David Shorthouse
@dshorthouse.bsky.social
father, husband, biodiversity informatician. Opinions mine and not those of my employer.
https://orcid.org/0000-0001-7618-5230
https://orcid.org/0000-0001-7618-5230
Reposted by David Shorthouse
“Overall, these findings suggest that the value of natural history collections as global research infrastructure is eroding due to decreased collecting of specimen data across species, locations, and time.“ doi.org/10.1038/s414... Interesting analysis based on @gbif.org data.
Global sampling decline erodes science potential of natural history collections - Nature Communications
Natural history collections hold over two billion specimens representing Earth’s biodiversity, but their scientific value depends on continued specimen collection and digitisation. This study demonstr...
doi.org
November 26, 2025 at 12:11 AM
“Overall, these findings suggest that the value of natural history collections as global research infrastructure is eroding due to decreased collecting of specimen data across species, locations, and time.“ doi.org/10.1038/s414... Interesting analysis based on @gbif.org data.
Reposted by David Shorthouse
Announcing the Gem Fellowship, a grant program for improvements to Ruby-related open source projects. https://gem.coop/fellowship/ Want to improve your favorite gem? Submit a proposal, starting next month.
gem.coop
gem.coop
November 20, 2025 at 11:58 PM
Announcing the Gem Fellowship, a grant program for improvements to Ruby-related open source projects. https://gem.coop/fellowship/ Want to improve your favorite gem? Submit a proposal, starting next month.
Reposted by David Shorthouse
Love to hear your thought on this. @rdmpage.bsky.social @dshorthouse.bsky.social @debpaul.bsky.social 🦉 I wrote a post on treating species identifiers with the same rigour as enterprise entity resolution. Not a new idea but we have to think about the scale. www.linkedin.com/pulse/one-sp...
One Species -> Many IDs: Applying enterprise "Entity Resolution" to Biodiversity Data
Here's a crazy idea. What if we treat species identifiers in the biodiversity data landscape the same way commercial organisations treat customers? Hear me out.
www.linkedin.com
November 16, 2025 at 2:06 PM
Love to hear your thought on this. @rdmpage.bsky.social @dshorthouse.bsky.social @debpaul.bsky.social 🦉 I wrote a post on treating species identifiers with the same rigour as enterprise entity resolution. Not a new idea but we have to think about the scale. www.linkedin.com/pulse/one-sp...
Received a notice that Akamai's long-in-the-tooth "Social Login" used by www.simplemappr.net will be retired Dec. 31, 2026. That means I have one year to either rewrite the integration (with considerable pain, tbh), hand it off to someone else to have a go, or shutdown SimpleMappr entirely. 🤔
SimpleMappr
Create free point maps for publications and presentations
www.simplemappr.net
November 5, 2025 at 4:25 PM
Received a notice that Akamai's long-in-the-tooth "Social Login" used by www.simplemappr.net will be retired Dec. 31, 2026. That means I have one year to either rewrite the integration (with considerable pain, tbh), hand it off to someone else to have a go, or shutdown SimpleMappr entirely. 🤔
Reposted by David Shorthouse
The end of an era: the Tree of Life Web Project is going dark after 3 decades. Anyone interested in communicating phylogeny online should read David's account of goals, history, and future. @bembidion.bsky.social
subulatepalpomere.com/2025/11/02/t...
subulatepalpomere.com/2025/11/02/t...
The Passing of the Tree of Life Web Project
The Tree of Life Web Project began its journey almost 40 years ago, and was formally announced in early 1996. It has served thousands of pages of information about the evolutionary tree of life and…
subulatepalpomere.com
November 3, 2025 at 3:54 PM
The end of an era: the Tree of Life Web Project is going dark after 3 decades. Anyone interested in communicating phylogeny online should read David's account of goals, history, and future. @bembidion.bsky.social
subulatepalpomere.com/2025/11/02/t...
subulatepalpomere.com/2025/11/02/t...
(Re-)stumbled onto @rdmpage.bsky.social 13 YEAR OLD (!!) iPhylo post about the stability of @gbif.org occurrenceIDs, iphylo.blogspot.com/2012/07/dear.... Great improvements to stability have been made since then & there is new awareness. But, the source of the instability remains exactly the same.
Dear GBIF, please stop changing occurrenceIDs!
Blog by Rod Page on biodiversity informatics, taxonomy, systematics, phylogeny, knowledge graphs, and other topics.
iphylo.blogspot.com
November 4, 2025 at 6:30 PM
(Re-)stumbled onto @rdmpage.bsky.social 13 YEAR OLD (!!) iPhylo post about the stability of @gbif.org occurrenceIDs, iphylo.blogspot.com/2012/07/dear.... Great improvements to stability have been made since then & there is new awareness. But, the source of the instability remains exactly the same.
Reposted by David Shorthouse
BHL had a strong presence at #LivingData2025 + the #GBIF #GB32 Governing Board Meeting in Bogotá 🇨🇴. We shared our transition progress, rallied support & strengthened collaborations for linked open biodiversity data. 🧪 🌎 📚 🌱🔗 Read more: blog.biodiversitylibrary.org/2025/11/livi... #OpenScience
BHL at Living Data 2025 & GBIF Governing Board Meeting
This month, members of the biodiversity community from across the globe gathered in Bogotá, Colombia, for two major meetings: the Global Biodiversity Information Facility (GBIF) Governing Board Mee…
blog.biodiversitylibrary.org
November 4, 2025 at 12:26 AM
BHL had a strong presence at #LivingData2025 + the #GBIF #GB32 Governing Board Meeting in Bogotá 🇨🇴. We shared our transition progress, rallied support & strengthened collaborations for linked open biodiversity data. 🧪 🌎 📚 🌱🔗 Read more: blog.biodiversitylibrary.org/2025/11/livi... #OpenScience
Reposted by David Shorthouse
New paper in Ecology Letters using @gbif.org mediated data:
Natural History Collections at the Crossroads: Shifting Priorities and Data‐Driven Opportunities 🇦🇺
#CiteTheDOI: ❌
https://doi.org/10.1111/ele.70188
Natural History Collections at the Crossroads: Shifting Priorities and Data‐Driven Opportunities 🇦🇺
#CiteTheDOI: ❌
https://doi.org/10.1111/ele.70188
Natural History Collections at the Crossroads: Shifting Priorities and Data‐Driven Opportunities
As environmental change and biodiversity crises accelerate, natural history collections face a critical juncture with collecting strategies remaining primarily taxonomically motivated, despite collec...
doi.org
October 29, 2025 at 2:39 PM
New paper in Ecology Letters using @gbif.org mediated data:
Natural History Collections at the Crossroads: Shifting Priorities and Data‐Driven Opportunities 🇦🇺
#CiteTheDOI: ❌
https://doi.org/10.1111/ele.70188
Natural History Collections at the Crossroads: Shifting Priorities and Data‐Driven Opportunities 🇦🇺
#CiteTheDOI: ❌
https://doi.org/10.1111/ele.70188
Solo paddling adventure last weekend in Algonquin Provincial Park in -4C weather was...adventurous. I flipped butt-over-teakettle, ironically fetching water for a late night tea. Many colourful words zinged Clamshell Lake. I later read this spot is 210ft deep, being the base of an old waterfall. 😬
October 27, 2025 at 4:34 PM
Solo paddling adventure last weekend in Algonquin Provincial Park in -4C weather was...adventurous. I flipped butt-over-teakettle, ironically fetching water for a late night tea. Many colourful words zinged Clamshell Lake. I later read this spot is 210ft deep, being the base of an old waterfall. 😬
Reposted by David Shorthouse
📣 Calling all biodiversity institutions! Meise Botanic Garden is supporting the continuation of BHL by auditing/cancelling non-Open Access journal subscriptions & diverting all saved funds to BHL. Patricia Mergen encourages other institutions to do the same 🧪 🌱🌎 #LivingData2025 #OpenAccess #ILoveBHL
October 23, 2025 at 7:37 PM
📣 Calling all biodiversity institutions! Meise Botanic Garden is supporting the continuation of BHL by auditing/cancelling non-Open Access journal subscriptions & diverting all saved funds to BHL. Patricia Mergen encourages other institutions to do the same 🧪 🌱🌎 #LivingData2025 #OpenAccess #ILoveBHL
Reposted by David Shorthouse
We are proud and delighted to announce the signing of a renewed partnership between OBIS and @gbif.org at #LivingData2025
With this, we strengthen our shared commitment to make marine biodiversity data more interoperable, accessible, and actionable!
⤵️ Read more
obis.org/2025/10/23/o...
With this, we strengthen our shared commitment to make marine biodiversity data more interoperable, accessible, and actionable!
⤵️ Read more
obis.org/2025/10/23/o...
October 23, 2025 at 9:00 PM
We are proud and delighted to announce the signing of a renewed partnership between OBIS and @gbif.org at #LivingData2025
With this, we strengthen our shared commitment to make marine biodiversity data more interoperable, accessible, and actionable!
⤵️ Read more
obis.org/2025/10/23/o...
With this, we strengthen our shared commitment to make marine biodiversity data more interoperable, accessible, and actionable!
⤵️ Read more
obis.org/2025/10/23/o...
Paddling solo in N. Algonquin Park starting tomorrow for three days. Marathon 8km of portaging (if I feel like it), a bit of rain, -4C at night, & unlikely to be any humans. Maybe moose and bears. A good fire will zap the chill. Bring it on!
October 23, 2025 at 5:27 PM
Paddling solo in N. Algonquin Park starting tomorrow for three days. Marathon 8km of portaging (if I feel like it), a bit of rain, -4C at night, & unlikely to be any humans. Maybe moose and bears. A good fire will zap the chill. Bring it on!
@gbif.org Do you have any docs on how you process the subtypes of checklists published via an IPT? This is an excellent guide ipt.gbif.org/manual/en/ip... but am looking if subtypes are differentially treated/processed.
Best Practices in Publishing Species Checklists :: GBIF IPT User Manual
ipt.gbif.org
October 23, 2025 at 1:28 PM
@gbif.org Do you have any docs on how you process the subtypes of checklists published via an IPT? This is an excellent guide ipt.gbif.org/manual/en/ip... but am looking if subtypes are differentially treated/processed.
Reposted by David Shorthouse
(1) 🥁 Announcing the 2025 Ebbe Nielsen Challenge winners!
First place: 🥇 @rukayaj.bsky.social (@gbifnorway.bsky.social) for BDQEmail
Sharing first place: 🥇 @daxkellie.bsky.social, Amanda Buyan, @shandiya.bsky.social and @rowdynerd.bsky.social (Atlas of Living Australia) for galaxias!
First place: 🥇 @rukayaj.bsky.social (@gbifnorway.bsky.social) for BDQEmail
Sharing first place: 🥇 @daxkellie.bsky.social, Amanda Buyan, @shandiya.bsky.social and @rowdynerd.bsky.social (Atlas of Living Australia) for galaxias!
October 22, 2025 at 3:00 PM
(1) 🥁 Announcing the 2025 Ebbe Nielsen Challenge winners!
First place: 🥇 @rukayaj.bsky.social (@gbifnorway.bsky.social) for BDQEmail
Sharing first place: 🥇 @daxkellie.bsky.social, Amanda Buyan, @shandiya.bsky.social and @rowdynerd.bsky.social (Atlas of Living Australia) for galaxias!
First place: 🥇 @rukayaj.bsky.social (@gbifnorway.bsky.social) for BDQEmail
Sharing first place: 🥇 @daxkellie.bsky.social, Amanda Buyan, @shandiya.bsky.social and @rowdynerd.bsky.social (Atlas of Living Australia) for galaxias!
Have some pancakes with maple syrup at sunrise in Algonquin Provincial Park. I’m sorry, I ate half.
October 13, 2025 at 12:12 AM
Have some pancakes with maple syrup at sunrise in Algonquin Provincial Park. I’m sorry, I ate half.
Preparing for a chilly Canadian Thanksgiving paddle with several 2km+ portages in Algonquin Provincial Park with a friend from my high school years. Might be the last one of the season. 🛶 💪 🦃 🥶
October 9, 2025 at 2:19 PM
Preparing for a chilly Canadian Thanksgiving paddle with several 2km+ portages in Algonquin Provincial Park with a friend from my high school years. Might be the last one of the season. 🛶 💪 🦃 🥶
First time I've not fully unpacked from the previous paddling adventure that the next one is underway. And, the first one where ticks are a consideration. Kawartha Highlands here I come with my eldest son. www.canoedaddy.com/home/trip-re...
Canoe Daddy - Serpentine Lake Loop
Total Distance: 20 km
Duration: 2 days (3 or more is recommended to explore the area)
No. of Portages: 7
Total Port. Distance: approx. 2700 m
Level of Difficulty: Novice (one long portage of 1500m)
www.canoedaddy.com
October 3, 2025 at 11:39 PM
First time I've not fully unpacked from the previous paddling adventure that the next one is underway. And, the first one where ticks are a consideration. Kawartha Highlands here I come with my eldest son. www.canoedaddy.com/home/trip-re...
Reposted by David Shorthouse
Very excited to have this opportunity!
Manaaki Whenua have appointed Siobhan Leachman as their Wikimedian in Residence!
Supporting staff to share their expertise, @siobhanleachman.bsky.social will be assisting the group with contributing content from their nationally significant collections to openly accessible Wikimedia platforms.
Supporting staff to share their expertise, @siobhanleachman.bsky.social will be assisting the group with contributing content from their nationally significant collections to openly accessible Wikimedia platforms.
From Collections to Commons: Announcing a Wikimedian in Residence at Manaaki Whenua
From Collections to Commons: Announcing a Wikimedian in Residence at Manaaki Whenua Manaaki Whenua – Landcare Research Group now have a Wikimedian in Residence on board, […]
www.wikimedia.nz
September 24, 2025 at 10:36 PM
Very excited to have this opportunity!
Reposted by David Shorthouse
Our article "Wikidata for botanists: benefits of collaborating and sharing Linked Open Data" is part of this new issue of @annbot.bsky.social
See: doi.org/10.1093/aob/...
Result of a great #collaboration @siobhanleachman.bsky.social @joaquimsantos1978.bsky.social Heidi Meudt! #Wikidata #LOD
See: doi.org/10.1093/aob/...
Result of a great #collaboration @siobhanleachman.bsky.social @joaquimsantos1978.bsky.social Heidi Meudt! #Wikidata #LOD
🆕 The new issue of Annals of Botany is now online!
🧬 Symbiosis, physiology & molecular responses
🌸 Pollination & plant–insect interactions
🌾 Nutrients & root processes
📊 Open data & measurements
🌱 Seeds, seedlings & climate change
New issue👉 botany.fyi/91590f
#PlantScience #Botany
🧬 Symbiosis, physiology & molecular responses
🌸 Pollination & plant–insect interactions
🌾 Nutrients & root processes
📊 Open data & measurements
🌱 Seeds, seedlings & climate change
New issue👉 botany.fyi/91590f
#PlantScience #Botany
![The cover image shows the Australian Queen of Sheba orchid, a plant which exhibits floral deception by mimicking buzz-pollinated tinsel lilies. Floral trait analyses, pollinator observations, and reproductive success metrics reveal how visual and olfactory signals interact to attract shared pollinators, advancing our understanding of the complex evolution of mimicry in deceptive pollination systems. [See Scaccabarozzi et al., pp. 583–595.]](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:qowz7hsvbml54nxg6hzo7rrg/bafkreict3cbx4a2wcbm42ai6jlkabu3dkhk2d3rxbtkg4qq2hfqe3tqnvm@jpeg)
October 3, 2025 at 11:17 AM
Our article "Wikidata for botanists: benefits of collaborating and sharing Linked Open Data" is part of this new issue of @annbot.bsky.social
See: doi.org/10.1093/aob/...
Result of a great #collaboration @siobhanleachman.bsky.social @joaquimsantos1978.bsky.social Heidi Meudt! #Wikidata #LOD
See: doi.org/10.1093/aob/...
Result of a great #collaboration @siobhanleachman.bsky.social @joaquimsantos1978.bsky.social Heidi Meudt! #Wikidata #LOD
Reposted by David Shorthouse
RIP #JaneGoodall - one of the modern pioneers of profound interconnections between people, animals and ecosystems. Her life was lived through science, compassion and tireless advocacy for the multiple values of nature - leaving a legacy that will endure for people and planet.
BREAKING: Jane Goodall, the conservationist renowned for chimpanzee research and environmental advocacy, has died.
Jane Goodall, conservationist renowned for chimpanzee research and environmental advocacy, has died
Jane Goodall, the conservationist renowned for her groundbreaking chimpanzee field research and globe-spanning environmental advocacy, has died. She was 91.
bit.ly
October 1, 2025 at 7:18 PM
RIP #JaneGoodall - one of the modern pioneers of profound interconnections between people, animals and ecosystems. Her life was lived through science, compassion and tireless advocacy for the multiple values of nature - leaving a legacy that will endure for people and planet.
Stunning and other-worldly solo canoe trip circumnavigating Philip Edward Island on the NE shore of Lake Huron in Ontario, Canada. Two nights and three days, not a cloud in the sky and what little wind there was, it was at my back.
October 1, 2025 at 12:26 AM
Stunning and other-worldly solo canoe trip circumnavigating Philip Edward Island on the NE shore of Lake Huron in Ontario, Canada. Two nights and three days, not a cloud in the sky and what little wind there was, it was at my back.
Departing on another paddling adventure to somewhere near here, the greatest concentration of freshwater islands in the world.
September 27, 2025 at 1:31 PM
Departing on another paddling adventure to somewhere near here, the greatest concentration of freshwater islands in the world.
Back from a 4-day solo canoe trip to N. Algonquin. Beaver dams, lift overs, lining, oh my! Been so luck with the weather on my adventures this summer.
September 3, 2025 at 12:28 AM
Back from a 4-day solo canoe trip to N. Algonquin. Beaver dams, lift overs, lining, oh my! Been so luck with the weather on my adventures this summer.
A four-day solo paddle with multiple, lengthy portages starts tomorrow morning. It's been at least 20 years since the last time I was truly all alone, fending for myself. I am grateful for my family who understand that I have been quietly aching for this. #MyLittleRedCanoe
August 30, 2025 at 12:00 AM
A four-day solo paddle with multiple, lengthy portages starts tomorrow morning. It's been at least 20 years since the last time I was truly all alone, fending for myself. I am grateful for my family who understand that I have been quietly aching for this. #MyLittleRedCanoe
What to do with scraps of uneaten dehydrated food from the last canoe trip? Plan another one!
Son and I couldn't complete this Algonquin trip in May; he had a rotten virus. Good on him to tap the mat. At that time we were deafened by spring peepers and an American Bittern youtu.be/bAxAEoAVmuc?...
Son and I couldn't complete this Algonquin trip in May; he had a rotten virus. Good on him to tap the mat. At that time we were deafened by spring peepers and an American Bittern youtu.be/bAxAEoAVmuc?...
August 27, 2025 at 3:53 AM
What to do with scraps of uneaten dehydrated food from the last canoe trip? Plan another one!
Son and I couldn't complete this Algonquin trip in May; he had a rotten virus. Good on him to tap the mat. At that time we were deafened by spring peepers and an American Bittern youtu.be/bAxAEoAVmuc?...
Son and I couldn't complete this Algonquin trip in May; he had a rotten virus. Good on him to tap the mat. At that time we were deafened by spring peepers and an American Bittern youtu.be/bAxAEoAVmuc?...