Μάρτιος 21, 2024

Annotation feedback

Recently, a number of GitHub issues related to annotations have been opened and discussed:

I wanted to take this opportunity to provide some feedback to the designers and developers without disrupting the GitHub issues. Hence this journal article.

Background: A group of us initiated and discussed a Proposal to replace the Plant Phenology annotation last November (2023). The proposal was not brought to a wider audience since it was felt that we lacked consensus on one or two key issues. In any case, I think some good points were raised, and apparently now is the time to surface these ideas to the designers and developers.

Briefly, the proposal is to replace the Plant Phenology annotation with the following annotation:

Reproductive Structures
1. Flower bud: At least one closed flower bud is visible
2. Flower: At least one open flower is visible
3. Fruit: At least one fruit or seed is visible
4. No reproductive structures: No sexual reproductive structures (in whole or part) are visible

Instead of modifying the current Plant Phenology annotation, can we modify the proposed Reproductive Structures annotation?

Here are some (out-of-band) comments on the GitHub issues:

#4046: See above for recommended annotation name, values, and mouseover definitions

#4047: The annotation name (Reproductive Structures) should be independent of the chart title. Put another way, user interface issues on the taxon page should not drive the choice of annotation name, values, or mouseover definitions.

#4049: No comment

Posted on Μάρτιος 21, 2024 0928 ΜΜ by trscavo trscavo | 2σχόλια | Αφήστε ένα σχόλιο

Φεβρουάριος 25, 2024

The confusing tick-trefoils

Desmodium glabellum (tall tick-trefoil) and Desmodium perplexum (perplexed tick-trefoil) are members of the Desmodium paniculatum complex. The specific name perplexum suggests these taxa are confusing, which is indeed true. Until recently, it was very difficult to distinguish Desmodium glabellum from Desmodium perplexum. In 2020, a breakthrough research result put these species on the map (both figuratively and literally). For more info:

The googledoc includes an identification key, references, and links. A short glossary is also included.

Posted on Φεβρουάριος 25, 2024 0130 ΜΜ by trscavo trscavo | 14σχόλια | Αφήστε ένα σχόλιο

Φεβρουάριος 10, 2024

Bristol Pond

Bristol Pond (also called Winona Lake on some maps) is a large wetland complex in the town of Bristol in Addison County, Vermont. Bristol Pond is the source of Pond Brook, which flows north through the adjacent town of Monkton before emptying into Lewis Creek (which itself empties in Lake Champlain). The Pond Brook Watershed is a significant natural resource (but that's a different story).

There are no hiking trails around Bristol Pond. The best way to experience the area is by canoe or kayak. For convenience, I made a geospatial PDF map of Bristol Pond. The blue area on the map is State land while the yellow area is private land owned by the A. Johnson Company.

I've only been to Bristol Pond once but my sense is that there's a lot to see and do here. You can browse the site's observations to get idea about biodiversity.

Have you been to Bristol Pond?

Posted on Φεβρουάριος 10, 2024 0838 ΜΜ by trscavo trscavo | 4σχόλια | Αφήστε ένα σχόλιο

Φεβρουάριος 04, 2024

A. Johnson Company is closed

As of the end of the December 2023, the A. Johnson (lumber) Company in Bristol, Vermont is closed. There's almost nothing online about this so I won't try to provide a link at this time (see the comments). If today's date were April 1st, I would wonder if this might be an April Fool's joke. If A. Johnson is closed, that's a Very Big Deal since they own many acres of forested land throughout the state.

Does anybody know more?

Posted on Φεβρουάριος 04, 2024 0643 ΜΜ by trscavo trscavo | 7σχόλια | Αφήστε ένα σχόλιο

Ιανουάριος 12, 2024

American ginseng

I've spent the last month reading and writing about American ginseng (Panax quinquefolius). What an amazing story! After somehow surviving 300 years of exploitation, this plant has earned my respect. For a quick introduction, see the lead paragraphs of the wikipedia article on American ginseng.

The following is from New Flora of Vermont [2015]:

QUOTE
Ginseng, "shang." Forests and woodlands, usually on soils derived from calcareous bedrock, near colluvial traprock or below talus slopes, often in the sugar maple-basswood-white ash association; frequent. Specimens seen from all except Essex, Franklin, and Bennington counties, but it probably occurs in all. There has been substantial trade in this species at various times in Vermont, probably beginning soon after its discovery in North America in 1720 (Thompson 1842). Its roots are still collected for sale. There has been some planting of it into the wild for this purpose, and it has also been commercially cultivated. Those collecting it have been called "shangers" and hunting for it has been called "shanging."
END

In my limited experience, this species is rather uncommon (not "frequent") in VT, with very few individuals per occurrence. What is your experience with this species?

Posted on Ιανουάριος 12, 2024 1124 ΜΜ by trscavo trscavo | 2σχόλια | Αφήστε ένα σχόλιο

Δεκέμβριος 02, 2023

Annotating the common witch-hazel

I’ve been obsessed with this species lately. It is one of the most interesting species I’ve ever studied.

All observations of the common witch-hazel (Hamamelis virginiana) in Vermont have been annotated (at least all observations that can be annotated). The results mostly agree with what’s in the literature but there are a couple of surprises. Check out the Plant Phenology chart on the taxon page (suitably restricted to Vermont). Briefly:

  • Flower budding: [July–]August–October
  • Flowering: September–November[–December]
  • Resting: [December–]January–April
  • Fruiting: May–October[–November]

Based on the number of iNat observations (a criterion that can be misleading), peak flower budding, peak flowering, and peak fruiting occur in September, October, and July, respectively. For more information:

Comments welcome.

Posted on Δεκέμβριος 02, 2023 0310 ΜΜ by trscavo trscavo | 15σχόλια | Αφήστε ένα σχόλιο

Νοέμβριος 30, 2023

Persistent plant part

By definition, a persistent plant part is retained after its normal function has been completed. I created an observation field for persistent plant part, with the following values:

  • bud scales
  • calyx
  • frond
  • fruit
  • seed
  • strobilus
  • style

The set of values may change as I continue to use this observation field. In particular, I may come to regret having separate fields for fruit and seed. Since a fruit is a container for seeds, those two values necessarily overlap. In practice, I choose the plant part that dominates the photo evidence.

Comments welcome!

Posted on Νοέμβριος 30, 2023 1202 ΜΜ by trscavo trscavo | 6σχόλια | Αφήστε ένα σχόλιο

Νοέμβριος 16, 2023

Proposal to replace the Plant Phenology annotation

The newly discovered annotation tooltips motivated a discussion regarding the Plant Phenology annotation. A proposal to replace the Plant Phenology annotation with a new annotation (called Reproductive Structures) grew out of the discussion:

Reproductive Structures

  1. Flower bud: At least one closed flower bud is visible and attached to the plant
  2. Flower: At least one open flower is visible and attached to the plant
  3. Fruit: At least one seed-bearing fruit is visible and attached to the plant
  4. No reproductive structures: No sexual reproductive structures (in whole or part) are visible

For details regarding the proposal, see:

If you support this proposal, please join the conversation!

Posted on Νοέμβριος 16, 2023 0105 ΜΜ by trscavo trscavo | 64σχόλια | Αφήστε ένα σχόλιο

Νοέμβριος 09, 2023

Flowering season of native plants in Vermont

Which native plant species have been observed in Vermont with a flower (or flower bud) either very early or very late in the season? The following search URLs can be used to answer this question:

Observations of native plants with flowers in Jan, Feb, and Mar: https://www.inaturalist.org/observations?introduced=false&month=1,2,3&place_id=47&subview=table&term_id=12&term_value_id=13&view=species

Observations of native plants with flower buds in Jan, Feb, and Mar: https://www.inaturalist.org/observations?introduced=false&month=1,2,3&place_id=47&subview=table&term_id=12&term_value_id=15&view=species

Observations of native plants with flowers in Nov and Dec: https://www.inaturalist.org/observations?introduced=false&month=11,12&place_id=47&subview=table&term_id=12&term_value_id=13&view=species

Observations of native plants with flower buds in Nov and Dec: https://www.inaturalist.org/observations?introduced=false&month=11,12&place_id=47&subview=table&term_id=12&term_value_id=15&view=species

Studying these lists, there are few authentic observations of flowers in Dec, Jan, or Feb. The aster observed on December 11 is one of my favorites. (There may be other non-annotated observations out there, I don’t know.)

Just for fun, here are my most extreme observations of native plants in VT with flowers:

Eastern Skunk Cabbage (Symplocarpus foetidus) observed on March 26:
https://www.inaturalist.org/observations/152724920

Rock Harlequin (Capnoides sempervirens) observed on November 8:
https://www.inaturalist.org/observations/105527264

What are yours?

Posted on Νοέμβριος 09, 2023 1000 ΜΜ by trscavo trscavo | 10σχόλια | Αφήστε ένα σχόλιο

Οκτώβριος 21, 2023

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?

Posted on Οκτώβριος 21, 2023 0339 ΜΜ by trscavo trscavo | 23σχόλια | Αφήστε ένα σχόλιο