperlinked to the Person Details record for that author (see Person Details), and the title of the publication. If the publication is an article in a periodical, the name of the periodical will be hyperlinked to another Bibliography Details page. The publication Bibliography page gives the title of the publication and notes about it, e.g., dates of actual publication.
Associated Multimedia Attachments
Below bibliography information, users will find the multimedia attachments, if any have been entered. There are three types of multimedia attachments: images, documents (e.g., Microsoft WORD documents, .pdf files), and links to other websites.
Images: These may be text (usually the protologs for the species) or images of the species from the publication. The images that appear on the Specimens Detail page are reduced, (thumbnail) versions. Clicking on the image will reveal the full size image of the specimen.
Documents: If the original publication is available in Microsoft Word format or .pdf format, the article may be attached to this record.
Website links: Links are included to websites that provide full or partial text of this publication or that give other information about it. In the case of an on-line book, the protolog page and illustrations will be linked to the Bibliography page that gives the page citation; if there is a second Bibliography page that relates to the publication, a link will be given to the opening page of the on-line version of the publication.
The Person Details Page
The Person Details page can be reached from the Specimen Details page, where it is linked through the name of the collector, or from the Bibliographic Details page, where it is linked through the name of the author of a publication.
The information on the Person Details page includes:
Person: The name of the person (abbreviated and full).
Dates: the birth and death dates of the person, if known.
Specialties: Groups of organisms studied by the person (e.g., Bryophytes, Pteridophytes, Spermatophytes, Fungi, Lichens).
Roles: Whether the person is an Author, Determiner, Collector, or some combination of these.
Details: For collectors, countries or regions where collections were made (generally not an exhaustive list).
Notes: The notes may contain other biographical details about the person or their research activities.
Associated Multimedia Attachments
Below the transcribed taxonomic information, users will find the multimedia attachments for this person, if any have been entered. There are three types of multimedia attachments: images, documents (e.g., Microsoft Word documents, .pdf files), and links to other websites.
Images: There may be a photograph or painting of the person. Images that appear on the Specimens Detail page are thumbnail images. Clicking on the image will reveal the full size image of the specimen.
Documents: Microsoft WORD files or .pdf files can be attached to a Person record; these will be published or unpublished biographical or bibliographical information pertaining to the person obtained from contributing authors, online repositories, or the archives of the LuEsther T. Mertz Library of the New York Botanical Garden.
Website links: Links are included to websites that provide additional biographical information about the person.
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