Sex field in extraction?

[pisum]

generally, there are 2 paths you can take.

option 1:

@pisum

i would download all observations first, and then separately download a set filtered for each annotation value i’m interested in. then use those subsets to populate a column (or multiple columns) in the “allt” set. (this is the easiest way to make sure you’re also capturing unannotated observations, when they exist.)

@pisum

a screenshot of one way you could get annotation data using the system as it currently exists (using Excel):

in the image above, the data in the two tabs come from two variants of a export / download query. below are the parameters for the queries:

• alive: quality_grade= any &identifications= any &taxon_id= 48662 &user_id= pisum &term_id= 17 &term_id_value= 18
• all: quality_grade= any &identifications= any &taxon_id= 48662 &user_id= pisum

also see: https://forum.inaturalist.org/t/how-to-export-annotated-observations/39708

option 2:

@pisum

for a set that is only ~15000 observations, it’s also possible to just get the observations via the API and parse out the annotations and observation fields you’re interested in. (i have a Juptyer notebook that could be adapted for this: https://jumear.github.io/stirpy/lab?path=iNat_APIv1_get_observations.ipynb, but there are lots of other ways to get this information, too.)

my example in the link above is based on Python, but here’s something written in R: https://forum.inaturalist.org/t/code-to-extract-annotations-from-exported-json/31950/31

… and of course, you could your own code using whatever other languages, tools, modules, etc. you prefer.

…

by the way, here are the “controlled terms” associated with different annotations:

@jdmore

&term_id= - the annotation group

• 1=Life Stage, 9=Sex, 12=Flowers and Fruits, 36=Leaves, 17=Alive or Dead, 22=Evidence of Presence, 33 Established (pilot test in Reptiles/Amphibians only)

&term_value_id= - the value within the group

• Life Stage: 2=Adult, 3=Teneral, 4=Pupa, 5=Nymph, 6=Larva, 7=Egg, 8=Juvenile, 16=Subimago
• Sex: 10=Female, 11=Male, 20 Cannot Be Determined
• Flowers and Fruits: 13=Flowers, 14=Fruits or Seeds, 15=Flower Buds, 21=No Flowers or Fruits
• Leaves: 37=Breaking Leaf Buds, 38=Green Leaves, 39=Colored Leaves, 40=No Live Leaves
• Alive or Dead: 18=Alive, 19=Dead, 20=Cannot Be Determined
• Evidence of Presence: 23=Feather, 24=Organism, 25=Scat, 26=Track, 27=Bone, 28=Molt, 29=Gall, 30=Egg, 31= Hair, 32=Leafmine, 35=Construction
• Established: 34=Not Established