GIS Unit - GeoCAT FAQs
Browse our Frequently Asked Questions for the GeoCAT tool.
Please note: GeoCAT is presently in beta. As GeoCAT is updated there may be a short delay in updating the FAQ, help and screencasts.
* Create a new project from scratch
* Upload your own occurrence data e.g. co-ordinates of specimens, field observations or plot samples from an existing dataset
* Manually add/edit occurrence points to the map and edit based on your own knowledge
* Import occurrence data from online sources such as GBIF or Flickr.
* Single-click analysis of Extent of Occurrence (EOO) and Area of Occupancy
* Visualise your results on Google Earth
* Download occurrence data used in the analysis
* Save your project and add more data later or share with partners in a collaboration
* View and save all the vital statistics as a report
No, it is very important to note that this is not a full Red List assessment. This tool provides a way of calculating some of the geospatial elements of a Red List assessment e.g. extent of occurrence (EOO) and area of occupancy (AOO). These measures are used in Criterion B. In order to qualify for a category you must fulfill the relevant sub-criteria - for example in Criterion B, as well as meeting the EOO or AOO threshold, your species must meet at least two of the following three subcriteria: severely fragmented or small number of locations, continuing decline and extreme fluctuations.
Also, it is important to consider that the AOO calculation is heavily dependent on collection effort and the area of suitable habitat.
A full Red List assessment also requires detailed documentation on threats, conservation actions, habitat and ecology and more. For more details of the full red listing process see the Red List training website:
Also, please see the detailed section on training materials relating to Red List assessments:
You may already have your own location data (latitude and longitude co-ordinates) for a species within a spreadsheet or database. It is easy to import this to the map editor via the .CSV import.
* From the map editor view click 'Add source'
* To upload your data click the 'Import .GeoCAT, .CSV' option
* Click the 'Browse' button and select your .CSV file
* Your file name should appear in the window - see the troubleshooting FAQ 7.1 and 7.2 if the file does not load
* Click the 'import' button and your points will be displayed on the map as blue dots and will appear in the 'Sources' menu as 'User occs'.
2.2 How do I create a .CSV file?
You can download the template .CSV file and add your own data or you can create a file from scratch. Many applications that deal with structured data, especially those with biological records, are able to produce comma separated value (CSV) files. If you are not sure how to do this check the help or contact your database administrator. Here are some examples:
Add data to a blank spreadsheet with the headings 'Latitude' and 'Longitude'
File > Save as > .csv
File > Export as > .csv
2.4 What are the default fields in the CSV
|basisOfRecord||Where the record is from||Observation, specimen, literature reference|
|catalogNumber||Unique catelogue ID||1|
|catalogue_id||Internal field used to identify sources||1|
|changed||Used for imported records from GBIF. Value is 'yes' if the record has been changed from the orginal, usually used to show a corrected or improved locality.||yes|
|collectionCode||Collection code||RBG Kew|
|collector||Who collected the specimen||A J Smith|
|coordinateUncertaintyText||Precision of the locality in text||1 km or within 3 km of Exford|
|coordinateuncertaintyinmeters||Actually the uncertainty in km used for the buffer||1km|
|county||County or district||Ambatofinandrahana|
|eventDate||Date when record was recorded either collection data or defaults to event date||14/02/2011|
|identifiedBy||Identifier of the record||A J Smith|
|institutionCode||Code for where collection is held||RBG Kew|
|latitude||Latitude in decimal degrees||-20.5654456|
|locality||Name of locality or extented text||Route National number 35, Near Itremo|
|longitude||Longitude in decimal degrees||46.59919739|
|occurrenceDetails||url link to any details here||https:\\www.asite.com|
|recordSource||Internal field showing where data is from||Added by user|
|scientificname||Taxon Name||Luzula acutifolia|
|stateProvince||State or province||Wales|
|verbatimElevation||Elevation in metre||100 m or 200-400 m|
2.5 Is there a template .CSV file?
The format should be decimal latitude and longitude pairs. Note that
decimal degrees = degrees +(minutes/60)+(seconds/3600). If latitude is west or longitude is south then these are negative. See Wikipedia for more details
* To import data from GBIF click the 'Add points from GBIF' option and the tool will query GBIF to see if there are any georeferenced occurrence records listed under the taxon name entered at the start screen
* The number of occurrences is reported in the window
* Add these to the map by clicking 'import'
* The GBIF occurrences will be displayed as green dots on the map and will display in the 'Sources' menu as 'GBIF points'
* To search Flickr for occurrences follow the same procedure, but click on 'Add points from Flickr' instead
You may wish to search GBIF with multiple names e.g. 'Ophrys apifera' or a synonym e.g. ‘Ophrys albiflora’. Only one name can be entered at a time and the search term is then used to label the data source layer. For Flickr searches you can use scientific names or common names e.g. ‘Bee Orchid'. See FAQ 3.1, to learn more about adding individual data sources.
3.3 Why are there only 1000 points from GBIF when the GBIF portal has many more points?
At present the tool provides the first 1000 points queried from GBIF. The maximum threshold for number of points that can be added to the tool has not yet been determined and may change in later versions. If you wish to add more you can export your data from GBIF as .CSV, edit the fields and import into the tool.
Use the pointer tool to select a point. Click the 'i' to open the information window. Click 'Edit' to open the Editing Metadata window. At the bottom of the window is the URL for the original occurrence record. Copy and paste this address into a browser to see the page. Alternatively you can just click 'Visit URL' and a new window will open directly to the original record page on GBIF or Flickr.
4.3 I have a .CSV file with occurrences for multiple species. Is it possible to carry out a batch analysis?
- IUCN default value
- User defined
*The AOO options are under review and may change in subsequent versions.
Due to the Google Maps projection the cells closer to the poles will appear elongated. The area reported is correct.
As with any analysis, the result is only as good as the data that is used. This tool allows data to be added from numerous sources e.g. Flickr, GBIF and the user must carry out their own review of the data to determine whether it is appropriate to include occurrence points for the analysis.
An important caveat to note is that AOO at the 2 x 2 km cell width is highly dependant on sampling effort. Although biological data can be systematically recorded e.g. quadrats, transects etc. the majority of occurrence data is based on a form of random collection (although not completely random due to factors such as accessibility). As a result you may have false absences e.g. 2 x 2 km cells where a species occurs, but has not been collected/observed yet (so appears to be absent). As a result, the AOO estimates based simply on known occurrences may underestimate true AOO at this scale. The user may reduce this error by manually adding points to areas where the species is known to occur based on expert knowledge.
4.8 The analysis of EOO and/or AOO suggests my species is Endangered - how do I make this a full assessment?
For a full Red List assessment you must ensure that all criteria and sub-criteria are met. At present, this tool only calculates values for EOO and AOO, measures that form part of the B criterion (B.1. and B.2.). To qualify for a full rating under Criterion B you must also fulfill the subcriteria e.g. at least two of a, b or c (severely fragmented or small number of locations, continuing decline and extreme fluctuations respectively).
4.9 Does the EOO value exclude 'discontinuities or disjunctions' e.g. areas of obviously unsuitable habitat?
No. At present the EOO value is generated using a convex hull or minimum convex polygon. If two populations are separated by clearly unsuitable areas e.g. sea then this will be included in the area measurement. Following Gaston and Fuller (2009) the EOO is measured including these discontinuities, thereby retaining a clear distinction between EOO and AOO.
You can save your data by clicking the green 'save project' button at the bottom of the page. This will create an .GeoCAT file which retains all the information about the analysis you have been working on including the points added and even the zoom level of the map. Depending on the browser you are using you will either be asked for a location in which to save the file or it will automatically save to your designated 'downloads' folder. If you are not sure where the file saved you can carry out a search for the .GeoCAT extension.
If you click the 'Close tool' button in the top right hand corner of the window and you have not saved your work you will be reminded and given the option to save your project:
* From the front page:
* From the sources menu:
An alternative way to add your .rla file is via the sources menu. Click on 'Add new source' and select 'Import .GeoCAT, .CSV'. Browse to the file and select it. The file will be added to the source menu and by clicking the 'import' button the project will be restored.
- Download .CSV
- Download .KML
Make sure you have the Latitude and Longitude fields in your file
Make sure you have saved a .CSV file
Make sure there are no erroneous values in the latitude and longitude fields
Make sure you do not have too many records ( > 2000)
7.6 Precision is reported in GBIF metadata, but why does it not show the same value in the error buffer?
The precision field reports the co-ordinate precision as defined in the original record. Because this field is not standardised the values cannot be used. However, the values are reported in the 'Precision' field so the user can interpret the value and set the precision using the precision slide bar.
See 9 below
9. Map and source editor
There are several ways to delete points within the map editor.
Click the pointer tool form the left hand sidebar, hover over a point to display a tooltip with three options: 'Information', 'Hide' and 'Delete'. Click the delete option to delete the point.
Delete points tool:
Click the 'Delete Points' tool from the left hand sidebar, hover over a point and click. Click 'Yes' to delete the point or 'cancel' to close the window.
Click the 'Marquee Select' tool from the left hand sidebar, draw a marquee over some points and click the 'x' to delete the points.
You may want to delete all points from a particular source e.g. all GBIF points. From the Sources menu click the 'x' on the right hand side. You will be asked if you want to confirm the deletion.
This is the tool tip that allows you to find out more information about your point as well as edit, hide and delete it.
To see more information about a point click the 'i'. A window will appear that displays some basic information such as Latitude, Longitude, Notes, Collector and Precision.
There are several options from the information window.
The 'Delete' button provides another way to delete a point.
The 'Hide/Show' button allows you to remove a point from the analysis without deleting it. For more information see FAQ 9.3
The 'Precision' slide bar allows you to manually adjust the error associated with your point. For more information see FAQ 10.1
The 'Edit' button allows you to view the point metadata. For more information see FAQ 10.2
You may wish to remove some points or an entire data source from the analysis without deleting them. Hidden points are still displayed on the map, but are hidden.
You can hide a source by clicking on the eye icon for that source.
Click on a point and click the 'o' button to hide
The hidden point will remain on the map, but will appear faded and will be excluded from the analysis
The shaded buffer around the points indicates the error associated with the precision of the point locality. For more information on georeferencing and precision see the paper by Wieczorek et al. (2004).
Use the pointer tool to select a point. Click the 'i' to open the information window. Click and drag the precision buffer at the bottom of the information window to the desired size.
As well as the latitude and longitude the meta-data window shows a number of fields relating to the occurrence record:
Basis of Record
See FAQ 2.4 for more details.
Yes all fields are editable.
Please also contact us if you have any comments on tool or check the feedback forum here: feedback
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