Tropicos.org Updates

Name Matching

2011-02-16T15:01:00.000-08:00

Recently, we added simple name matching capabilities to Tropicos®.

Basically, all that you need to do is point to a tab-delimited file that contains the list of names you want to check and click a button.

The first row of the file needs to be a header row of column names. Your file needs to contain a column called "FullNameNoAuthors" (e.g. "Ochlopoa annua"), and/or a column called "FullNameWithAuthors" (e.g. "Ochlopoa annua (L.) H. Scholz"). If your file contains both columns, we will first attempt to match on the name with authors; then (if there is not a match) we will attempt to match on the name without authors.

Here is an example input file:
http://www.tropicos.org/docs/namematchexample.txt

To try this out, click on the following link (or click "Name Matching" in the Tools menu): http://www.tropicos.org/NameMatching.aspx

Click on the "Browse" button to locate the file on your local machine.

Then, click the "Match Names" button.

When processing is complete, an output file will be returned with the original columns, plus the following additional columns (from Tropicos data):

OutputNameID - Tropicos NameID (if matched)
OutputHowMatched - which column was matched
OutputFullNameWithAuthors - name with authors
OutputAbbreviatedTitle - publication abbreviation (where the name was published)
OutputCollation - publication collation
OutputVolume - publication volume
OutputIssue - publication issue
OutputPage - publication page
OutputTitlePageYear - publication title page year
OutputYearPublished - publication year published (if different from title page)
OutputNomenclatureStatus - Legitimate, No opinion, or nom. cons.
OutputBHLLink - link to the protologue in BHL
OutputBatchID - internal tracking number for the record batch

Browse Tropicos® Specimens in Google Earth

2010-07-26T13:55:00.000-07:00

Many of our specimens can now be browsed in Google Earth. To try this out, download the latest version of Google Earth and click on the following link:
http://services.tropicos.org/mobotspecimenfeed.kml

In Google Earth, this will add a "Missouri Botanical Garden - Specimens (via Tropicos®)" folder to your "Temporary Places".

Pan and zoom into your area of interest, and up to 100 representative specimens will be shown for the area in view. As you zoom in further, more specimens are retrieved.

At any time, you can uncheck the folder to suspend display of the specimens.

If you would like to keep this folder, you can right click on the folder and select "Save to My Places". Alternatively, when you close Google Earth, it will prompt you "You have unsaved items in your 'Temporary Places' folder. Would you like to save them to your 'My Places' folder?". Select Yes to keep this folder available when you use Google Earth again.

Execute a Tropicos name search directly from your browser

2010-02-19T09:40:00.000-08:00

We have added an OpenSearch description document (http://www.opensearch.org/Home) to our site so that name searches can be executed from your browser (regardless of what page you are currently on).

If you are using Chrome, visiting the Tropicos home page (http://www.tropicos.org) will automatically add Tropicos as a search provider.

For Firefox (2.0 and up) and Internet explorer (7 and up), click the "Add Tropicos as a browser search provider" link on the home page.

Digitizing Engelmann's Herbarium

2009-07-31T04:29:00.000-07:00

The Missouri Botanical Garden has been awarded a 2009 Museums for America Collections Stewardship grant from the Institute of Museum and Library Services (IMLS) for its project "Digitizing Engelmann's Legacy: Providing Web Access To Plant Specimens Documenting the Great American Frontier." The project will run from 1 November 2009 through 31 October 2010, and is online at http://www.tropicos.org/project/engelmann.

About the project

The Missouri Botanical Garden has identified the digitization and online public display of the George Engelmann Herbarium of plant specimens as a priority collection stewardship activity. The approximately 8,000 specimens gathered during pioneering expeditions into the native American West following those of Lewis and Clark are the first scientific record of the plants growing in the vast wilderness west of the Mississippi River. As such, they form the earliest verifiable documentation of species occurrences before the rapid migration west permanently altered that pristine landscape through human alterations and the introduction of invasive species. These specimens will provide an historic complement to the 3.6 million specimens already databased and accessible through Tropicos, MBG’s botanical information system.

This project is structured to accomplish three primary goals:

Goal 1: Provide web-based search and query access to the Engelmann Herbarium via Tropicos. The 8,000 historic specimens in the Engelmann Herbarium documenting America’s westward expansion will be databased and barcoded by Herbarium Assistants, making their scientific data available for query and analysis through the Tropicos web site at www.tropicos.org. The approximately 900 type specimens within the Engelmann Herbarium will be scanned and published alongside their transcribed scientific data.

Goal 2: Digitize field literature and published reports associated with collecting expeditions in the American West. MBG Library staff will select more than 100 volumes of botanical literature generated from these expeditions for scanning. Using well-established procedures and existing equipment, Imaging Technicians will digitize the selected reports and references, and will publish them using existing workflow via the Botanicus web site at www.botanicus.org. Tropicos will be updated to include links to the Botanicus materials, enabling a cross reference between historic museum collections and the public domain literature describing the artifacts within taxonomic publications.

Goal 3: Provide web interfaces for geospatial analysis and data modeling into the Engelmann Herbarium and Tropicos. New geospatial software developed by academic institutions and commercial software companies such as ESRI can be used to provide enhanced query interfaces into these historic collections. Programming is required to integrate these components into the core Tropicos system, enabling rich map-based visualization and analysis.

Project activities will be managed by an existing team comprised of staff from the MBG Herbarium, Library, and Bioinformatics Departments. Project activities have been scheduled for a duration of one year, starting November 1, 2009. Upon completion, MBG will have provided online public access to a collection of previously unavailable historic specimens and public domain library references, and provided novel analytical interfaces into these datasets. These products will be of use to a wide audience of scientists, students, and the general public, and will help inform users of the historic distributions of species throughout the native American landscape.

Contact: Dr. Robert Magill

 Senior Vice President for Research 
314-577-5161; bob.magill@mobot.org

Image courtesy of Wikipedia: http://en.wikipedia.org/wiki/George_Engelmann

Tropicos Images now available through OAI-PMH

2008-12-05T10:46:00.000-08:00

Missouri Botanical Garden is pleased to announce that our specimen and plant images are now under preservation management using the Fedora Commons repository software, and are available for harvesting using the Open Archives Initiative Protocol for Metadata Harvesting (OAI-PMH). To access the Tropicos Images OAI provider, use the following:

http://fedora.mobot.org:8180/fedora/oai?verb=Identify
http://fedora.mobot.org:8180/fedora/oai?verb=ListRecords&metadataPrefix=oai_dc

Added MBG Specimen Distribution Map

2008-12-04T08:12:00.000-08:00

Last night, we added an "MBG Specimen Distribution Map" link to the home page, which shows the distribution of Specimens stored in our database. We used Google Charts (http://code.google.com/apis/chart/), specifically the "Map" chart type. Below the map, we show the counts by country, as well.

New features added

2008-04-16T12:38:00.000-07:00

New Features were released today to improve functionality. They include:

Added new tab to Name for literature-based distribution

Example for Poa annua L.

Enhanced image search to show results with thumbnails (can toggle between thumbnails and previous detail view)

Go to Images search and select Rosaceae in Family dropdown.

Added country dropdown for Name->Specimens and Name->Distribution

Example for Zea mays L.

Added link to “Project” page to “More” menu. Contains links to project portal pages (e.g. IPCN page)

Launch of www.tropicos.org

2008-03-18T19:18:00.000-07:00

After months of work by a core team of scientists and developers lead by Bob Magill and Jay Paige, the new release of the Tropicos web site has been published at www.tropicos.org. To submit questions or report an issue on the new site, please use the Feedback form.

Release candidate available

2008-03-09T12:53:00.000-07:00

A candidate for the Tropicos portal upgrade has been released at http://test.tropicos.org/.

The release includes the following features:

Improved paging controls on search results, displaying options at top and bottom of list.
Enhanced interface for viewing and exporting specimens for a given name, such as specimens of Poa annua L.
Revised interface for viewing Subordinate Taxa.

Tropicos development can be tracked online through Missouri Botanical Garden's issue tracking application, available at:
http://www.mobot.org/gemini/Issues.aspx?pi=4&m=1

Submit feedback to http://test.tropicos.org/Feedback.aspx.