brahms - biodiversity informatics training...

BRAHMS stores data and images from herbaria, field surveys, botanic gardens, seed banks and literature.

The system is used to:

§ catalogue and curate collections § support taxonomic research § prepare checklists and floras § analyse and map plant diversity § publish online

BRAHMS BOTANICAL RESEARCH AND

HERBARIUM MANAGEMENT SYSTEM §  BRAHMS projects are active in about

60 countries, many in species diverse tropical or subtropical regions.

§  The country with the highest number of individual projects is presently Brazil. The Amazonian region herbaria are almost 100% databased and imaged.

§  The largest databases are in the Netherlands and South Africa where national BRAHMS networks are established.

§  Globally, about 7 million specimen records catalogued.

Denis Filer Andrew Liddell University of Oxford

About BRAHMS Data Some projects Publishing GIS BRAHMS online Curation

http://herbaria.plants.ox.ac.uk/bol/


Taxa

Botanical records

Specimens

Literature

Geodata

Plot samples

Living collections

Seed

Details about plant taxa

Details about places

Plant collections

Herbarium sheets, spirit, DNA, etc.

Botanical survey data

Botanic gardens

Seed banks

Bibliographic references

Images All categories

Categories of data managed in BRAHMS


Taxonomic data

All BRAHMS databases include a central list of taxonomic names. New projects can import names from IPNI and other sources. All details about names can be stored at all taxon levels. For example, taxonomic status, authors, validity, legitimacy, protologues, selected references, synonymy, descriptive texts, habit, conservation coding, etc. Tools to assemble and format taxonomic data lie at the heart of the reporting system.


Botanical records Botanical records are species x locality records. Material may be collected to make one or more physical specimens although a botanical record may only be an observation.


Specimens Specimens are physical objects like herbarium sheets, fruit, seed, wood samples, leaf collections for DNA analysis. A single botanical record may have many specimens including duplicated herbarium sheets. Specimens often have barcodes, an accession number. a type status and more than one determination.

Specimen categories are added as required


Botanical surveys

This module manages plots, small and large. They may be temporary or permanent and have multiple research objectives. Plot data files may only register species presence. More complex files used for e.g. forest inventory, may include species ID, tree #, DBH, HT, images, voucher references, etc. There are no restrictions on the data fields added. Plot data can be combined with other data for diversity analysis


Living collections

§  Description of plants in botanical gardens

§  Images of plants

§  Original source of the material

§  Identification

§  Management events including garden inventories


Seed bank module

§  Developed in collaboration with the Millennium Seed Bank, RBG Kew.

§  Stores all details about seed including processing and testing.

§  All these data can be published online.


Images of plants, specimens, labels, maps, illustrations, etc. can be registered in BRAHMS. Images can be linked to any record.

Images


database

§  If BRAHMS does not include data fields you need, you can add these to your BRAHMS database.

§  These fields are added to link files which are like extensions to the main files.

Add the fields SPINES, USES,

CONSERVE, ECOLOGY

to the species link file

§  Data are normally added using flexible external files called Rapid Data Entry (RDE) files.

§  These data are then checked and transferred to your database.

RDE


Herbarium curation


Producing labels and various categories of list are typical functions of BRAHMS in the herbarium.


§  Loans can be made and processed online.

§  In Oxford, we distribute data + images for loans online.

§  Determinations are returned via a website service.


Creating maps


How to produce a map?

1.  Select the data to map 2.  Send the data to selected GIS 3.  Choose base map and add your points

Conifer distribution in Africa on a raster relief map

Podocarpus totara in New Zealand – simple black/white map


Publishing taxonomic revisions, checklists,

floras, etc. from BRAHMS


It is very difficult to convert from word

processor to database

Database


And incredibly boring typing and formatting data for journals…


Using a database, you can create many

outputs and keep these updated.

Lobostemon database


Making a checklist that includes common names and distribution summary.


Getting online


§ BRAHMS online (BOL) is a unique website service created for the BRAHMS project.

§ Anyone who has developed a BRAHMS database can create a website from BRAHMS.

What is BRAHMS online?


§  Many projects under strong pressure to publish their data and images online.

§  Online herbaria are better known than those that are not.

§  Feedback on determinations.

§  Much important taxonomic work (e.g. doctoral theses) remains hidden. A website distributes data effectively.

§  A website presents data widely and benefits research.

§  A good website with quality data is excellent publicity for your institute or project.

§  A website can be cited as a publication for your CV.

The advantages of putting your data online


Local database

Server database

BRAHMS WebConnect is the software that connects BRAHMS to BOL allowing you to: § Develop and edit websites.

§ Upload selected data and additional resource files.


§  BRAHMS onlne can be used to publish e-floras and e-monographs.

§  Online reports can designed and saved as part of your website.

§  Reports use HTML templates and can include any of the data fields you have uploaded.

§  Online e-floras and e-monographs provide more flexibility than the traditionally printed volumes, are low cost and easily updated.


Images can be sorted and grouped and displayed in different ways.


§  Maps can be prepared using Google Maps or Google Earth and use point clustering where possible.

§  Descriptions of point data are provided in the right margin.

§  Images associated with individual data points can be displayed on the map and/or in the margin.

§  KML layers be added to your online project and selectively added or removed.


Some example projects available online

Training •  Extensive online documentation (

http://herbaria.plants.ox.ac.uk/bol/brahms/GroupResources) –  Entering data from images –  Living collections –  Online loans –  Reporting –  BRAHMS Online setup –  Example data files

•  In-person training courses –  Often held at conferences (November 2013: Brazilian National

Botanical Conference) –  Can request and fund your own course (October 2013: BRAHMS

network in South Africa launched)


BRAHMS 8

•  Development continues, BRAHMS 8 is being developed in collaboration with the Royal Botanic Gardens, Kew

•  Estimated release by April 2014

Contact

Denis Filer ([email protected])


brahms - biodiversity informatics training...

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