UCJEPS: Consortium detail page help

Supplementary information for CCH search and detail pages

About the records displayed

Records are from botanical specimens. Collection dates may range from the mid-19th Century to the present. Applicable taxonomy and geographic distributions may have changed since collection. Curation of specimens varies by institution and accuracy of data varies by collector.

Specimen number

Most of the herbaria have a number fixed to each specimen. This number, sometimes called the accession number, serves as a unique identifier in the database when associated with a herbarium abbreviation. Some herbaria have such a number only for the database, and it does not appear on the sheet.

Determination; scientific name

The name under which the specimen is currently filed. Note that participating herbaria may use different names for what is the same taxon. The author of the name is not given, but may be retrieved, along with other taxonomic information, by clicking on "More information: Jepson Online Interchange".

Botanical "scientific" names ("taxon" names) of plants are governed by an internationally agreed upon Code. Forms of botanical names differ according to the classificatory rank of the taxon being named. For example, names of families and genera are single words (uninomials), such as Pinaceae, Fabaceae, Juniperus, Astragalus, and so on.

Names of taxa at species rank comprise two words (they are binomials): Pinus alba, Rosa woodsii, and so on.

Names of taxa at ranks below species comprise four elements: genus nmae, species epithet, indicator of rank (forma, subspecies, or variety), and infraspecific epithet: Rosa woodsii subsp. gratissima, Rosa woodsii var. gratissima, Rosa woodsii var. glabrata and so on. Note that statements such as Rosa woodsii subsp. gratissima var. glabrata, consisting of more than four elements, do not constitue botanical names, though they may be thought of as statements of classification.

Collector, number, date

The collector is the person or people recorded on the label as having collected the specimen. Only the last name of the first collector is used for searching and sorting. That is, Hall and Michener will sort with H. M. Hall and a search for Michener will not turn up specimens collected by Hall and Michener. The collector name is linked to the Harvard Index of Botanists, or for a few collectors, to other sources of biographical information. The collector number is the number used by the collector to index the specimen. Collector numbers have a variety of formats. For the purposes of searching and sorting, the collector number is assumed to contain an alphanumeric prefix followed by a numeric stem followed by an alphanumeric suffix, of which only the stem is pertinent. The date is the date or date range on which the specimen was collected. It is stored in the database both as it occurs on the label, and as early and late Julian dates. The Julian dates, which are used for searches, accommodate date ranges. Searches for specific dates (e.g., June 6 1946), will also retrieve specimen data with a date range that includes the specific date (e.g., Jun 1946 or 1946). The date on the detail display is formatted as in the database. The date in the primary result set is formatted consistently: month, day, year. Jepson's collection numbers are linked to images of his field books, as are Brewer's and Bolander's Geological Survey collection numbers, and some of the numbers of C.A. Purpus and Annie Alexander.

County

The California county (spelling standardized) as it appears on the label, unless that is in error. Note that during the history of botanical collection in California, county boundaries have been altered several times. If the county does not appear on the label it has either been entered as "Unknown" or secondarily determined by a data enterer or user.

Locality

The name of the place the specimen was collected, or a description of how to reach that place. Locality information is not standardized in any way and a wide variety of spellings or usages for the same place may be encountered. Users should not expect to retrieve the data for all specimens collected from Yosemite National Park by searching for "Yosemite". The SMASCH database at Berkeley was designed with four locality fields: loc_place, for a referenced place (e.g., Clark's Ranch); loc_distance, for an indication of direction or distance from the referenced place (e.g., 3 mi NW of); loc_other, for other locality terms on the label (e.g., Yosemite --usually more encompassing terms); loc_verbatim (a more or less verbatim capture of the label data, usually used in place of the other three fields). In the Consortium display, these four fields are concatenated, with an attempt made to approximate the original label and reduce redundancy. The attempt is algorithmic, and not 100% successful.
Locality searches: Words in the locality search box are anded. Results will be returned only if all the words are found. Very common words are disregarded. If the search box is filled with a quoted 2 or 3 word phrase, only records containing that exact phrase will be returned.
Geographic region searches: Geographic regions are defined by rectangular bounding boxes; therefore, it is likely that some anomalous records will be included. Furthermore, records can only be returned if they include coordinates, so some will be missed.

Elevation

If you want to search within an elevation range, fill out both the Upper and the Lower field. On the detail page the elevation in feet or meters (units indicated) of the collection site. Elevation may be determined by instrument, map, or estimation. Accuracy should not be relied upon. Apparent accuracy may result from conversion. For the primary result set, all elevations are displayed as meters.

Habitat

Physiographic or biological details about the collection site.

Coordinates

From coordinates on the label or in a database (less than 10% of specimens). Source and precision is not known. Errors on the label are frequent and derive from misreading maps, mistyping figures, missetting GPS units, and computer operation errors. Labels are often not made by the collector, but are transcribed from a fieldbook or other medium by someone who may or may not be familiar with the collection region. The label typer sometimes adds coordinates
From descriptive information on the label, evaluated using archival material at the herbaria: collector's field books/itineraries, historical maps, etc.
Converted from TRS data on label. Many labels bear Township, Range, and Section data without other coordinate data. These figures can be converted using the program TRS2LL. If no section is given, we assign a section in the middle. Coordinates assigned this way can be off by several miles (or much more if the original TRS numbers are not accurately entered). We have found that TRS coordinates are troublesome because is easy to misenter them originally from a map, and easy to confuse east and west, north and south, or mistype the numbers. There is the additional complication of 3 baselines in California.
These were assigned in the past by the Biogeomancer program, which has not been supported for a number of years. A replacement for Biogeomancer can be found on Manisnet.org: Georeferencing Calculator.
This application can be used to supply coordinates for localities that are represented as one place--Coalinga, Peanut, Yreka. Other types can also be calculated, such as 4 miles W of Coalinga is georeferenced as 4 air miles due west of Coalinga, whereas the location is probably 4 road miles along a road trending west rather than east. The location of a stream is georeferenced as as the mouth of the stream. -->
Assigned by people interpreting the databased locality data using the mapping program Terrain Navigator, which allows quick lookup of a referenced locality and fairly easy measuring along a road or line. We extract locality data into an Access file by county and one georeferencer works on one county. The error assigned in this process takes into account uncertainty of the reference point and other uncertainty. This system was developed by the Museum of Vertebrate Zoology at Berkeley.
Regarding herbarium specimens from cultivation: In these cases there are two localities of interest: the place where the plant was cultivated, and the provenance of the source material: the place in the wild from which seeds, bulbs, rhizomes, cuttings, etc. were derived. Both localities are useful and interesting in different ways, but only one set of coordinates can be mapped. In an effort to most accurately represent the biodiversity of California plants, the CCH prefers to display coordinates for source material, if that information is available. When only the locality of cultivation is available, we prefer to still serve the record while masking the coordinates; in some records, however, the fact that a plant was cultivated is not expressed precisely enough that it can be automatically detected. When specimens are mapped to their garden location, they are very likely to display as a yellow flag. In these cases we encourage users to write to Jason Alexander so that the record can be modified accordingly.

There is a paper on georeferencing protocol by Arthur D. Chapman and John Wieczorek (the latter the developer of the system we are using) at https://www.gbif.org/document/80536/biogeomancer-guide-to-best-practices-in-georeferencing
The BerkeleyMapper application plots position using the coordinates from the database; it does not assign coordinates.
NOTE: Coordinates have not yet (Winter, 2012) been systematically verified.

Coordinate source

Derivation of latitude and longitude figures. Herbaria participating in the Consortium use a variety of protocols for evaluating locality descriptions and obtaining coordinates. At SBBG, coordinates for specimens that lack a longitude-latitude statement are found using MAPTECH Terrain Navigator, backed up by SBBG map archives and field notes (especially for Channel Islands and military bases). As of Winter, 2006, coordinates are not uniformly tagged as to their derivation. If the source is listed as "Not recorded", it could have come from a label or it could have been derived secondarily. If the coordinates are obtained by georeferencing at UC/JEPS using the Terrain Navigator, Biogeomancer, or TRS2LL programs, then this is indicated.

TRS

Township, Range, Section are frequently indicated on labels, and not always correctly. It is easy to mistranscribe TRS from a map and easy to miscopy the combination of numbers and letters. In California, there is the additional complication of three meridians: Humboldt, Mount Diablo, and San Bernardino.

Datum

...Read Wikipedia article

Voucher information

Information from a variety of fields. Sometimes merely the fact that a certain kind of information occurs on the label is recorded.

Annotations and/or curatorial actions

Some of the participant databases store annotations that have been posted on the specimen sheet: reidentifications, assignments to an infraspecific rank, etc. Sometimes, in accordance with a recent taxonomic treatment, a curator transfers all specimens assigned to a species from one genus to another, without evaluating the specimens. This is what is meant by "curatorial action". Usually, but not always, the specimen is filed in accordance with the most recent annotation.

Comments

We welcome comments and corrections of the specimen data that we display here. Action on the comments will be taken by the curators of the participating herbaria. You should provide helpful explanatory information if you can. Incorporating the comments into the database is time-consuming because in most cases it is necessary to examine the specimen label before amending the database. Often a discrepancy can be caused by more than one error, and investigation of an error sometimes reveals related problems.