Tab delimited GBIF file for the Biological Records Tool

I am using the FSC QGIS Biological Records Tool for analysis of a very large (2GB) GBIF dataset. The problem is the dataset is a tab-delimited csv rather than comma-separated. The dataset can be imported into QGIS fine, but trying to open it in excel crashes my computer. Under the data specification tab in the FSC BRT I can import my csv but it reads it incorrectly since it is tab-delimited. The QGIS base program can import tab-delminited files fine but I can’t seem to find the option for how to do it with the BRT. I’m trying to do it in QGIS because I can’t open the file in excel to convert it to comma separated. Am I overlooking how to get the BRT to read tab-delimited csvs? Any help would be great

@rburkmar

Hi, welcome to the forum! :raised_hand_with_fingers_splayed:

What platform are you using, Windows, Mac or Linux?

I am using QGIS v3.4 on a Mac

Are you able to send a small sample of your dataset? It will help me test the solution I’m going to propose. No worries if not.

All of the data from GBIF.org is open access, I merely downloaded a subset of their giant repository. I’ve uploaded my dataset to the following two websites

fil.email/KI5cLxF6

Also check out my reply on the suggest new features thread

Great, thanks! I missed the fact you got it from GBIF – sorry, should have spotted that. I will take a closer look at this when I’m back on my laptop a bit later.

I did see the feature request – many thanks, that’s great. I will move it to it’s own thread rather than being a reply to the original general thread there. This will make it easier to keep discussion about it neatly together. I’ll wait for @rburkmar to reply as he’s the developer of the plugin.

Thanks again!

Thanks, hopefully we can get this resolved soon

And I made two feature requests in the feature request post, I hope the part about subspecies concatenation isn’t lost or forgotten

I think I’ve fixed the issue. I opened the file normally in QGIS, then right clicked on it within QGIS and exported it as a CSV. This created a new CSV file where the tabs were replaced by commas

Now the only immediate issue I have left is the subspecies concatenation problem. The obvious solution for my dataset would be to open the file then create a new column in the csv file itself that concatenates only the values in the genus and species columns, and not the subspecies columns. The problem is that opening the CSV crashes my computer. I didn’t resolve the tab-delimited issue by opening the file at all. So I’d say a fix for the program could be to add, instead of a taxon drop down bar, a genus dropdown bar and a species dropdown bar to reference those two columns from CSVs, rather than reference a single speciesID column. This would make sorting better anyways, and eliminate issues related to typos in the speciesID column, or capitalization of the species name, or the inclusion of a space/no space between the genus and species name

1 Like

There’s no need to export as a CSV file. If you can open in QGIS as a point layer - which I assume you have done when you say that you opened in QGIS - you can work directly with this point layer from the Biological Records tool - just select it from the drop-down list. No need to import a CSV.

1 Like