Living Collections - Oxford Plant Systematics

Document prepared by Denis Filer, Plant Sciences, University of Oxford
April 2015
Oxford Botanic Garden looking towards Magdalen College tower. Oxford Botanic Garden has
kept records in some form or another since it began, including a catalogue listing all plants at
the Garden. The sample page above right is from Bobart the Elder’s Catologus Plantarum
published in 1648. Jacob Bobart the Younger, a son of Jacob Bobart the Elder (1599-1680),
and succeeded his father as Hortus Praefectus of the Oxford Botanic Garden.
http://herbaria.plants.ox.ac.uk/bol/bobart.
CONTENTS
SUMMARY ................................................................................................................. 5
GETTING STARTED ..................................................................................................... 7
MANAGING SPECIES NAMES ................................................................................... 11
ACCESSIONS, PLANTS, REQUESTS AND EVENTS ...................................................... 15
BOTANIC GARDEN AREAS AND LOCATIONS ............................................................ 21
CONTACTS, SUPPLIERS AND OTHER ADDRESSES ..................................................... 23
MANAGING IMAGES ................................................................................................ 24
MAPPING ................................................................................................................. 27
DATA CAPTURE USING RDE ..................................................................................... 30
QUERYING LIVING COLLECTIONS DATA ................................................................... 32
REPORTS AND EXPORTING DATA ............................................................................ 34
GARDEN EXCHANGES AND RELATED TRANSACTIONS ............................................. 39
VIRTUAL BOTANIC GARDENS AND ONLINE CATALOGUES ....................................... 41
ANNEXES.................................................................................................................. 44
Thanks to The Morton Arboretum, Oxford Botanic Garden and Hortus Botanicus,
Leiden for screens and images used in this document and to Tim Pearce at RBG Kew
for his comments on the text.
Summary
The Living Collections module is designed to manage data and images in botanic
gardens, arboreta and other horticultural projects.
The module benefits from all standard BRAHMS features
to edit, query, report, map, export and publish online with
additional features for the management of garden
accessions and plants. There are also tools to sort, filter,
calculate and analyse data and images. As the living
collections module is integrated within BRAHMS, it
becomes possible to develop a comprehensive
management system for gardens that shares data and
resources with other system components.
Accession records include details of the type and amount
of material received, from who or where, the original or
derived source and initial identification.
Plant records hold details of plants in the garden from planting out to disposal or
death. A history of management events, requests and observations for plants can be
added. These may include, as examples, standard garden maintenance and stockchecks; name changes; propagation activities; plant movements; periodic observations
on features such as leaf flush, flowering, fruiting, disease and cause of death. Event
categories are defined to suit your project management procedures and objectives.
PDF files, Excel sheets and other documents/files can be linked to accessions, individual
plants, species and other records. Examples are material transfer documents and
species level spreadsheets.
Plant location can be recorded from a defined garden area or theme zone down to
pinpoint map location with options to record bed and grid numbering as used locally.
Images of plants in their original habitat or in the garden can be linked to records in the
database as appropriate. Images of herbarium specimen vouchers and other associated
specimens or illustrations can be added.
Individual projects can extend the standard data file structures by editing the BRAHMS
‘link files’. For example, if a project wanted to store more specific details about plant
condition, perhaps linked to a research project, additional data fields can be registered
and become a permanent part of the database.
5|P a g e
The module is supported by Rapid Data Entry which can be used to capture new data
and to transfer data from other formats such as Excel worksheets. RDE can also be
used to batch upload stock-checks and plant observations for plant accessions.
The living collection module is linked to the
main BRAHMS taxonomic framework.
Detailed information can be stored about
individual taxa from plant order through
family and genus to infra-specific levels,
cultivars and hybrids. This may include
synonymy, common names, descriptions,
known distribution, hardiness, conservation
status and more.
Voucher specimens (herbarium specimen, DNA, wood, seed, etc.) can be linked
through to the main botanical records file. Vouchers may be from original wild
collections and/or from established garden plants. Data and images from herbaria and
living collections can be united in a single database.
Online, you can design your own website and publish a virtual botanic garden or online
plant catalogue directly from BRAHMS using its WebConnect features.
The BRAHMS training guide, while not explicitly dealing with living collections, provides
the necessary background information you need to install BRAHMS and get started
with RDE and BRAHMS itself. See:
http://herbaria.plants.ox.ac.uk/bol/Content/Groups/brahms/Resources/BRAHMStraining2013.pdf
6|P a g e
Getting started
The Living Collections module enabled
To include the living collections module in your menu selection, use Utilities > My
setup/profile > Active modules. This is a user specific setting. Once enabled, the main
LivingCollections menu option appears. Note that the options available to the user
within this menu are controlled by the access rights provided by the system
administrator.
System-wide and personal configuration
BRAHMS can be configured to accommodate the needs of different categories and
levels of user. There is no need to expose a garden volunteer whose interests are to
add new plant records or garden observations to the same system complexity as a
researcher wanting to manage images, link herbarium and plant records, analyse plant
diversity and design new report templates.
The task of the system administrator is to understand how the system can be
configured appropriately for the whole user team and for the different categories of
user. On networks, the administrator can add users with access rights that range from
complete access to all functionality to that which might only allow data capture or the
editing of selected categories of data. Further details on assigning user access rights are
provided in the BRAHMS guide.
7|P a g e
A partial screen showing how the system administrator can assign user access rights
All users, within the access rights they have been assigned, can adjust their personal
settings using Utilities > My setup/profile. New users quickly learn how the options
here are adjusted to suit. Examples are adjusting the modules that appear on the main
menu, colours of highlighted data columns and rows and the way data grids are
displayed.
An example menu set to provide limited access
An example menu set to provide access to a wider range of modules
Transfer existing data to BRAHMS
If you already have data stored in another format, it is almost always possible to avoid
re-typing data and transfer these to BRAHMS using the Rapid Data Entry (RDE) module.
Examples of data you can transfer are accession and plant data (with details of naming,
origin, garden location, etc.); names and addresses of suppliers; taxa and details about
these taxa; herbarium vouchers; links between images and data.
8|P a g e
If you have large numbers of accession records or plant observations to add from paper
records or other data files (e.g. MS Access, Excel), the best procedure is to use the RDE
module. RDE is briefly introduced in this short guide but more detail is provided in the
training guide and manual.
Designing RDE data capture templates
If you plan to use RDE for data entry, you can optimize RDE use by designing data
capture templates that are the most suitable for your project.
An RDE data template is like an Excel spreadsheet with only those data columns you
need, and these arranged in the best order. Templates can be designed for different
tasks, for example capturing new accessions, garden maintenance data or plant
observations.
The standard BRAHMS table designer is used to create data capture templates which are then
available to all users
Custom lookups
Your database will benefit from access to customized lookup lists, for example, lists of
options for taxa, garden locations, provenance and propagation history types, habit
classes, plant hardiness codes, plant status categories, etc. BRAHMS has two broad
categories of lookup list:
a)
b)
The main BRAHMS dictionaries themselves act as lists to choose from. These
include lists of family, genus and species names; country to individual
geographic locations; garden areas from the main divisions to specific named
beds or theme areas; names and address; and a few other files relevant to
living collections.
Smaller lookup lists that are stored in the BRAHMS custom lookups dictionary
and can be developed by each project. These are generally smaller lists of
values for any field where you have a standard list of options. Typical
examples for living collections are lists of plant habit, hardiness and growth
9|P a g e
form categories; plant provenance codes (W, Z, G, U); and options you care
to use for the status of garden plants (Alive/Active, Dead/Inactive, etc.).
Mechanisms to develop both lists from your data are provided. For example, lists of
species and places are auto-built when data are imported. Custom lookup lists can be
edited manually using Admin > Custom lookups and you can also import your own lists
or use standard lists provided in the BRAHMS living collections setup folder. Clean
lookup lists save time typing and help standardise data entry.
Example entries in the custom lookup dictionary, here for the fields PROVTYPE (Provenance type)
and PROPHIST (Propagation history). Lookup lists can be developed for any field in your database.
Reporting introduced
All projects use report templates to generate formatted outputs. The reports required
vary from project to project although typically, they range from simple lists to more
detailed plant and seed catalogues.
BRAHMS provides the tools that enable you to design your own reporting templates.
There are two main types of reports in BRAHMS known as ‘Visual reports’ and ‘Text
reports’. Visual reports are normally printed directly from BRAHMS (lists, labels and the
like) while text reports are sent to your word processor as documents where they can
be further edited before printing. Text reports are often used to create checklists and
more complex outputs such as plant and seed catalogues. Information about report
design is available in:
http://herbaria.plants.ox.ac.uk/bol/Content/Groups/brahms/Resources/BRAHMStraining2013.pdf
http://herbaria.plants.ox.ac.uk/bol/Content/Projects/brahms/Resources/Textreporting.pdf
Although reports can be created from all BRAHMS files, they are usually used with data
in query files. Thus you can query the data you want to include in the report and then
choose one of your report templates. Learning to design reports, while somewhat
‘challenging’ – opens up endless scope to create an almost limitless range of reports
based on the data you query from BRAHMS.
10 | P a g e
Managing species names
The family, genus and species files are centre stage in the living collections module. All
plant records are linked to a species record and through that, to the genus and family
tables. The species file stores all names below genus including infra-specific taxa,
cultivars and hybrids.
You have the option to store as many facts about species as you want. As examples,
you can add details such as common names, conservation status, CITES and red list
details, range (for botanic garden labels) habit and hardiness. If relevant to your
project, you can store more complete taxonomic profiles that may include synonyms,
publication details, nomenclature notes and literature links. Links can be added to
online resources.
You can also store descriptive texts for names at any taxonomic level and subsequently
include these in reports. Examples are general plant descriptions, local and/or global
distribution notes, conservation status, ecology and plant uses. In nurseries and
botanic gardens, the focus may be on more practical issues such as best germination
practice, optimal treatments in seedbeds and nurseries, compost mix, stress tolerance
(drought, frost), pruning regimes and other useful details, all of which can be searched
on and included in formatted reports. Another use of the species file would be to build
up details for education programmes with a focus on topics such as how a plant is used
locally, poisons, the origin of the Latin name, how it reproduces and what are its close
relatives.
Individual text entries can be linked to references as needed.
Snapshot of a species file in data grid mode showing some cultivar names
11 | P a g e
Common names for species are stored at the family and species level. Families can be
given a single common name such as the ‘Bindweed family. Species can be assigned
many common names and these can be linked geographically, ideally via vouchers.
Species common names are stored in the separate common names file open using Taxa
> Uses and common names. Each species can also be given a primary common name
which is stored in the main species file.
Sample from the Morton Arboretum showing common names in the family file.
Sample from the Morton Arboretum showing common names of some cultivars in the species file.
Taxa can be added manually to the respective files using the data grid or screen forms
or using Rapid Data Entry files. Thus, to add a new species record, you select Taxa >
View/edit species records and add a new record using the Add toolbar.
12 | P a g e
If you are starting a new project, it makes sense to use RDE to add names as a batch
process. You may have a list of names in Excel or some other format and these can be
added to BRAHMS via RDE.
Note that new names are also auto-added when transferring a living collection RDE
into BRAHMS.
If BRAHMS does not have one or more data fields for the data you wish to store, you
can add these to your system using the species link file. Unlike the main species file,
link file structure can be modified and the changes you make then become a
permanent part of your database.
A field view in the species file showing calculated fields for Alive and Dead/Disposed plants.
13 | P a g e
Species can also be viewed and editing using a form. Here in the conifer database on the Synonyms
tab. The right panel provides a summary of specimen data for the current species.
If creating an online service, you can upload selected details about taxa. Here, these include red list
criteria, TDWG distribution codes, a text distribution summary, name origin and common names.
14 | P a g e
Accessions, plants, requests and events
At the heart of the living collections module are the files shown below. These files
connect to other BRAHMS components not shown here including those for taxa,
geography, vouchers and images.
Accessions file
The accession file is opened using LivingCollections > View/edit living collection
ACCESSIONS. This file keeps records of plant material received, often in batches, from a
supplier or directly a wild source. Each accession will be of one species and from the
same source. All fields are listed in Annex 1.
Numbering systems vary from project to project. The system ensures accession IDs are
unique. A common approach is to use a sequential number combined with the
accession year, for example 2015-01, 2015-02, etc. The numbering system used can be
added to a configuration setting so that the next available number can be autocalculated for a given receipt year.
15 | P a g e
Some of the system configuration settings for accession number calculation
Where accessions have a known wild origin, the record is linked through to a botanical
record (= collection event). This allows you to record the collection details such as
collector, field number, date, collection location, the habitat of the collection site and
more.
As accessions are usually added in relatively small numbers, it’s convenient to add
these directly into BRAHMS. However, it is also possible to add new accessions to an
RDE file and then transfer these to BRAHMS. RDE is especially useful for batch loading
large number of records including data migrated from other systems.
As with all BRAHMS files, plant accessions can be viewed, sorted, filtered and edited
using the data grid (spreadsheet) view.
A sample data grid with a field view selected. Accessions are accessed by selecting
LivingCollections > View/edit living collection ACCESSIONS.
Forms, where available, are opened using the
toolbar. Most forms float on top of
the grid and can be dragged to another monitor if you have that facility. The living
collections form is divided into logical tabs for editing purposes and you can use the
additional tab options on the right-side area of the form for various tasks. Form
banners are selected using a setup option.
16 | P a g e
The accession/receipt tab on the living collection form showing a summary of the material
received.
The accession/Summary tab on the living collection form showing a summary of plants for the
current accession.
17 | P a g e
Plant records
Garden plant records are stored in the main living collections table with links to the
relevant BRAHMS tables, for example the taxa and botanic garden locations files. All
fields are listed in Annex 2.
As with accessions, plant numbering systems
vary from project to project. The system
ensures plant IDs are unique.
A common approach is to use a sequential
number or letter before or after the
accession number.
In this example, plant IDs are a sequential number added to the accession number, separated by *.
The plant ID numbering system used can be added to a configuration setting so that
the next available plant ID can be auto-calculated for a given accession.
Adding a new plant ID. This plant record represents a group of 12 plants planted in a patch.
18 | P a g e
Form mode, Garden location tab. The form allows access to all accession and plant level details.
Some further features about plant data storage:





Plant records can be vouchered with links to the botanical collections module
recording any physical specimen (herbarium material, DNA, wood sample,
etc.). Each plant can have multiple vouchers. Determinations between
herbarium and garden can be matched.
Images are easily linked to plant records.
Living collection ‘events’ are used to record things that happen to plants from
their acquisition through to possible death. Examples are sowing, potting,
plant movement, spraying and tree surgery. You can also store observations
such as flowering and fruiting times. A plant record may have many
registered events, each with an event type and name, the date and various
descriptive fields. Events are stored in a separate file linked to the main plant
file. You can add and edit events directly in this file or from the form when
browsing through the main accessions file.
Requests (plant actions requested) can be logged in the plant request file.
Requests, once processed, are transferred to the events file.
Flexibility with data storage is provided through the living collection ‘link file’.
This means that you can augment the standard living collection file structure
by adding custom fields. The new fields become a part of your database, can
be queried and included in reports.
19 | P a g e
The history of things that happen to plants over time can be recorded as ‘Events’. Events are also
used to record observations such as flowering and fruiting.
Projects can extend default file structures by adding new fields. These fields become a part of your
database, can be queried and included in reports.
20 | P a g e
Botanic garden areas and locations
Botanic gardens have a structure that can be
defined as you wish, divided into major and
minor areas. For example, you might have
student teaching and public display order
beds, theme zone areas (e.g. arid forest,
‘Japan’ and rockery), glass houses of different
types and nurseries. Zones, locations and
structures can be registered in a separate file
selecting LivingCollections > Principle garden divisions and LivingCollections > Garden
locations.
Snapshot of the locations file showing some of its fields. The field LVTOTALA (alive) and LVTOTALD
(dead/disposed) are examples of calculated fields updated using Calculate > Update calculated
fields.
21 | P a g e
Another view of the garden locations file.
As well as linking each plant accession to a garden region in the above dictionary,
plants can be given garden grid, sub-grid and row numbers as well as precise
coordinates. Plants can also be assigned a sequence number to help with inventory and
public trail hand-outs.
You can store descriptions of areas with images and other linked documents. Areas can
be assigned map and garden grid references.
Showing a section of a living collection plants file with various garden location fields.
Store images of garden areas
22 | P a g e
Contacts, suppliers and other addresses
The names and addresses of suppliers and all other contacts are maintained in a
separate file opened using LivingCollections > Botanic gardens, sources and suppliers.
Records can be edited in data grid and/or form mode. Names/addresses can be
imported from an external file.
Editing the list contacts in form mode.
23 | P a g e
Managing images
There are many positive reasons to add images of plants, of herbarium vouchers, of
garden areas and more to your database. Images bring a database to life. They can
used for a variety of research, education and public interest purposes as well as helping
with identification on and offline.
Images of all types (jpg, png, etc.) and of any reasonable size can be linked to records in
BRAHMS. When you attach an image, a link is created between the image and the
record and the image file name and path is registered in your image file. As the images
themselves are not stored in the database, you can link many thousands of images
without inflating database size. Images can also be stored in RDE files in the memo field
IMAGELIST. Images can also be stored by adding the URL to the image file field
IMAGEURL e.g. http://medialib.naturalis.nl/file/id/WAG.1288083/format/medium
Where large numbers of images are involved, folder naming and organisation becomes
important. Images can be easily moved to different folders and tools are provided in
BRAHMS to help with this.
Image paths are registered in and can be viewed from the main image library. Tools are provided
to edit folder names and rename the image files themselves. Image renaming can be based on the
data the images are linked to.
24 | P a g e
You can link multiple images to each record in the database.
Images can be linked to any category of data. For botanic gardens, typically, this will be
to either the plants themselves in the garden or to species records. You may also have
images that represent families and genera and these can be linked to those files.
Images of garden regions (order beds, glass houses, etc.) would be linked to the garden
location file.
There are several ways to link images to records. One of the easiest ways is to open the
image viewer (Camera toolbar) and then drag images from your file explorer onto the
image viewer form.
Images dragged to the image viewer are auto-linked to the current record. Image links can be
removed using the delete option on the image viewer toolbar.
There are also methods to batch link images to records in BRAHMS based on their file
names.
25 | P a g e
Keeping the original camera names, while possible, is not recommended. BRAHMS has
functions to rename image files based on one or more fields from the record the image
is linked to. This is discussed further in:
http://herbaria.plants.ox.ac.uk/bol/Content/Groups/brahms/Resources/EnteringDataFromImages
.pdf
Images of plants and specimens can be displayed online. Images can be displayed in raw format or
pre-processed via Zoomify. Online, images, together with key-wording and search filters, can be
developed into an online plant identification system.
26 | P a g e
Mapping
Maps can be produced for garden plants as well as the sites the plants were originally
collected from. The accuracy of points depends on your data. If your map data have 6
decimal places, you can plot with pin-point accuracy. In desktop mode, you can choose
which GIS to plot to (ArcGIS, DIVA, etc.). You can also plot to Google maps and Google
Earth. You can map collections of records using the main mapping form options or
individual records using the record level map toolbar.
You are also able to plot KML shapes and layers. Thus, if you have shape files for
garden areas, these can be superimposed on your map. Online, images can be
displayed with map points.
Data are stored as numeric values in the fields LAT/LONG (origin) and BGLAT/BGLONG
(garden) with their respect NS and EW fields. Map units can be DMS, DD or DM and this
is specified in your overall system configuration map setup and/or in the record level
LLUNIT and BGLLUNIT fields in your data files. All data are auto-converted to DD when
sent to your GIS. Different map units can be mixed within the same database.
Web toolbars are selectively enabled using Utilities > My setup > WebToolbars.
Maps can be created from any file where the
toolbar is enabled. The choice of GIS
depends on what you have installed locally or is accessible on your network. DIVA GIS is
freely available on http://www.diva-gis.org/.
Map projects created in ArcMap or DIVA can be registered in a BRAHMS map projects
file and selected when creating a new map. A project may include many GIS layers and
a reference to the data file of points to plot.
27 | P a g e
The mapping form. By selecting the ‘Map botanic garden points’ option, the mapper uses data in
the BGLAT/BGLONG fields. Otherwise, the mapper will use the LAT/LONG fields which are used to
store origin data as provided.
Bird eye view of living Quercus plants mapped across the Morton Arboretum
28 | P a g e
A botanic garden database may hold a wider range of data allowing you extend the
mapping functions to plot species distribution and/or calculate diversity of taxa.
An example online map showing locations of Oak trees in England, filtered on ancient, pollard
trees.
Global richness for all Conifers calculated online as species per ¼ degree. Red areas most diverse.
Richness maps can be calculated for different cell sizes for collections, families, genera and species.
29 | P a g e
Data capture using RDE
While living collections and living collection events can be added directly to BRAHMS,
where large numbers of accessions are being added or transferred from elsewhere,
Rapid Data Entry (RDE) is faster. RDE, a key module of BRAHMS is described in the
BRAHMS guide and manual.
RDE files are independent, external DBF data files, rather like Excel worksheets with a
flexible structure. You can re-structure RDE files to include only those data fields you
need for your project. RDE has functions to speed up, check-as-you-type and
standardize data entry. If your database already includes data, you can access these as
you add data to RDE files using AutoComplete, AutoMatching or standard lookup
functions. You can also link images of accessions to RDE files to assist when adding or
editing data in RDE. The BRAHMS RDE manager keeps track of your RDE files.
30 | P a g e
An example RDE file screen with the record summary Zoom panel opened. In RDE, data are entered
into an external DBF file. Once checked, these data are transferred into your main database.
RDE is also a fast way to add garden inventory, stock check and observation data. You
can create RDE files already populated with a batch of accession numbers queried from
our database. This latter function is especially useful for garden stock-checks. For
example, imagine you are about to do a stock-check from the “Japanese zone” of your
garden (or choose another region…). First query your database for all (living) plants
from that garden zone; Use the query file Tools option to create an RDE file based on
these plant records; Edit the RDE file as required, perhaps simply confirming the plant
status as dead or alive; finally transfer the RDE data to BRAHMS. The event records are
linked to the plant records in the database.
31 | P a g e
Querying living collections data
The process for querying plant records in botanic gardens is the same as for other
categories of data and is explained in the BRAHMS training guide section ‘Querying
data – making extract files’.
When you query data, records are assembled from your main database files and copied
to one or more temporary query result files. These ‘extract files’ are created when you
want to prepare outputs and reports, for example general lists of plants, labels, a
determination list, a map, a checklist, an index of collections, a species list, etc.
For most reporting tasks, you would first query out the data you want and then decide
how to report on these selected records. This division of tasks provides flexibility.
Query options are selected from the main query form, for example, to extract all
garden plants by garden location or family. Options can be combined (as in the
example screen below). You can also use tags and tag groups to query your database
and this provide almost limitless querying flexibility. Thus, you could manually tag
individual plant records or use a function to tag a group of records with something in
common and then simply extract tagged records. You can tag records in the main
family, genus and species files and then use these tags to query all garden records
associated with these tagged records.
Select Living collections > Extract/Query data to open the extract form and choose one
of the search options.
A typical query screen, here combining garden location, family and living collection status. You can
extend the query options provided by adding custom SQL queries.
32 | P a g e
Query results are delivered to user-specific extract files. Thus on networks, users can
assemble and subsequently process their own query results. As these files are copied
from the main database files, they can be edited and manipulated as required with no
changes in your main files.
In the following example, the objective is to query the database for all living accessions
that belong to species with “9” in the HARDINESS field. The encoding for hardiness
here uses USDA climate zonation.
1.
2.
Select Taxa > View/edit species in database.
Use the menu option Tag > Clear all tags to ensure no records are tagged.
3.
Using the
toolbar, apply a filter on the species field HARDINESS to
include the text “9”. This will filter to all records that include e.g. “9”, “3 – 9”.
If you wanted only “9”, the filter to be set as equals “9”
4.
5.
6.
7.
Select Tag > Tag all. This will tag all records within your filter selection.
Close the species file and select Living Collections > Extract/Query data.
Here, chose Tagged > Tagged species.
Proceed to query the data.
A section of the query result file showing records with status Alive, all records belonging to ZONE*9
taxa. In this screen, the Zoom option is enabled providing a summary of the records in the right
panel.
33 | P a g e
Reports and exporting data
Reporting
BRAHMS has tools that enable you to design your own report templates. These
templates are saved and registered in your system and are then used to create reports
based on the data you choose to include. Although reports can be created from any file
or module, they are mostly generated from data in RDE and query files. BRAHMS is
delivered with some sample report templates.
The guide has further sections on visual and text reports:
http://herbaria.plants.ox.ac.uk/bol/Content/Projects/brahms/Resources/BRAHMStraining2013.pdf
For more details on text reporting:
http://herbaria.plants.ox.ac.uk/bol/Content/Projects/brahms/Resources/Textreporting.pdf
Report examples commonly needed in botanic gardens are plant lists and catalogues,
species lists, seed indexes, labels and periodic inventory reports.
There are two categories of report - Visual and Text. ‘Visual reports’ are normally used
to generate lists, labels and other outputs that are printed directly from BRAHMS. The
Visual report options are similar to MS Access reporting options. ‘Text reports’ are used
to prepare documents such as checklists, catalogues and other products that will be
opened in your word processor. Text reports are HTML based although no knowledge
of HTML is needed to design them in BRAHMS.
Reports are often created from data in a query file.
34 | P a g e
A simple landscape, tabular list of garden accessions produced using a Visual Report with a few
graphic features added.
A simple Text report with a list of accessions generated directly from an RDE file.
Labels for herbarium specimens and plant accession can be designed and printed using
Visual reports. For garden labels, data are normally exported to MS Excel and then fed
into an engraving printer.
Label design is entirely flexible. For engraved labels, data can be fed to special machinery using
Excel or another format as required.
35 | P a g e
A more complex text report for a single species.
36 | P a g e
An example ‘Index Seminum’ prepared using text reporting and exported to a PDF. Data provided
by Thomas Jansen, Humboldt-Universität zu Berlin, Späth-Arboretum, Berlin. Reports such as this
are completely customizable and can be adapted to any preferred format.
Exporting data
As well as creating text reports (which in itself is a form of data export), data can be
saved in a variety of well-known formats such as Excel, CSV, MS Access and Delimited
Text. While you can export data from any file, the normal procedure is to first query
data and then export the results to the selected file type using File > Copy/Save as… or
the Copy/Save toolbar equivalent.
37 | P a g e
In the above example, tagged records are being exported to Excel, respecting the current field
view.
An example export where the data are being opened in Excel.
38 | P a g e
Garden exchanges and related transactions
Living collection records can be linked to transactions of different types, providing a
mechanism to track incoming and outgoing accessions. You can also print transaction
reports which are similar to herbarium loan list. The categories are edited using Living
collections > Transactions > Transaction categories.
Transactions are organized into categories.
The basic transaction record is added via using Living collections > Transactions >
Transactions file. Here you would add the type of transaction, its ID reference number
and if outgoing, the name of the recipient.
Each transaction can be opened using the
toolbar and accessions added one by one. A faster
method is to extract the records to link to the transaction and in the extract file, select Tools >
Transactions > Link tagged to transaction.
39 | P a g e
As with labels, transaction lists are designed using Visual Reports.
40 | P a g e
Virtual botanic gardens and online catalogues
If you already have your own web platform, botanic garden accessions can be exported
from BRAHMS into a selected format and then uploaded to your website. Alternatively,
you can develop your website directly from BRAHMS and upload those data you wish
to for online access on BRAHMS Online (BOL). BOL is separate software to BRAHMS and
it can be installed on your own server.
BOL web pages are bootstrap based and offer almost limitless design flexibility with
options for pages in multiple languages. The services offered can be used by those with
no web design skills or knowledge on HTML, CSS and related web language features.
Web design and data upload features are provided on the PublishOnline menu.
Uploading a website banner.
You can upload almost all categories of data including living collections. Upload
restrictions can be separately defined and applied at either the record or the field level.
For example, you can upload only tagged or queried records, exclude protected taxa
and exclude entire selected fields. Data, once uploaded can be refreshed or removed.
Once online, your data can be queried and presented in tables (similar to those used in
BRAHMS itself) or developed into reports. Default online report templates are provided
41 | P a g e
but you can also design your own. Online, data can be mapped as plants in your garden
with pinpoint accuracy; or referring to the original collection sites. Images can also be
uploaded and by combining text, maps and images, you can prepare a virtual botanic
garden.
A sample home page with a dynamic image map providing quick access to selected plants.
42 | P a g e
A species report presented online
The Summary option displays record counts per selected column in the right panel. Summaries can
also be charted. Here showing total botanical records collected in Indonesia and Malaysia for all
families.
43 | P a g e
Annexes
Plant accession field list
Some fields from related tables are included. Fields from further related tables not
documented here are visible when opening the accession file. Field views in BRAHMS
are often project specific and are configurable.
Field name
Tag
Del
ID
Accession
Accession status
Comments
Quantity received
Received date
Full name
Rootstock
Source/supplier
Source notes
Source reference
Supplied as
Received as taxa
Justification
Breeding system
Provenance type
Prop history
Origin note
Source reference
Source location
Prop number
Prop container
Prop site
Finish number
Surplus
Restrict
Documents
Collectors
Number
Collection date
Country
Major area
Minor area
Description
Processing field for record selection
Processing field for record deletion
Unique record ID - read only
Plant accession ID
Status of accession
General notes
Number of items received
Day Month Year
Species full name
Rootstock/understock
Source of plant/accession
Notes an source
Source reference
Cutting, plant, seed, etc.
Species name on receipt
Justification for acquisition
Breeding system of plant
Provenance of the accession (W,Z,G,U)
Propagation history of plant (VB, SB, SA, …)
Origin notes
ID of immediate parent plant
Location of parent plant
Numb. of plants sent to prop
Propagation container
Propagation site
Target to propagate
Notes on surplus available
Restriction documentation
Other documentation
Collector name
Field number
Day Month Year
Country of collection
Major area
Minor area
44 | P a g e
Locality
Locality notes
Lat
NS
Long
EW
LLunit
LLres
QDS
Altitude
Max altitude
Habitat text
Plant description
Cost
Notonline
Edithist
Rdefile
Mydocs
Images
Planttotal
Lctotala
Lctotald
Accesssum
Checkdate
Checknote
Checkwho
Entrydate
Who
Location name
Location notes
Map reference
North South
Map reference
East West
Map units (DD DMS DM)
Map resolution
QDS grid square
Altitude (or min alt)
Max altitude
Habitat text notes
Plant description notes
Purchase cost
Marked * if not to go online
Track changes
Source file if imported from RDE
Calc. linked total documents e.g. MTA
Calc. linked total images
Calc. Number of plant records
Calc. Number of plant records – alive
Calc. Number of plant records - dead/disposed
Calc. Summary of plants
Date last checked
Check notes/comments
Checked by
Entry date
Entered by
Light blue rows refers to fields linked via a botanic record (wild origin). The botanical record link
file can be used to add project specific descriptor fields describing the collection event, for example
‘biome’, ‘soiltype’, ‘terrain’, etc. Dark blue rows are calculated fields updated using options on the
Calculate menu.
45 | P a g e
Plants file field list
Some fields from related tables are included. Fields from further related tables not
documented here are visible when opening the plants file. Field views in BRAHMS are
often project specific and are configurable.
Field name
Tag
Del
ID
Accession
Plantid
Plant status
Comments
Loss date
Losswhy
Loss notes/cause
Disposed
Plant treatment
Stump treatment
Order
Family
Genus
Taxstat
Fullname
Common name
Growthform
Hardiness
Detby
Det date
Detstatus
Detnotes
Barcode
IPEN
Bgregister
Main garden division
Garden location
Garden location code
Garden area category
Layout
Plantcount
Subarea1, 2
Bed
Row number
Description
Processing field for record selection
Processing field for record deletion
Unique record ID – read only
Accession ID
Plant ID
Status of plant in garden
General notes
Loss date
Loss why (death, disposed)
Specific loss causes
Number of plants disposed
Treatment of plant
Treatment of tree stump
Plant order
Family
Genus
Status of name
Full species name
Main common name
Growth form
Hardiness coding
Det by who
Determination date
Status of det
Det notes
Barcode
International exchange ID
National plant register ID
Main garden division name
Garden location name
Garden location code
Garden area category
Formation of plants (patch, …)
Number of plants in a plant group
Garden sub-area IDs
Bed number
Row number
46 | P a g e
Sequence
Garden locnotes
Grid
Subgrid
BGLat NS
BGLong EW
BGLLunit
Hazard code
Hazard notes
Plantedby
Plant date
Labelprint
Label date
Needslabel
Label type/size
Label total
Label notes/text
Species range
Commemoration category
Commemoration text
Commemoration person
Commemoration date
Commemoration end date
Commemoration notes
Sponsor
Fields from accession file
Catalogue
Mystring
Rdefile
Edithist
Images
Voucher total
Mydocs
Checkdate
Checknote
Checkwho
Entrydate
Who
Sequence number for inventory/trail
General notes on garden site
Garden grid
Garden subgrid
Latitude of plant + NS
Longitude of plant + EW
Map units (DD DMS DM)
Hazard coding
Hazard notes
Planted by who
Planting date
Print labels for…
Label last produced
Indicate if a label needed
Label size/type
Labels to print
Text to print on label
Range from species file
Commemoration category (in memory)
Commemoration
Commemoration person
Commemoration date/start date
Commemoration end date
Commemoration notes
Name of sponsor(s)
Is plant in garden catalogue
General processing field
Source file if imported from RDE
Track changes
Calc. linked total images
Calc. linked vouchers
Calc. linked documents
Date last checked
Check notes/comments
Checked by
Entry date
Entered by
Light green refers to fields linked via the main species file. Light blue rows refer to fields in the
garden locations file. Dark blue rows are calculated fields updated using options on the Calculate
menu.
47 | P a g e
48 | P a g e
49 | P a g e
Botanical Research And Herbarium Management System
BRAHMS is a widely used database management system providing extensive and
innovative functionality for herbaria, botanic gardens, seed banks and research
botanists. Developed to assemble, edit, analyse and publish botanical data, the system
is used by small research projects as well as by the largest herbaria, botanic gardens
and ‘industrial scale’ botanical surveys and analyses.
The BRAHMS project is part of the plant diversity and systematics research group at the
University of Oxford.
BRAHMS Project
Department of Plant Sciences
University of Oxford
South Parks Road
Oxford OX1 3RB, UK
email: [email protected]
url: http://herbaria.plants.ox.ac.uk/bol/