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ABOUT BRAHMS v8

Development priorities
A modular system
User friendly and brandable
A sustainable future


SAMPLE APPLICATIONS

Managing natural history collections
Taxonomic research
Botanic gardens and living collections
Seed banks
Samples and surveys
Publishing online


SOME v8 FEATURES

Data store, scalability, portability
Language
Context sensitive menus and toolbars
Spreadsheets and forms
Opening and linking multiple tables
Find anything - anywhere
Explore, query, filter
Sorting records
Column summaries
Selecting visible columns
Design your own Tree Views
Calculated fields
Module specific tools
Editing data
Adding comments
Custom fields
Taxon names in v8
Descriptive text for taxa
Adding literature
Importing data from Excel
Matching data from Excel
Exporting
Reporting
Transactions
Tagging records
Tag Group Manager
Mapping
Map searching and analysis
Mobile technology for gardens
Images
Documents
Dynamic web links
Transferring data from v7 to v8

The list of topics is gradually being extended.



ABOUT BRAHMS v8

Development priorities

BRAHMS v8 has been developed as a scalable research and curation management system for preserved and living natural history collections. While derived from earlier versions of BRAHMS with respect to much of its functionality, v8 is an entirely new system with updated technologies and data store. Based on almost 30 years of database development and implementation, v8 is being phased in during 2018. Development has been undertaken in consultation with many different categories of project, many of these long term v7 users. Wherever beneficial, the system follows published management standards for preserved and living collections.

The development priorities for BRAHMS v8:

  • easy to install and maintain, intuitive to use;
  • scalable from small research projects to large, multi-site enterprise systems;
  • extendable, allowing projects to add custom storage fields;
  • modular, allowing others to add components including web-based add-ons;
  • international with respect to data store and user interface;
  • capable of managing and integrating all categories preserved and living collection;
  • a sustainable solution with the potential for distributed development.

A modular system: bringing your data together

BRAHMS has a flexible, 3-tiered and modular architecture with common services utilized as required. Individual modules may have their own internal services for specialized purposes. Data are fully integrated system-wide. The modular architecture opens up options for shared development.

  • a flexible, 3-tiered and modular architecture with common services.
  • each module may have its own internal services for specialized purposes.
  • the modular architecture opens up options for shared development.
  • modules and their components can be developed independently of each other.
  • the current user interface is written using WPF (XAML) as a ‘Desktop application’.
  • the UI is independent of the services and data store access and therefore could relatively easily be substituted by other technologies such as a web-browser UI.

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For collection managers in museums, botanic gardens, herbaria and seed banks and for those undertaking taxonomic and biogeographic studies, BRAHMS helps integrate your data for collection management and research, increasing outputs and productivity.

User friendly and brandable

BRAHMS v8 is highly intuitive using dynamic, context sensitive ribbon technology similar to that used in MS Office applications. Menu text, tooltips and related help messaging are held in translatable resource files. Setup options allow the selection of background imagery and form banners.

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Context sensitive menus and toolbars are intuitive and easy to use. Data can be viewed and edited in versatile data grids or using forms, both dockable.

A sustainable future

BRAHMS licensing and support are now managed through Oxford University Innovation. OUI provide rigour to the entire project and through appropriate licensing, ensure our projects get the service and support they require. With OUI backing, a sustainable and long-term future for BRAHMS is secured.

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Oxford University Innovation is a wholly-owned subsidiary company of the University of Oxford.

SAMPLE APPLICATIONS

Natural history collections

BRAHMS v8 has been developed to store all categories of natural history collection. Above family, taxa levels including Kingdom, Phylum, Class, Order and Suborder are provided as standard higher classification fields. However, depending on the collections you are managing, you can define as many new taxonomic ranks as required, both above and below family level (superfamily, subfamily, tribe, subtribe, etc.). Read more about using BRAHMS for museum management.

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BRAHMS v8 has been developed to store all categories of natural history collection.

Taxonomic research

While some projects require only a simple list of species names, others assemble comprehensive details about each name as required for different types of research publication. In this respect, BRAHMS manages all details of nomenclature for taxonomic research. The ability to select, format and publish taxonomic information for different purposes, including online, is a key BRAHMS priority. Read more about using BRAHMS for taxonomic research.

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A comprehensive online resource for the Papaya family with full nomenclature, imaged and geo-referenced specimens, species descriptions, keys and references. Visit the e-monograph.

Botanic gardens and living collections

The BRAHMS living collections module manages data and images for botanic gardens, arboreta and other horticultural projects. The module uses all the standard BRAHMS features to edit, query, report, map, export and publish online with additional features to manage garden accessions and plants. As living collections data are fully integrated within BRAHMS, it becomes possible to develop a comprehensive system for both curation and research. Read more about managing living collections in BRAHMS.

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The Living Collections module in BRAHMS has been developed collaboratively with The Oxford Botanic Garden and The Morton Arboretum, Illinois.

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The Morton Arboretum database brings together data about their garden plants and herbarium vouchers. Here, zooming in online to a selection of their Malus collection. Visit the Morton Arboretum Malus collection.

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As a celebration and count-down to this anniversary, the University of Oxford Botanic Garden and Harcourt Arboretum, together with the Oxford University Herbaria and the Department of Plant Sciences, will highlight 400 plants of scientific and cultural significance. One plant is profiled weekly using BRAHMS online, and illustrated with images from Oxford University's living and preserved collections. Visit the Plants 400 website.

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BRAHMS is also used to publish images and illustrations. An example is the collection of watercolours by Charlotte Georgina Trower. Visit the Trower Botanical Illustrations website.

Seed banks

The seed module, developed collaboratively with the Millennium Seed Bank at RBG Kew, has broad curation and research applications for projects and institutions that collect, store, test and distribute seed. Seed accession and test data, related vouchers and images are all integrated and can be published online. Read more about the seed bank module in BRAHMS.

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The Millennium Seed Bank, the world’s largest seed banking project, uses BRAHMS to bring together seed accession and test data from across the many partners in the Millennium seed Bank Partnership covering some 53 countries and 123 organisations. Visit the MSBP Data Warehouse.

Samples and surveys

The survey module manages data from temporary and permanent plots which may be small, irregularly shaped survey sites or industrial scale forest grid blocks. The simplest samples may only register species presence. More complex surveys may include many more measurements. For example, a forest survey may add data about trees - tree numbers with their provisional identification, diameter, height, stem form, field images, specimen vouchers and more, depending on the research objectives. Plot data, combined with other data stored in BRAHMS, can be used for diversity and bio-quality analysis. Read more about using the sample and survey module in BRAHMS.

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Use survey data to calculate meaningful local richness, diversity and bioquality indices. http://herbaria.plants.ox.ac.uk/bol/trin

Publishing online

BRAHMS online allows you to design websites and manage your data and images online for curation and/or research use. Websites can be created for herbaria; botanic gardens; seed banks; taxonomic groups; geographic areas; images, paintings and illustrations; or any combination of these. Specialist websites can also be created, for example, websites for historical collections or all collections of a particular collector. Read more about publishing online from BRAHMS.

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The South African National Biodiversity Institute (SANBI) brings together species and collection data for southern Africa. Visit the SANBI database online.


SOME v8 FEATURES

Data store, scalability, portability

One of the key challenges in developing v8 has been to provide a system that can be scaled up to enterprise level projects with the capability to manage many millions of specimens on servers with suitable IT support - but is equally accessible to the itinerant researcher needing to copy his or her entire database onto a memory stick.

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As well as providing database support to individiual researchers, BRAHMS v8 has been developed for enterprise level projects. Stress test results with the largest existing BRAHMS database [National Herbarium of the Netherlands with 650,000 taxa records and 5.7 million preserved specimen records, each with a linked media library image] using a MSSQL Server data store, with multiple, simultaneous logins, are excellent.

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BRAHMS is easily connected to different data stores. In this example, using the option to Manage Data Sources, the data store is set to a MSSQL Data Provider where a database (catalogue) oxforduniversityherbaria2018 has been created.

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Databases are scalable to any size. Record numbers per table are displayed on the grid tools tab.

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National herbarium of the Netherlands, the largest BRAHMS project storing over 5.5 million specimens and images. Visit the Naturalis database online.

Language

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BRAHMS v8 is international with respect to the interface and the storage of data. Translatable resources files are used to manage interface components. Variable formatting (date, time, numbers, currency, etc.) and other processing features are language independent. Data storage is Unicode with no restriction on the character data stored across languages.

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New languages can be added on request - a new language column is added to the v8 text resource file. This can be translated locally and then returned to the BRAHMS project to update the system.

Context sensitive menus and toolbars

Context sensitive ribbon toolbars similar to those used in Microsoft Office applications, offer all the features that long term v7 users have voted for. These include record tagging, two step deletion, zoom, column summaries and column selection. They also make BRAHMS v8 intuitive - easy to learn and use.

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Some example ribbon menu toolbars.

Spreadsheets and forms

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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Data can be viewed and edited using grids or forms. Forms can be resized, docked or dragged to separate monitors.

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Forms can include calculated summaries, here, a quick list of botanical records for the current species with a summary of collection details.

Opening and linking 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.

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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.

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

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.

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Explore, query, filter

BRAHMS v8 includes comprehensive search functionality. The top 'filter row' feature provides an extremely fast way to add multiple filters. You can also quickly filter to the value in any cell, adding further cell value filters using the Selection and +Selection toolbar options. Using the main Query tool form, you can design and save your own queries. These queries, which generate visible SQL commands, can mix and match fields of any type. Column summaries and Tree Views provide additional mechanism to quickly locate and query your data.

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Data grids have a handy filter row where you can enter values to filter on multiple columns. This option allows the use of ranges as well as AND and OR clauses.

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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.

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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.

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Here, we are querying the living collections file with several fields selected including 'Needs a label'. Frequently used command combinations can be named and saved.

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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.

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Data in all tables can be sorted using single or multiple fields in ascending or descending order. Shift+click headers to combine columns.

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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.

Column summaries

Column summaries are a powerful way to list all the different values in the current column. Moving to a different column updates the summary. Furthermore, you can 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 month.

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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.

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.

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A view showing species names with text descriptions and the text opened in a separate window.

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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Here a field view has been created to show some of the calculated fields in the main species file. All calculated fields are updated using the Recalculate option. In this example, the table has a descending sort on the number of living plant records linked to each species.

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An example showing some calculated fields in the main family table.

Design your own 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.

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

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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.

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

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

Module specific tools

Module specific data processing tools help with many different tasks, for example, checking data quality and editing records in batches.

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

Editing data

All data editing is initiated using the Edit toolbar. Context sensitive editing applies throughout BRAHMS. Thus, if you are in a date field, a date editor is used while with map points, the map point editor will be available. All changes are tracked and can be reversed in steps.

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Record creation and modification details are stored in each table. Thus records are easily sorted by create or last edit date. Here a column summary shows the number of records created per date.

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Context specific data editors are available to change your data, the example here for a map point.

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Here editing the genus name in the main species table. The grid editor lists genus names matching the Search value entered. If the genus name is changed, this edit is auto recorded in the Edit History.

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Changes to your data are tracked and can be reversed using the Undo option.

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All additions, deletions and updates are registered in a central Edit History file, here filtered to show Updates and, taking advantage of the system-wide column summary tool, showing the number of updates per table.

Adding comments

Comments are easily added to any record using the data tools Comments option.

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Adding a comment to a species record.

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 your main data grids with equal status to BRAHMS default fields. Custom fields can be added to any table.

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Here showing the addition of custom fields to a Rapid Data Entry file. The fields Shelf Number, Scanned and Spirit material available have been added to this RDE file.

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Custom fields here viewed in the main collection event table. They are display in a different font to standard fields.

Taxon names in v8

BRAHMS has separate tables for Higher Classification, Families, Genera and Species. The first three of these store details from Kingdom through Phylum, Class and Sub Class down to the Order, family and genus. In each of these tables, you can define further taxonomic levels as needed for particular taxa groups, examples being suborder, superfamily, subgenus, tribe, section and series. Each name can be assigned an authority and be linked to publication details. Further standard fields are provided for commonly stored data and again, you can extend the tables by adding your own custom fields.

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You can define further custom higher classification taxonomic levels as needed for particular taxa groups.

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Species and infraspecific names are stored in the species table. Here, unlike BRAHMS v7, default fields are Species, Subspecies, Variety, Forma and Cultivar. As with the other tables you can extend the table by adding further taxon levels as custom fields. The use of the v7 rank fields has been dropped. Taxon rank descriptors such as subsp., var. and f., are added to calculated name strings and are formatted into reports as appropriate.

Descriptive text for taxa

You can store descriptive text 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.

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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.

Literature

You can add literature references to the main literature table, linking these to any record in your database. Typically, links will be to species but you may want to store reference entries for people, genera, seed collections, plants, etc.

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An example list of literature references with a filter on 'magnolia'. A column summary is displayed for the literature category.

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 XLSX 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.

Exporting

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Export data to Excel or CSV formats respecting the sort order and visible column selection. Additional export options are being added.

Reports

Adding to the existing report features, we have connected BRAHMS v8 to a reporting suite that effectively replaces the functions of Text and Visual reporting in v7. As with the ArcGIS API, links to Stimulsoft Reporting have been fully embedded in BRAHMS v8. This new reporter, which comes licensed with BRAHMS, provides 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. Stimulsoft report wizards are provided and there are guides and videos available online for those wanting to stretch their report design legs. Some ready to use examples are provided with BRAHMS, together with some start up notes. For those familiar with v7 reporting, there are many familiar features such as a visual designer; report bands for headers, data, footers and summaries; and text formatting and style setting. Although not needed, you can refer to the full reporter user manual.

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

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Report wizards help learn the ropes with the report designer.

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..

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

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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.

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.

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

Tag Group Manager

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

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Here, the three IUCN Red List categories CR, EN and VU have been tagged using the colour coded numbers 1, 2 and 3 respectively and saved as a tag group. The tags have been restored to the species table. The Manager also allows you to set quick filters on one or more of the saved tag categories.

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Mapping

Mapping options include dynamic links to the in-built ArcGIS and externally, by passing data to ArcGIS, Google Earth, DIVA, QGIS and GeoCAT. Any data with map references (collection events, botanic garden plants, etc.) can be mapped.

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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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Mapping plants in a botanic garden. Here, the map is opened with a filter set to garden areas using a user-defined Tree View.

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Combining maps with the query tool. The yellow point represents the current record. Clicking on any map point locates the grid record, a great way to pin down map errors.

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ArcGIS map opened with a data grid, Tree View and Google images.

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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.

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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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Map searching can be used with botanic garden maps, here again showing the different taxa located in the search area.

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Useful mapping functions are being added. One example is calculating the Extent of Occurrence (EOO).

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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.

Mobile technology for gardens

The mobile app developed by the Morton arboretum is currently optimized for any 7 inch tablet and is soon to be optimized for different sizes of the screen.

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The Morton Arboretum app displays plants near the user and allows entry of plant events and plant requests, feeding these directly to BRAHMS v8 RDE files awaiting verification and import.

Images

Images can be linked to any record category in BRAHMS and you can link multiple images to the same record. Some images may also be linked to multiple data records. All your images are listed in the central images table with their full pathname or URL. Images can be viewed from the main file and/or wherever they are linked. Various options are provided to link images and you can also drag and drop images to the image viewer. Images may be stored in any location including in media libraries and on cloud servers. Read more about managing images in BRAHMS.

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Images of different categories can be published online. Visit the Flora of Namibia online.

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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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Combining image viewing with a Tree View in the main specimen file. The data grid is showing the calculated field for image total per record.

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The image viewer has various handy functions including zoom and copy.

Documents

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.

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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.

Web links

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Dynamic links to external websites. Web pages are updated as you scroll through your data, in this example, Kew Science Plants of the World Online (POWO).

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Opening multiple websites.

Transferring data from v7 to v8

Data stored in v7 can be transferred to v8 using the administrative function provided in the latest versions of v7. The procedure creates a sequence of XML files in a designated folder, ready for the transfer to v8. As part of this process, detailed checks are carried out on your v7 database to ensure there are no data integrity errors.

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The export process transfers all data from v7 including your custom fields and edit history.