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A selection of BRAHMS features

Updated March 2024


BRAHMS RDE Reporting Query Data Store Garden app Publish Online Custom Fields Integrated Mapping Sorting Darwin Core

Botanic gardens

The living collections module manages data and images for botanic gardens, arboreta, estates and other horticultural projects. A comprehensive range of functions is provided to manage all aspects of garden management from initial accessioning on. This module is closely linked to the BRAHMS modules for managing taxa, vouchers, images, documents and maps. Daa can be added quickly using Rapid Data Entry and garden inventories can make use of BRAHMS garden app.

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BRAHMS is used to manage a wide range of gardens and arboreta, small and large. Projects include The Royal Horticultural Society (RHS) and The Royal Botanic Gardens, Kew.

Botanic gardens app

The botanical gardens mobile app is used to gather data and images for plants in botanic gardens or similar areas. As the app works both on and off line, you can gather data in garden areas that have no internet/phone signal. Example uses are to undertake stock-checks; check plant names; request labels/maintenace tasks; add map references; take images; and to log observations such as flowering.

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The app includes map and image management tools.

Calculated Fields

Many tables have one or more calculated fields. These are handy fields that provide a range of numeric totals and calculated text strings. Examples are to total up the number of images or documents per record; the number of collections made by different collectors; and the number of genera and species per family. Calculated fields have multiple uses with viewing, reporting and error checking, as well as simply knowing what's in your database.

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An example showing some calculated fields in the main species table. All calculated fields are updated using the Recalculate option.

Selecting visible columns

You can customise the visible columns from the Grid Tools menu. Multiple column views can be saved for each table and then selected from a drop down list. There are a number of ways to select or hide columns.

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A view of the species file showing the publication details and the calculated collection totals.

Column summaries - single and multi-column

class="v8textintro">Column summaries are a powerful way to list different values in the current column. Moving to a new column updates the summary. You can also use the column summary tool to quickly filter on one or more of the listed values.

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The simple use of the column summary function to total up the number of collection events per family.
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Column summaries can be opened with other features such as maps - here the map is updated to reflect the two selected values.
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Multi-column summaries are used to total the number of records for any combination of columns. In this example, the count shows the number of collection events per country per family.

Adding custom fields

If BRAHMS does not have the storage fields you need, you can add your own custom fields. These fields are fully integrated with your database and appear in the main data grids with equal status to standard BRAHMS fields. Custom fields can be added to any table.

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Here showing the addition of custom fields to the main species table.

Darwin Core Archive (DwC) transfers

Create DwC archive files for taxa and occurrence data.

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Creating DwC output from specimen table.

Documents - files and URL links

Multiple documents of any type can be linked to any record in BRAHMS. This could be a PDF material transfer agreement or collection permit linked to a specimen, accession or transaction; a protologue description linked to a species; a sound file linked to an animal entry; or perhaps a video or slideshow linked to a botanic garden greenhouse record. You can link any category of media including URLs.

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Linking pdf, docx, wav, pptx and xlsx documents to a species record. Media and documents can be opened using the Open option or double-clicking on the linked entry.
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Linking a sound file to a bird record in the species table, here showing the document and image viewers opened at the same time.

Editing data

All data editing is initiated using the Edit toolbar. User restrictions can be applied per module.

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The upper image shows a grid which is not in Edit mode. The lower image is in Edit mode with context sensive data editors enabled in the grid and on the form.

Edit History and Undo

All edits are recorded in a central edit history table. Edits can be viewed and reversed from any table.

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Edits for all fields in the current record are easily tracked using the Edit History option.
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Edits for specific fields can be reversed using the Undo option.

Exporting to Excel/CSV

Tagged records from any table can be easily exported to Excel/CSV format. This function will export data from your currently selected columns respecting any filters and sort order you may have set.

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Exporting data to Excel.

Importing data from Excel

Using the Excel Import Wizard, Excel tables can be opened and imported directly into Rapid Data Entry files and then, after checking/editing, transferred into BRAHMS itself. The Import Wizard is accessed when an RDE file is opened.

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Step one is to locate the Excel file you want to import.
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The Wizard allows you to match columns in the Excel spreadsheet to the columns in your RDE file. This means that Excel tables with differently named fields, perhaps in foreign languages, can still be imported.
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The data in the Excel table are then listed and you can opt to import all or a selection of records. Once in RDE, the data can be checked, edited as needed and then transferred to BRAHMS.

Matching data from Excel

Match records provided in an Excel table to records in BRAHMS using any combination of fields, tagging the matched records. Examples uses: match a list of species provided in Excel to your own species list; match a list of museum specimens or seed accessions based on a list of barcodes provided in Excel.

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Here matching a list of seed accessions provided in Excel using the seed accession number and family name.
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Matching a list of species names.

Find anything - anywhere

When you open any data grid, you can use the Find option to locate any text or a number in any grid cell. Cells that include your text are highlighted in yellow. Using the search box navigation arrows, you can move to the next or previous matching cell.

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The find function is a quick way to locate text or a number anywhere in the data grid.

Data grids and forms

class="v8textintro">By default, BRAHMS uses versatile data grids with context sensitive toolbar options to locate, select, sort, query and analyze your data.

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A typical data grid with associated toolbar options. Data grids provide a powerful way to view and explore your data with options to tag, sort, analyse, calculate, query, export and report.
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The species table form, here configured for botanists. As well as providing a way to edit your data record by record, forms include additional calculate and list options.
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List synonyms on the main species form.

Images

Images can be linked to any record in BRAHMS and you can link multiple images to the same record. All images are listed in the central images table with their full pathname or web URL. Images may be located in any location including in media libraries and cloud servers. Read more about managing images in BRAHMS. You can store links to images using a URL - you do not need to have a copy of the image file. Read more about managing images in BRAHMS.

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Images are easily dragged to the image viewer and stored in your central images library where they can be further organised and managed.
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Viewing images from the main image library.
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When viewing images in the main species table, the system assembles images of linked collection events and specimens. In this example, the species table is filtered to taxa with > 50 linked collections in the family Lecythidaceae. Taken from the Naturalis herbarium database.
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The image viewer has various handy functions including zoom and copy.
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Images of different categories can be published online. Visit the Flora of Namibia online.

Mapping - ArcGIS

Mapping options include dynamic links to the in-built ArcGIS and externally, by passing data to ArcMAP, Google Earth, DIVA, QGIS and GeoCAT. Any data with map references (collection events, botanic garden plants, etc.) can be mapped. The internal ArcGIS mapper requires no installation but you do need to be online. Training videos on mapping in BRAHMS are available on the training video page.

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Map options are selected from the Maps toolbar which is enabled when mapping data are available.
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ArcGIS is integrated with v8 and requires no installation. Dynamic links between grid and map allow point highlighting.
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Hightlighting one species in Sarawak using tag colouring.
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Mapping wild origin sites of seed accessions using a tree view to filter on seed supplier.
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Combining maps and images online.

Mapping - QGIS

QGIS is a mapping package freely available on https://www.qgis.org. BRAHMS can connect and pass data to QGIS – but you have to install the QGIS software locally first. You can open QGIS directly from BRAHMS, passing data to saved QGIS map projects. Training videos on mapping to QGIS from BRAHMS including creating species richness maps are available on the training video page.

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Mapping the species Pinus devoniana to QGIS.

Map point editing

The map point editor and location search option can be used in any table with map points. The editor opens a dynamic online map form. Records with existing map points will be mapped using your selected base map. A right-click on the map resets the point position and either auto-saves this to the grid or awaits conformation with via the Save option.

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The map location editor displaying the current point, set to Auto-save. In this mode, a right-click on the map will update the Latitude and Longitude values in the data grid without using the Save option.
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Zoom to a different scale.

Map search and analysis

The integrated ArcGIS is being extended in phases to provide search and analysis features.

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Map searching updates the associated data in the data grid. Here a species list for the search area is created using the summary tool.
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The internal mapper has a range of features including calculating the Extent of Occurrence (EOO) and map screen capture.
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An example map connection to GeoCAT for conservation assessments.
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BRAHMS online includes features to map richness and diversity with different scales and themes. One example is the conifer database published on http://herbaria.plants.ox.ac.uk/bol/conifers. The red areas have the highest numbers of different taxa.

Menus and toolbars

Context sensitive ribbon toolbars similar to those used in Microsoft Office applications are used throughout BRAHMS making the system intuitive, easy to learn and use.

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Some example ribbon menu toolbars.

MS SQL Server as a Data Store

MS SQL Server is an industry standard DMBS and as with PostgreSQL, is secure, highly scalable, and can be configured to optimise performance. Databases can be accessed simultanously by multiple users. The Standard (Express) edition is free but the Enterprise editon must be licenced.

Create an MS SQL Server data store directly from BRAHMS using the Data Connections option provided.

Spread out on multiple monitors

Data grids, forms, images, weblinks, maps and calculation screens can all be undocked and used on separate monitors. Toolbar options always apply to the last selected window.

An example using a second monitor for the ArcGIS mapping. Maps are dynamically updated as you adjust your grid filters.

Multiple tables

In BRAHMS v8, you can open as many tables as you wish at the same time. Table docking can be arranged as needed and using different monitors. Where tables are related, for example, [Family -> Genus -> Species -> Collection event -> Specimen] or ... [Species -> Garden Accession -> Garden Plant -> Plant Events], you can relate these tables to dynamically update as you select records on your data grids. This also applies to maps and external weblinks.

Multiple tables and features can remain open at the same time. In this example, the family, genus, species, garden accession and garden plant tables are opened and linked ensuring that they dynamically update as you browse.

Maps and web pages update as you move through your records.

Multi-Value (list) searches

The Multi-Value Search enables you to copy or enter a list of values to locate and tag records in the current table. For example, you may have a list of species names, plant accession IDs, collector numbers, publication years, barcodes or transaction IDs that you wish to locate.

Searching for a list of barcodes in the specimen table. The barcode list was copied into the Multi-Value search window from Excel.

Museum Collections

BRAHMS has been developed to store all categories of natural history collection - examples are birds, insects, fungi, ferns and higher plants. Specimens may have accession numbers and/or barcodes and be of any physical category. A specimen may have multiple determinations (annotations) over time and these are recorded with dates and the name of the person providinvg the name. Types can be recorded. Each specimen is linked to a collection event where comprehensive details can be stored on the origin of the material. With some categories of collection, for example plant material, a collection may result in multiple specimens, potentially distributed to different institutions. Specimes may be linked to boxes and/or folders and these in turn can be numbered or barcoded. Multiple images (files or URLs) can be associated with each specimen. Additional curation tools are provided across the collection management module, notably adding transactions for loans and exchanges. BRAHMS encourages the use of these data to catalyse research initiatives.

BRAHMS can equally be used to manage collection for a research project as for the world's largest collections. There are no meaningful limits to the number of collection records that can be stored.

Permits and Permissions

The Legal option under Data Tools provides access to all details on permits, permissions and other issues related to the legal status of material and its movement. You can store details on permits of different types with links to material transfer agreements, notes on due diligence and other documents. Entries can be categorized as Nagoya (2014 onwards), CBD (1991 - 2014 ) or pre-CBD.

Permits and Permissions records can be linked to physical specimens, plants or seed collections.

Documents associated with the record can be dragged to the lower panel.

PostgreSQL as a Data Store

For larger databases, especially those with many simultanous users, PostgreSQL is one of the data store options. As with MS SQL Server, PostgreSQL is secure, highly scalable, and can be configured to optimise performance. It can manage extremely large 'industry standard' databases accessed simultanously by multiple users. PostgreSQL is open source/free.

Create a PostreSQL data store directly from BRAHMS using the Data Connections option provided.

Publish Online

Create, design and publish your own websites directly to BRAHMS Online (BOL) using the Publish Online features.

The WebConnect tools provided on the Publish Online menu enable you to create and design multi-page websites using bootstrap with full control over the menu system and CSS file. Data and images can be directly uploaded from your database.

Query and Filter

BRAHMS includes powerful search functionality in all tables. The top data grid 'filter row' feature provides a fast way to add multiple filters. You can also instantly filter to the value in any selected cell using the Selection and +Selection toolbar options. And for those wishing to develop and save complex queries, the Query form can be used. Queries can mix and match fields of any data type.

Data grids have a handy yellow filter row at the top of the grids where you can enter values to filter on multiple columns. This option allows the use of ranges, wildcards as well as AND and OR clauses. Even if the data grid is linked to a table with millions of records, the filter row is very fast.

Using the Selection option, quickly set a filter on the current cell value, adding further filter selections using +Selection. In this example, Araucariaceae and Papua New Guinea have been selected.

Using the main query form, more complex queries can be built using data fields of any type. Queries can be selectively enabled and / or saved for future use.

Rapid Data Entry

While data can be entered directly into BRAHMS, RDE is recommended for entering larger numbers of records and also as a first step when importing or transferring data from other software packages such as Excel. RDE files are entirely separate mini-databases linked to your main BRAHMS database. Training videos on RDE are available on the training video page.

RDE is the fastest way to add multiple data records for most categories of data.

Reporting

BRAHMS is delivered with a powerful and flexible suite of reporting tools that are fully embedded in the system. BRAHMS reporting options provide almost limitless power to generate lists, master detail reports, labels, charts, cross-tabs and more. You can print, send to documents, attach as email or publish online. Those wishing to go the extra mile can refer to the full reporter user manual. Training videos on how to create reports are available on the training video page.

Designing report templates for almost any category of report is possible.

Sorting records

The ability to sort records, vital for reporting, is also useful to simply locate records and to find errors. Tables can be sorted on single or multiple columns by clicking and shift-clicking on the headers. Complex sorts are carried out and saved using the sorting tool.

Data in all tables can be sorted using single or multiple fields in ascending or descending order. Shift+click headers to combine columns. You can quickly sort on Last Modified date. Various further specialised sort functions are provided.

Using the sort form, any combination of character, numeric, date and logical field can be selected to sort your records. Complex commands can be named and saved for future use.

Tagging records

By tagging a record in any table, you add a character or number to the TAG field. Tagging opens up numerous options for subsequent record selections, processing and analysis. A simple example would be to tag a selection of collection events or garden plants manually or using a function - and then when mapping, restrict to tagged. Tagged records are dynamically coloured. All tags are user specific. Thus, on networked systems, your tagging operations do not interfere with those of another user.

Tagging is used throughout BRAHMS for record selection, querying, grouping records and more.

Tag Groups

The Tag Group option allows you to save profiles of tagged records in any table. You can mark up records with any of the available tag symbols and then save these tags to a named group. Examples are 'Medicinal species', 'My research taxa', 'Garden plants of special interest', 'Localities of special interest'. Tags from your saved tag groups can be loaded/restored to the respective table. Tag groups can optionally be shared with all users.

Once saved, you can quicky restore the tags from any group - this will add the tags to the records in your data grid.

Managing taxon names

Central to all BRAHMS databases, be they for curation or research, are the core taxon dictionaries. Designed equally for zoologists and botanists, data for any rank from kingdom down to the infra-specific ranks can be stored. Aside from names and their authors, it's possible to add full nomeclatural details for each name, cross-referencing to online resources and literature links.

Working with the RHS, innovative new methods are being developed to manage the complexity of plant names.

An example data processing tool, checking for possible spelling errors in the main species file.

Descriptive texts for taxa

You can store descriptive texts for all taxa levels, defining as many text categories as you need. For example, you may want to store details of recommended seed germination procedures at the species level, notes on species hardiness or preferred water requirement or sun tolerance, perhaps a technical description of a genus. All these texts are stored in a central table and can be viewed/edited there or when viewing the respective taxa records themselves.

All descriptions are held in a single table, here with a column summary showing the numbers of entries per text category.

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Descriptive text can be added at all taxa levels and displayed from the main taxa files. Text categories can be defined as needed.

Transactions - loans, gifts, exchanges and similar

Managing transactions is an important feature in BRAHMS v8 - be these for preserved or living material. Transactions are linked to the categories you choose to add to your database. After adding a transaction record, you can link or unlink items; print packing notes and correspondence; record material as returned; edit determinations; and review all transactions using any of the standard data grid features. Transactions, best managed using barcoded material, can be uploaded to BRAHMS onliine as Image based transactions..

The main transactions table records all details of incoming and outgoing material, both preserved and living.

The form also includes options to list linked specimens with barcoding features to link and unlink material or mark material as returned. Incoming determintations can be edited here directly.

Tree Views

Tree Views provide an excellent way to locate, explore and filter data as well as tracking down spelling errors. The Tree View designer allows you to create and save your own views with up to 10 hierarchical levels, as many as you need per table. Once opened, you can then use the locate and filter options offered, for example 'filter on selection' when you click on any tree level.

You can design and save your own Tree Views for each table.

This example shows a single level view to explore by country. With 'Filter on selection' selected, clicking on a Tree View entry filters to that value and updates any linked data, in this case, the map.

A Tree View with 3 levels. Tree View windows can be docked to suit.

A example Tree View for botanic garden events, with the plant events organised by group.

Dynamic Web Links

You can consult a range of handy online references from the Weblink toolbar. As a rule, these locate an online source for the species name for the current record - and this will update as you browse through the data grid. For example, you may want to check an author name on IPNI, check nomenclature on Tropicos or simply check out google images.

Dynamic links to external websites. Web pages are updated as you scroll through your data.