Journal archives for March 2019

March 20, 2019

add metadata to an observation in an iNaturalist-controlled way rather than relying on the free-for-all that is observation fields

[code]annotations are key /
value pairs associated with observations, so kind of like observation
fields, but *controlled*, i.e. the site admins determine what kind of
annotations can get added to avoid the giant duplicative mess that
became of observation fields. A type of annotation, e.g. "Life Stage",
has a bunch of potential values, and types and values can be
associated with different taxa, so "Life Stage" is currently
associated with everything, "Life Stage = Adult" is only associated
with Animalia, and "Life Stage = Pupa" is only associated with
Arthropoda. Most annotations can only have one value per type per
observation, but some, like "Plant Phenology," can have multiple.
Currently we can't associate a type with more than one taxon, or
provide exceptions (e.g. "Plant Phenology = Flowering" for all plants
except bryophytes or something), but we're hoping to build tha
http://www.inaturalist.org/pages/annotations
[/code]

[quote]
Actually to be honest I'm thinking of quitting again, since this really irritates me. There are so many very interesting pictures in iNaturalist and I can't even filter on plumage/ age/ sex/ observation method.
There are tags and fields, but there is no good way to filter on them or search on them.
And everybody is using new fields and new tags since they are extremely hard to find (even more difficult in the new observation screens).
You really can't expect me to make hundreds of separate observations because the system can't handle making a single simple observation: Mallerd: 3 pulli, one adult male, one male eclips, 3 adult female.

[/quote]

So in 2017, iNaturalist introduced annotations 4, which is a way to add metadata to an observation in an iNaturalist-controlled way rather than relying on the free-for-all that is observation fields. We wanted to start out with some basic ones, such as Sex and Life Stage, as well as Plant Phenology (which, I know, many botanists have argued should be Flowering Phenology) and there were many other requests 2, but the subject died down without anything else being added by iNat, aside from some taxonomic tweaks.

I’d like to revive that discussion here and see if we can add at least a few more annotations to iNaturalist and reduce some observation field confusion. So please reply with a request, if you have one. It would be best to define the annotation, possible values, and which taxa it would be applicable to.

Please keep the following in mind:

Annotations should be attributes that can be independently determined from an image or sound and are useful in the places where we use annotations, eg the taxon page charts and the taxon page photo browser.

We want to restrict annotations to qualitative values, so annotations with numerical values will not be added. Values should not be arbitrary, either.

These are not photo-level annotations, so the annotation should describe the observation as a whole.

In general I’d prefer that the annotation not be of very niche use but can be used for a good number of observations.

We can’t promise your suggestion will be added, especially until we implement a user interface that will not display15 annotations on an observation’s page all at once.

I’ve submitted a GitHub issue 1 to make observation field search results be ranked by the number of observations a field has been used with, to at least bring up the more often-used fields from a list of fields with duplicative functions. I’m hoping this will cause some to be more used than others.

I’ve also posted an Annotations topic 4 in General as a way to get some more standardized metadata fields available for certain taxa. I know this is something we dropped the ball on in 2017.

I’ll add your requests for better Obs Field search options to our team document for our planned upgrade of Search.

https://forum.inaturalist.org/t/lets-talk-annotations/627

https://groups.google.com/forum/#!searchin/inaturalist/controlled$20terms%7Csort:date/inaturalist/V06_UTD1cTU/_GPBDUbrBAAJ

http://www.inaturalist.org/pages/annotations

Posted on March 20, 2019 13:09 by ahospers ahospers | 0 comments | Leave a comment

March 25, 2019

Additional info:earch for maverick IDs,Identify grasshoppers and scorpions:

==
Is there some way to view a list of all observations that have had a particular ID applied to them, even if it’s not currently the community ID? Say, someone IDs a madrone tree as a walnut, a second user corrects it to “Madrone” but no-one else adds an ID so it remains at “dicots”. I’m hoping there’s a way to view all the observations that have had a “madrone” ID applied to them (even if it’s a maverick).
https://forum.inaturalist.org/t/identification-filter/991/7
g for me: https://www.inaturalist.org/observations?ident_taxon_id=68912,797562
I haven’t been able to find a way to do it either. What I really want is not just to be able to sort for observations that have a particular ID, but ones that have a particular ID made by a particular user. So if I know user X is an expert on taxon Y, I can look for observations where they made an ID for taxon Y, even if the community ID is something else.

Which should show all observations that have an active ID of the taxon you enter. For example, this should show observations which have an active Dysdera crocata ID, a commonly misidentified spider.

https://www.inaturalist.org/observations?ident_taxon_id=68912 3

Edit: I know how to filter on particular IDs, but I’m interested in filtering on observations with IDs, i.e. through https://www.inaturalist.org/observations/identify.
For anyone interested in filtering on IDs, it’s under https://www.inaturalist.org/identifications, e.g. https://www.inaturalist.org/identifications?user_id=username&taxon_id=12345 will give you identifications of taxon 12345 made by user username, regardless of the observation ID.

this shows all cases where I have entered Blue Jay as an Id with no filter on if the community agrees with me
https://www.inaturalist.org/identifications?taxon_id=8229&user_id=cmcheatle
==

ou can search for maverick IDs, e.g. https://www.inaturalist.org/identifications?category=maverick&taxon_id=46259

here’s also something about searching for observations where most agree, some agree, most disagree, but it doesn’t seem to work quite the way I expect it to. Maybe someone knows how it works?
You can find it built into the search function for a single user’s observations, but I think it’s also possible to stick it in the identify URL, e.g. https://www.inaturalist.org/observations/identify?identifications=most_disagree 3. https://discourse-cdn-sjc1.com/business6/uploads/inaturalist/original/1X/f4b1f41d4002b12f1df97aeb0eeecfb86ff03e13.png

https://www.inaturalist.org/observations/identify?identifications=most_disagree&lrank=order 7 meet your original request?

This originally came in as a feature request but I popped it over in General instead because you should be able to do these searches with some existing tools:

Identify grasshoppers and scorpions: https://www.inaturalist.org/observations/identify?taxon_id=48894,47651 1
Identify gastropods, but not nudibranchs: https://www.inaturalist.org/observations/identify?taxon_id=47114&without_taxon_id=47113 3
You can read more about some modifications to search URLs that aren’t in the website’s user interface filters here: https://forum.inaturalist.org/t/how-to-use-inaturalists-search-urls-wiki/63

== ATLASSES
Atlases aren’t a fully fleshed out feature. Right now only curators have a link to create and view atlases on each taxon page. It’s in the Curation drop-down. Unfortunately I don’t think there’s a way for you to search atlases to find out if one exists yet for a particular taxon…

hanks. I used to just rely on calflora.org. But now that the taxonomy of iNaturalist diverges more from calflora.org, I use BONAP. Neither had a map of the plant I’m looking for. So I look forward to when correct maps are somehow on iNaturalist instead of just maps of right and wrong identifications.

Same here. When I am investigating a particular taxon, first thing I do is go to the map tab on the Taxon page, and visit the pins that seem to be out of place. Most often it’s a mis-ID, but sometimes it can be a captive observation.

Next thing I do is check the observations for “similar species” to find mis-IDs that are really my taxon of interest. Curation is a never-ending process for everyone on iNaturalist. Just the nature of the beast, so to speak.
Reverse populating from GBIF is an interesting idea. I’m not sure it has to be an either/or, but I would actually focus on using it to populate the checklists first before the atlases.

Checklists are much more user available, and I’m not sure the site has quite figured out the use case for atlases yet, Right now they have a kind of ‘solution in search of a problem’ feel to them.

One concern I would have is that sites like GBIF dont tend to update their records when taxonomy is updated. For example, the Northern and Hen Harriers of North America and Europe respectively used to be considered a single species under the name Circus cyaneus.

If you go look at the GBIF page for C. cyaneus https://www.gbif.org/species/2480487

It has thousands of records for North America that are no longer valid, which would get imported. Cleaning up stuff like that, and any potential impact on if they add geographic intelligence into the computer vision system could be a nightmare. And then making sure if cleaned, it does not simply return should the process ever be run a 2nd time.

= = =
There are some things you can only search for by editing the URL directly, in this case, by adding taxon_geoprivacy=obscured to the URL.

More info here:
How to use iNaturalist’s Search URLs - Wiki 5

= = =
A workaround:

https://www.inaturalist.org/observations?place_id=any&verifiable=any&taxon_geoprivacy=obscured&user_id=er1kksen 3

Posted on March 25, 2019 21:01 by ahospers ahospers | 1 comments | Leave a comment