Tom.bio QGIS Biological Recording Plugin

QGIS logoTom.bio productivity tools

This is a QGIS plugin designed specifically for biological recorders. The plugin streamlines many of the tasks commonly required from GIS by biological recordes including viewing NBN maps (via the NBN WMS), displaying biological records derived from CSV file, working with OS grid references and registering raster map images from the internet.

YouTube logoMost of the help is provided by means of Youtube tutorial videos (see below) which you can link to from this page. If you want a flavour of the power of the tools, have a look at the video on creating batch atlas maps or the one on mashing up maps. If you are particularly interested in getting data from the NBN Gateway into QGIS, then look at he videos in this playlist. The tool is available from the QGIS plugin repository (see foot of this page for further information and a tutorial video showing how the tool can be installed).

As well as the videos showing how to use the Tom.bio plugin tools, our YouTube channel also has other videos relating to QGIS and others relating to biological recording. The best way to see everything we've got is to go to our channel and look at the playlists. We organise everything by playlist. So, for example, there's a playlist on there called 'QGIS tips for biological recorders' which contains videos not listed on this page.

OSGR Tool

The OSGR tool is designed to make working with Ordance Survey grid references easy in QGIS. Using this tool you can find the grid reference at any place (and at any resolution), centre the map on a given grid reference and generate layers of grid reference squares at any resolution.

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QGIS OSGR tool: basic use

How to use the FSC Tom.bio productivity tools plugin for QGIS to work with Ordnance Survey grid references. This explains how to retrieve OS grid references in QGIS and how to reposition the map to a specific grid reference. (Note that the QGIS CRS - coordinate reference system - for the map window must be set to an OSGB CRS such as EPSG:27700.)

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QGIS OSGR tool: generating OS grid squares

How to use the FSC Tom.bio productivity tools plugin for QGIS to generate grids of squares aligned to the Ordnance Survey grid. This explains how to generate grid square features by dragging a square over the map or by selecting a map feature. (Note that the QGIS CRS - coordinate reference system - for the map window must be set to an OSGB CRS such as EPSG:27700.)

Biological Records Tool

This tool is enables the rapid creation of map layers showing the distribution of biological records contained in CSV files (easily created from any spreadsheet). Map layers can be created for entire spreadsheets or for particular species within the spreadsheet. Records can be represented by points or collated to produce atlas distribution maps at any OS resolution. Map layers can be created singly or in batches. Batching map production makes the generation of atlas maps very easy and very quick. Images of map layers can be automatically created in batch mode to make the generation of maps for online or paper atlases a simple matter.

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QGIS Biological Records tool: the basics

How to use the FSC Tom.bio productivity tools plugin for QGIS to generate generate maps of biological records from spreadsheet data. This video explains the basics of the Biological Records tool - creating point and atlas maps from records in CSV files.

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QGIS Biological Records tool: mapping by species

How to use the FSC Tom.bio productivity tools plugin for QGIS to generate generate species maps from spreadsheets of biological records. This video explains how to build a selectable list of taxa from your spreadsheet and generate maps for each species.

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QGIS Biological Records tool: batch generating atlas maps

How to use the FSC Tom.bio productivity tools plugin for QGIS to generate generate species maps from spreadsheets of biological records. This video explains how to batch generate large numbers of high quality species distribution maps - ideal for atlas projects.

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QGIS Biological Records tool: Irish grid example

Example of using the QGIS Biological Records tool to generate 'atlas' style maps in the Irish context. In this example the CSV input file as data geocoded as easting/northings aligned to the Irish National Grid.

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QGIS Biological Records tool: WGS84 example

Example of using the QGIS Biological Records tool to generate 'atlas' style maps in an international context. In this example the CSV input file as data geocoded as latitude and longitude to the WGS84 CRS.

NBN Tool

The NBN tool simplifies the process of generating map layers for individual species from NBN records via the NBN Gateway Web Mapping Service (WMS). The tool includes a link to the UK Species Inventory and you start by searching the inventory in order to get the unique key (Taxon Version Key) which is used in the call to the NBN WMS.

Youtube link
QGIS NBN tool: viewing NBN distribution maps in QGIS

How to use the FSC Tom.bio productivity tools plugin for QGIS to view species distribution maps from the NBN Gateway via the NBN Web Mapping Service. This video explains how to query the UK species inventory to find the correct key for the species you want and then to retrieve distribution maps for that species from the NBN.

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QGIS NBN tool (V2): viewing NBN distribution grid maps in QGIS

How to use the FSC Tom.bio productivity tools plugin for QGIS to view species distribution maps and species density maps for datasets and designations from the NBN Gateway via the NBN Web Mapping Service. This video looks as the new tool it is best viewed after the video "QGIS NBN tool: viewing NBN distribution maps in QGIS".

Youtube link
QGIS NBN tool (V2): downloading NBN records for QGIS

How to use the FSC Tom.bio productivity tools plugin for QGIS to download raw species observation records from the NBN Gateway and use them in QGIS. This video explains the basic use of the tool for doing this and how to specify filters etc. It does not demonstrate spatial filters which is the subject of another video.

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QGIS NBN tool (V2): downloading NBN records for QGIS with spatial filters

How to use the FSC Tom.bio productivity tools plugin for QGIS to download raw species observation records from the NBN Gateway and use them in QGIS using spatial queries. This video explains how to use spatial filters to download records including known site boundaries (e.g. LRC, VC and protected sites), grid references and user-defined search polygons. It also demonstrations the convenience tool for creating circular search polygons by specifying a point and buffer.

Map Mashup Tool

The Map Mashup tool vastly simplifies the process of registering raster map images within QGIS when you are repeatedly registering images of the same size and showing the same area. It takes advantage of the fact that QGIS can use external registration files - world files (WLD extension) - to store the georeferencing information for a raster map.

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QGIS: registering raster images - creating WLD files

This tutorial shows you how to take an image of a map and register it as a raster map layer in QGIS. It shows how to generate a WLD file to do this. The power of these WLD files leveraged to the full in the Tom.bio Map Mashup tool - so this is an important step in realising the full potential of that tool.

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QGIS: using raster images

This tutorial shows that the result of registering a raster map in QGIS is a rich information layer that allows you to fully explore and visualise data in more powerful ways.

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QGIS Map Mashup tool: introduction & adding WLD files

How to use the FSC Tom.bio productivity tools plugin for QGIS to quickly register and display raster maps from the internet. This video introduces the interface of the Map Mashup tool and explains how to set and maintain the list of WLD files used to display raster map images from the internet.

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QGIS Map Mashup tool: mashup the maps!

How to use the FSC Tom.bio productivity tools plugin for QGIS to mashup raster map images from the internet and use them as georeferenced maps in QGIS. This video shows you what is possible.

Other Tom.bio productivity suite tutorials

This section contains ancillary information for the Tom.bio productivity tools.

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QGIS Tom.bio productivity tools: installation

A quick demonstration of how to find and install the FSC Tom.bio productivity tools plugin using the QGIS plugin manager.

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QGIS Tom.bio productivity tools: setting environment variables

How to set environment variables for the FSC Tom.bio productivity tools plugin for QGIS.

Download plugin

The plugin is available from from QGIS via the plugin repository (see tutorial video above). Once you have installed it, you will be able to find a folder called 'TomBio' in your QGIS python plugins folder (e.g. 'C:\Users\username\.qgis2\python\plugins').  In that folder there is a sub-folder called 'TestingData' containing some useful files for testing - including WLD files that will work with the many of the raster map data sources shown in the Map Mashup tutorial.

Release history

For a full release history, look at the QGIS plugin repository page for the tool (https://plugins.qgis.org/plugins/TomBio/) and select the 'Versions' tab.

Comments

Are there any plans for an Irish Grid System plugin that can accept Irish Grid References without using Easting and Northing?

It's on the wish-list. Would it be useful? If there is a decent demand for it, it will climb higher up the list.

There has been a surge of interest in recording over the last few years in Ireland. I, for one, would like to use it to produce spider distribution maps for Northern Ireland. I know of a number of active recorders of other groups who would find it useful.

Yes, I too would endorse the provision of an Irish Grid facility Rich - I don't have more than a few thousand Irish records (Galway area mainly) but I would still find it useful.

Are there still plans for Irish Grid integration or have they been put on hold? Thanks.