Tech Tip Tuesday: Exporting Observations

I don’t know about you, but I was pretty excited for our recent snow storm, even though I knew that it meant more shoveling. From my weather app (ah, the wonders of modern technology), I knew that the storm would begin around 4pm, so I set out for my favorite hillside at 3:15pm to watch it approach. I love how still the air gets as a storm draws near – so calm, it’s almost as if the whole world is holding its breath. As I stood under the nearly naked limbs of an old oak, I watched as the mountains were slowly erased, merging with the pale grey sky. Suddenly, I felt the air change on my face, plunging from frosty yet mild to damp and chilly. Within a few minutes, there was an exhale and the last oak leaves above me began gently stirring. When I finally turned to leave, the mountains were gone and snow was beginning to drift from the sky.

I love watching the weather like this and believe that it’s truly a hidden joy. With all of our apps, we need not look at the sky nor pay attention to the air to know that the weather is about to shift. However, there’s something very grounding about sensing the change – an ancient knowledge forgotten among touch screens and keyboards. I find that if I watch closely, I can also tell when a storm is coming based on the behavior of wildlife. There’s often a burst of activity followed by stillness as the storm gets closer. I clearly remember walking in the woods right before a big snow storm during my sophomore year of college and watching a shrew scurrying about unconcerned with my presence, chewing on some ice remnants. Next time a big storm is predicted, I suggest stepping outside to see what animals around you are preparing for the inclement weather.

This Week on Tech Tip Tuesday

If you prefer to watch the snow fall from a comfortable window seat, there are still plenty of ways to learn about the wildlife beyond your front door. If you love using data as a tool to better understand the natural world, than this week’s TTT is for you! Although many people may think that the data produced by iNaturalist is exclusively for scientists and other conservation professionals, it’s actually accessible to anyone. In a couple of simple steps, you can export observation data and begin using it to explore.

There are two ways you can get to the “Export Observations” page. The first way is to go to the “Explore” page and select “Filters”. In the “Filters” box, you will see a button that says “Download” in the bottom right corner. Click on that. This will set you up to export data from anywhere in iNaturalist. By following these same steps, except from your personal observations’ page, you can export data from your own observations.

The other way is to visit the Vermont Atlas of Life project page and scroll down to the “Members” box to the right of the map. The fourth option down is “Export Observations” – click on that. This method prepares you to export data from the Vermont Atlas of Life project. If you want to export data from a wider area, simply delete “Vermont Atlas of Life” from any textbox you see it in. You can also do this as you walk through the next steps.

Regardless of which method you use, you should now be on the “Export Observations” page. If you want, you can delete the text in the box at the top of step 1 – this will get filled in as you walk through the options below. Please note, you don’t have to fill in the information for all of the steps below. Only fill in the information you want to see in your exported data.

  1. Find a specific species or place. This is one way to input a particular species, place, or other field you’re interested in. To figure out what you can search, click the dropdown menu at the end of the search bar. You can test out this feature by searching for a species, place, tag, or anything else described there. There are other ways to input this information later on as well. You can also leave this blank.
  2. Filters. Here, you can add filters to specify the type of observations you want. Maybe you only want observations with sound or ones that are not marked “captive/cultivated”. Selecting these options will narrow the range of observations you receive.
  3. Show only. The next line allows you to select the groups you want displayed. For example, if you only want to export insect observations, then select “Insects” and leave all other boxes unchecked. This is best if you want all the species for a particular group. This step is not necessary if you are interested in a specific species. Hover over each option with your cursor to see what they are. Notice that there is a category for “unknown” observations.
  4. Taxon and Observed on. These are pretty straight forward. “Taxon” asks you to select which species or group of species you’re most interested in (if you did not do so in step 1). “Observed on” allows you to select observations made on a specific date.
  5. Rank. In this next line, you can specify the taxonomic rank you’re interested in. For example, maybe you only want observations that have been identified to the Genus level. If this is the case, you would select “Genus” out of the dropdown list under “Exact Rank”. If you want any observations with a “genus” identification and higher rankings, then you would select “Genus” under the dropdown list for “Lowest Rank”. If you want anything with a “genus” identification and lower rankings (i.e. species, subspecies), then you select “Genus” under the “Highest Rank” dropdown menu.
  6. User, Project ID, Taxon IDs, Date Range, Created on. These are areas where you can add additional information. Under “User”, you can provide a specific user’s name or their ID number to export only their observations or all of your own. For “Project ID”, you enter the project ID number or URL slug (appears at the end of the web address) for the project you want to export data from. For example, the URL slug for the Vermont Atlas of Life is vermont-atlas-of-life. “Taxon IDs” are the number associated with the taxon on iNaturalist. You can enter multiple numbers if you’re interested in multiple species. You can find this number by going to the taxon’s page (see TTT #7) and selecting the “id” number in its URL. “Date Range” allows you to select the range of dates you want observations from and “created on” let’s you choose observations that were created (not observed) on a specific date.
  7. Step 2. This section shows you a preview of what your data will look like. Take a glance at this to make sure that the data displays the information you need. If it doesn’t look correct, return to the steps above and make the necessary changes.
  8. Step 3, Basic. This section allows you to choose all of the columns you want to export. Look this over carefully and decide what information is most meaningful to you. You can leave all options selected, however this will create a huge file that may be difficult to sift through, so it’s best to stick with the necessary information. Some good choices when looking to gather basic data could be: id, observed_on, user_id, image_url, description, and out_of_range. Ultimately, it just depends on what is important to you.
  9. Step 3, Geo. Similar to above, this is where you can select what location columns you want. Latitude and longitude are some good basic ones. This is another instance where unchecking columns that you’re not interested in is helpful, otherwise you could end up with an enormous datasheet. Once again, it’s all about what’s important to you.
  10. Step 3, Taxon extras. These usually appear unchecked by default. They’re useful if you’re interested in looking for patterns in larger taxonomic groups, but otherwise they’re not really necessary for most basic functions.

Helpful tip: if you’re confused about what any of these checkable items mean, you can hover over them with your cursor and they will offer a brief explanation.

  1. Step 4. Yay, you’re done! Hit “Export” under step 4. A green box with a “Download” button should appear at the top of your screen shortly. Sometimes larger file sizes take longer to export, so don’t panic if it doesn’t immediately appear. You can also choose to have iNaturalist email you when the export is complete if it’s taking a really long time.
  2. Download. Once you hit download, click on the new file that appears. It should display the file in your computer’s “Downloads” folder. From here, you can drag it to move it to your desktop or a different folder on your computer.
  3. Open file. Go ahead and open the file. It should open in Excel (at least it does on my computer) and from there you can begin exploring the data or move it to a preferred data processing platform.

One final note: this tool is best used for data that you don’t intend to publish. If you’re looking for data that you can publish, it’s better to export directly from the geoprivacy preferences set either for specific species or by specific users.

TTT Task of the Week

Now that you know how to export data, it’s time to give it a try! Think about what aspect of iNaturalist you may want to explore for patterns and start filling out the “Export Observations” page. If you have any questions along the way, don’t hesitate to reach out!

Thank you for helping us map Vermont’s biodiversity and happy observing!

Posted on 03 December, 2019 18:53 by emilyanderson2 emilyanderson2


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