Annotation tooltips

I discovered these short, official definitions for annotations just the other day:

Alive or Dead:

  • Alive: Organism is living and shows no signs of imminent death
  • Cannot Be Determined: Cannot be determined from the evidence provided
  • Dead: Organism is dead or shows signs of imminent death

Evidence of Presence:

  • Bone: Predominantly endoskeleton remains; partial bone exposure in an otherwise intact organism should be labelled [sic] “organism”
  • Feather: One or more feathers not attached to an organism
  • Gall: Deformed plant tissue outgrowth caused by a parasitic organism
  • Molt: Discarded skin or exoskeleton
  • Organism: Whole or partial organism
  • Scat: Fecal matter (not owl pellets or other regurgitated matter)
  • Track: Impression in ground or snow made by organism

Life Stage:

  • Adult: BUG
  • Egg: BUG
  • Juvenile: BUG
  • Larva: BUG
  • Nymph: BUG
  • Pupa: BUG
  • Subimago: BUG
  • Teneral: Adult that has recently emerged but has not yet achieved its final adult form

Plant Phenology:

  • Flower budding: Flower buds visible but not open
  • Flowering: Flowers visible, open, and still attached to the plant
  • Fruiting: Fruit visible and still attached to the plant
  • No evidence of flowering: Media provides no evidence of reproductive structures

Sex:

  • Cannot Be Determined: Cannot be determined from the evidence provided
  • Female: Evidence indicates that organism can produce ova for use in sexual reproduction
  • Male: Evidence indicates that organism can produce sperm for use in sexual reproduction

At this time, not all of the values have definitions since some of the annotation tooltips are affected by a bug.

Apparently these definitions are not widely known since the tooltips are visible only after the annotation has been applied. For example:

  1. Browse: https://www.inaturalist.org/observations/165124188
  2. Hover over the annotation “bone”
  3. The tooltip will display as: Predominantly endoskeleton remains; partial bone exposure in an otherwise intact organism should be labelled “organism”

Note: In the previous tooltip, it should be “labeled”, not “labelled”, but hey, that's a minor point!

I was really surprised to learn about these definitions after all this time. I'm curious, did you know about these before now?

Publicado el sábado, 21 de octubre de 2023 a las 03:39 PM por trscavo trscavo

Comentarios

Great post! Translators translate these tooltips, so they are aware of them.. In Dutch you can also see the tooltip text before they are choosen as annotation.

controlled_term_labels:
#Value displayed when a filter is not filtering by a specific value for this attribute
any_sex: Alle
#Value displayed when a filter is not filtering by a specific value for this attribute

sex: Geslacht
male: Mannelijk
female: Vrouwelijk
plant_phenology: Plantenfenologie
budding: Ontluikend
flower_budding: Bloemknoppen
flowering: Bloeiend
fruiting: Vruchtdragend
life_stage: Levensstadium
adult: Volwassen
teneral: Net verveld
subimago: Subimago
pupa: Pop
no_evidence_of_flowering: Geen bewijs voor bloei
nymph: Nimf
larva: Larve
egg: Ei
juvenile: Juveniel
alive_or_dead: Levend of dood
alive: Levend
dead: Dood
cannot_be_determined: Kan niet worden vastgesteld
evidence_of_presence: Bewijs van voorkomst
#As in the feather on a bird
feather: Veer
#Abnormal growth
gall: Gal
#Refers to an observation that depicts the actual organism and not some
#kind of secondary evidence like a footprint
organism: Organisme
#Fecal matter, not regurgitated matter
scat: Uitwerpselen
#Impression made by the organism on the ground or in snow, like a footprint
track: Spoor
#Endoskeletal remains, like a deer bone
bone: Bot
#Skin or exoskeleton shed by a reptile or arthropod, not a particular
#plumage in a bird or seasonal hair/fur in a mammal
molt: Vervellingshuid
controlled_term_definitions:
alive: Organisme leeft en vertoont geen tekenen stervende te zijn
bone: |
Vooral endoskelet-resten; gedeeltelijke blootstelling van bot in een verder intact organisme moet worden gelabeld als "organisme"
cannot_be_determined: Kan niet worden gedetermineerd met het geleverde bewijs
dead: Organisme is dood of vertoont tekenen stervende te zijn
feather: Een of meer veren die niet zijn bevestigd aan een organisme
flower_budding: Bloemknoppen zijn zichtbaar maar niet open
flowering: Bloemen zichtbaar, open, en nog vast aan de plant
fruiting: Vruchten zichtbaar en nog vast aan de plant
gall: Misvormde uitgroei van plantenweefsel veroorzaakt door een parasitair organisme
molt: Afgeworpen huid of exoskelet
no_evidence_of_flowering: Media levert geen bewijs van reproductieve structuren
organism: Heel of gedeeltelijk organisme
scat: Feces (geen uileballen of andere uitgebraakte dingen)
teneral: Volwassene die onlangs ontpopt is maar nog niet zijn uiteindelijke volwassen vorm heeft
track: Afdruk in grond of sneeuw gemaakt door organisme

controlled_term_definitions:
alive: Organism is living and shows no signs of imminent death
bone: |
Predominantly endoskeletal remains; partial bone exposure in an otherwise
intact organism should be labelled "organism"
cannot_be_determined: Cannot be determined from the evidence provided
dead: Organism is dead or shows signs of imminent death
feather: One or more feathers not attached to an organism
flower_budding: Flower buds are visible but not open
flowering: Flowers visible, open, and still attached to the plant
fruiting: Fruit visible and still attached to the plant
gall: Deformed plant tissue outgrowth caused by a parasitic organism
molt: Discarded skin or exoskeleton
no_evidence_of_flowering: Media provides no evidence of reproductive structures
organism: Whole or partial organism
scat: Fecal matter (not owl pellets or other regurgitated matter)
teneral: Adult that has recently emerged but has not yet achieved its final adult form

track: Impression in ground or snow made by organism

https://github.com/inaturalist/inaturalist/blob/main/config/locales/en.yml
https://github.com/inaturalist/inaturalist/blob/main/config/locales/nl.yml

Anotado por optilete hace 4 meses

Thanks optilete!

Anotado por trscavo hace 4 meses

Thank you for writing up this summary. I had not been aware of these definitions before this week.

Anotado por tsn hace 4 meses

No, I did not know about the definitions until I read your post. Thanks for sharing this information! The fruiting definition is interesting. Sometimes, well into the spring of the following year, I will see dried up fruits still attached to a plant, such as a rose or Viburnum opulus (the birds leave these highbush cranberry fruits until last because they're so sour). Somehow, it seems as if choosing the annotation "fruiting" would be misleading, but the definition would seem to allow for the choice.

Love the [sic]! Good Latin!

Anotado por cgbb2004 hace 4 meses

Yes, the annotation "fruiting" is an oddball in the following sense. Note how "fruiting" (and the others in that category) are verbs (or maybe adjectives, I don't know) while most of the other annotations are nouns (with a couple of adjectives thrown in). Yet the definition is clearly intended for a "fruit". I'm not surprised since it's fairly easy to define "fruit" in a few words.

The annotation "flowering" is even less understood. That word can be used as either a verb or an adjective. In the latter case, we say "flowering plant" but that phrase is ambiguous. It requires context to be understood. Beginners have difficulty with that phrase. I know I did.

For awhile now, long before I learned of the tooltips, I stopped using the phrases "flower budding", "flowering", and "fruiting" in comments and other writings. I use the nouns instead. So for me, the definitions make complete sense.

Anotado por trscavo hace 4 meses

Ha! You're a grammarian, too! Here are a couple of other little thoughts:

As well as acting either as a noun or an adjective, depending on sentence structure, the "-ing" form can be a gerund, a noun. Hiking in the Green Mountains is one of Tom's favorite activities!

Oh, and while we're at it, it should be "Media provide..." rather than "Media provides...."

Then again, rules of grammar definitely evolve -- witness the recent evolution of pronouns!

Anotado por cgbb2004 hace 4 meses

Thanks @cgbb2004 your example bolsters my point: The -ing form of a verb is inherently ambiguous. Instead the annotation should use nouns:

Reproductive structures:

Flower bud: One or more flower buds visible but not open
Flower: One of more flowers visible, open, and still attached to the plant
Fruit: One or more fruits visible and still attached to the plant
Other: Other reproductive structures visible such as flower stalk, withered flower, or dried fruit
None: Media provide no evidence of reproductive structures

This is simpler (and therefore better imo) but it's still not perfect. Comments welcome.

Anotado por trscavo hace 4 meses

Nice improvement! In your proposed scheme, if a dried fruit is still attached to the plant, would that count as Fruit or Other?

Anotado por tsn hace 4 meses

Agreed. Definitely an improvement. As well, the question re "Fruit" or "Other" points to further ambiguity.
😏

Anotado por cgbb2004 hace 4 meses

Further modifications based on comments:

Reproductive structures:

Flower bud: One or more flower buds visible but not open
Flower: One of more flowers visible, open, and still attached to the plant
Fruit: One or more fruits visible and still attached to the plant
Other: Other reproductive structures visible such as flower stalk, withered flower, or empty seed pod
None: Media provide no evidence of reproductive structures

@tsn does that help?

@cgbb2004 I'm not following you…can you elaborate?

I begrudgingly added "other". There's a tradeoff between simplicity and the desire for an exhaustive list. By adding "other", I claim that every observation may be annotated (if desired). Otherwise you end up revisiting an unannotated observation (using the Identify tool).

Anotado por trscavo hace 4 meses

If simplicity is your primary goal, the following annotation might be preferred:

Plant structures:

Flower bud: One or more flower buds visible, not open, and attached to the plant
Flower: One of more flowers visible, open, and attached to the plant
Fruit: One or more fruits visible, with seeds, and attached to the plant
Leaf: One or more leaves or leaflets visible and attached to the plant

Gut reactions welcome.

Anotado por trscavo hace 4 meses

Yes, I like your modified version of the Reproductive Structures list better. In the old (current) system, there are some situations in which none of the annotation options fits (such as when an empty seed pod is visible, so that even "No evidence of reproduction" isn't accurate). Your "Other" category fixes that. Might I suggest calling it "Other Evidence of Reproduction" instead, or is that too long?

One gray area that we probably can't resolve is the question of exactly when a spent flower crosses the line into becoming a developing (unripe) fruit. That will remain a judgment call, different for different plants, no matter what labels we apply.

Anotado por tsn hace 4 meses

I am not keen on adding a "Leaf" annotation. That would apply in such a large percentage of observations that I suspect most people would never use it, so the data would be meaningless.

Anotado por tsn hace 4 meses

Okay, I tweaked the names and values for clarity:

Reproductive structures:

Flower bud: One or more flower buds visible, not open, and attached to the plant
Flower: One of more flowers visible, open, and attached to the plant
Fruit: One or more fruits visible, with seeds, and attached to the plant
Other reproductive structures: Other reproductive structures visible such as flower stalk, withered flower, or empty seed pod
No evidence of reproductive structures: No visible reproductive structures of any kind

I agree that the stage between flower and fruit is not doable. Some plants don't even traverse that stage.

You're probably right about "leaf" but it is tempting. With leaf data, the corresponding chart on the taxon page (similar to the "Plant Phenology" chart) would illustrate the full growing season of the plant and help dispel misconceptions such as those surrounding "spring ephemerals".

Anotado por trscavo hace 4 meses

@trscavo -- I was just wondering if "Fruit" would be an appropriate annotation for a dried up fruit from the previous year (when the plant had produced fruit, say, in August, but the fruit is observed still clinging to the plant the following April or even May). It happens rarely, so I'm not invested in an answer. Thanks for doing all this work!

Anotado por cgbb2004 hace 4 meses

Thanks @cgbb2004 actually, that is precisely the use case that prompted me to dive into this in the first place. Numerous disagreeing annotations were recently added to a bunch of my observations, and so I started a forum discussion on this topic. Not everyone agrees but most people annotate a "fruit" in the situation you describe.

I've been asking for formal definitions for a long time. Lo and behold! The definitions exist but are hidden from view. No one realized they were buried in the user interface! So that's my immediate goal—to make the definitions more widely known.

Anotado por trscavo hace 4 meses

A worthy project. Well done!

Anotado por cgbb2004 hace 4 meses

To clarify, which (if any) annotation would you suggest that we use in the case where fruits are visible on the ground underneath (but no longer attached to) the plant?

Anotado por tsn hace 4 meses

Thanks for asking this! Up until now, I've been annotating that situation as "fruiting", which seemed like the natural thing to do. Just the other day, @hollyyoung and I had a brief discussion about this. She annotates that as "fruiting" as well. @tsn @cgbb2004 what do you currently do in this case?

The current definitions of "flowering" and "fruiting" specify that the flower or fruit be "still attached to the plant". Maybe we should relax that requirement under the new definitions? If so, that would look something like this:

Reproductive structures:

Flower bud: One or more flower buds visible but not open
Flower: One of more flowers visible and open
Fruit: One or more fruits visible and with seeds
Other reproductive structures: Other reproductive structures visible such as flowerless stalk, withered flower, or empty seed pod
No evidence of reproductive structures: No visible reproductive structures of any kind

Anotado por trscavo hace 4 meses

I'll catch up with you and follow this comment thread when I'm off the road. Heading to Florida and exploring a bit on the way. Buds, flowers and fruits to follow :-)

Anotado por hollyyoung hace 4 meses

Up until last week, when you pointed out that the current official definitions require that the fruit be still attached to the plant, I was using the "Fruiting" annotation also in the case where the fruits are visible on the ground underneath the plant. My reasoning was that I frequently find it useful to go to the photo gallery on a taxon page and filter for fruiting phenology, in order to learn what the fruit of a particular species looks like. Excluding photos of fruits on the ground would make it more difficult for me to learn what I want to learn. However, in this case, I would not propose such a significant change to the official definition without first understanding why someone decided in the first place to include only fruits still attached to the plant.

Anotado por tsn hace 4 meses

Okay, we don't have to decide right now whether or not fruits should be attached to the plant. That can remain an open issue.

Anotado por trscavo hace 4 meses

It all does get complicated, does it not! I haven't ever noted fruits lying on the ground, probably because I've just about always seen attached fruits!

Safe travels @hollyyoung :-)

Anotado por cgbb2004 hace 4 meses

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