Rod Page

@rdmpage

Expat Kiwi, emeritus Professor of Taxonomy at Glasgow University, inclined to say that something sucks at every available opportunity. Biodiversity informatics, phylogeny, knowledge graphs.

1,281 Following1,262 Followers734 Posts

Bluesky

Is this your profile?Claim it and rdmpage.dirty.social is yours.Claim profile

Rod Page@rdmpage· 20d

New in @biodivlibrary.bsky.social are the chapters of "Vertebrate palaeontology of Australasia", including one of my favourite images, a giant goanna chasing a mihirung (Genyornis) www.biodiversitylibrary.org/page/39941042

Figure 7. Reconstruction (by P. Trusler) of the dromomithid Genyornis newtoni being attacked by the giant goanna, Megalania prisca, both known from the Pleistocene of Australia.

Rod Page@rdmpage· Jul 13

More #bhlsunday updates, I've now added articles to "Abhandlungen und Berichte des Königl. Zoologischen und Anthropologisch-Etnographischen Museums zu Dresden" biostor.org/issn/0233-125X, featuring a mix of anthropology, zoology, and reports on museums in the U.S. & Europe @biodivlibrary.bsky.social

Rod Page@rdmpage· Jul 5

Argh! I posted low resolution images, these are a bit crisper.

Rod Page@rdmpage· Jul 5

New for #bhlsunday is a volume of Arkiv för zoologi which includes "Über einen neuen Riesenkäfer (Goliathus meleagris) aus Süd-Kongo. Nebst einer Revision der Gattung Goliathus (♂♂)" with some elegant drawings of goliath beetles www.biodiversitylibrary.org/page/65710175 @biodivlibrary.bsky.social

Rod Page@rdmpage· Jul 1

I can't resist pointing out that you can see this work online in @biodivlibrary.bsky.social, e.g. www.biodiversitylibrary.org/page/47135898 (Tafel 7 from v.1 of Systême silurien du centre de la Bohême).

Tafel 7 from v.1 of Systême silurien du centre de la Bohême

Rod Page@rdmpage· Jun 30

I've added nicer domain name for my "BOLD View"project which explores an alternative interface to the DNA barcoding data in @boldsystems.bsky.social, you can now view it at boldview.iphylo.org. Very much a work in progress, I keep getting distracted by how badly DNA barcode data needs curation.

Rod Page@rdmpage· Jun 30

When querying for "bat" in a demo tool I created to search @biodivlibrary.bsky.social images I get manta rays popping up iphylo.org/bhl-image-se..., and it's only now that I see that rays resemble bats (although I can't help wonder if the underlying model has also been trained on images of Batman?)

Screen shot of https://iphylo.org/bhl-image-search/?q=bat&k=12 BHl image search showing results of querying for "bat" and getting manta rays as well.

Rod Page@rdmpage· Jun 24

Part of the process of generating the Darwin Core Archive for @GBIF creates a GeoJSON file, which GitHub displays as a map, enabling a quick check that the geographic coordinates make sense.

Rod Page@rdmpage· Jun 4

I agree that search box and nothing else can be a bit daunting (e.g., OpenAlex). That does lkeave the question of what would be good starting points for browsing...? Re a Zotero-like interface, this feels a bit like a slippery slope to creating a bibliography manager online.

Home page for OpenAlex https://openalex.org

Rod Page@rdmpage· May 30

If you are having trouble getting published, spare a thought for William Barnwell whose article "in the time oſ the Yellow ſever the copy was miſlaid and it was unavoidably poﬅponed" so this is all we get www.biodiversitylibrary.org/page/12181248 @biodivlibrary.bsky.social

(288 )
No. XXXIV.
An Attempt to inveﬅigate the Cauſes why the Winters in
North America are colder than the Winters in Europe,
in the ſame Latitudes; and why the Eaﬅern ſides oſ both
the Northern Continents are colder than the Weﬅern.
By Dr. WiLLIAM BARNWELL-Should have been
inſerted here, and ſome part oſ it was printed; but in
the time oſ the Yellow ſever the copy was miſlaid and
it was unavoidably poﬅponed.

Rod Page@rdmpage· May 28

This is very preliminary, but this is an overview of every species in the Open Tree of Life, colour coded by whether their position in the tree is based on taxonomy only (dark colour) or includes phylogenetic information (blue). Phylogenetic coverage is sparse, mostly plants and vertebrates.

Hilbert curve for every species in the Open Tree of Life, colour coded by whether their position in the tree is based on taxonomy only (dark colour) or includes phylogenetic information (blue)

Rod Page@rdmpage· May 25

For "fun" I have created a MCP server for the Open Tree of Life and I asked it to interpret the definition of "Acrodonta". It found a node that matches the definition, but it is not labelled Acrodonta in the tree because Priscagama gobiensis is sister to all the other Acrodonta.

Ok here is a challenge. This is the definition of Acrodonta according to https://phyloregnum.org:
The crown clade originating in the most recent common ancestor of Agama (originally Lacerta) agama(Linnaeus 1758), Chamaeleo (originally Lacerta) chamaeleon (Linnaeus 1758), Uromastyx (originally Lacerta)aegyptia (Forsskål 1775) and Leiolepis guttata Cuvier 1829.

Can you locate this node in the OTT tree?

17:46
Good challenge — this is a phyloreference, so I need to find the MRCA of those four species in the synthesis tree.

Mrca
Mrca
Found it. The Acrodonta crown clade as defined by the phyloreference resolves in the OTT synthesis tree to node mrcaott2417ott4812, an 833-tip clade.

All four specifier species resolved cleanly (Agama agama, Leiolepis guttata, Chamaeleo chamaeleon, Uromastyx aegyptia), and their MRCA gives a node labelled — using two arbitrary descendant tips — as Phrynocephalus forsythii + Trioceros harennae. Per the lesson from earlier, the label is incidental; the node's biological content is the clade uniting agamids (including Agama, Uromastyx, Leiolepis, Phrynocephalus) with chamaeleonids (including Chamaeleo, Trioceros) — which is exactly what Acrodonta is meant to circumscribe.

Want me to pull node_info on it to look at how well-supported this node is, or check what it's sister to?

Rod Page@rdmpage· May 24

Also adding more information about the studies that are relevant to each node. A lot of studies conflict with claim that rheas are sister to elephant birds + kiwis + emus + cassowaries, e.g. doi.org/10.1093%2Fsy... versus doi.org/10.1016%2Fj....

Rod Page@rdmpage· May 24

Messing about with adding PhyloPic images to the tree of life, e.g. iphylo.org/ott-viewer/i...

Rod Page@rdmpage· May 13

More displacement activity, I've added a bunch of articles from Journal and proceedings of the Asiatic Society of Bengal to BioStor biostor.org/issn/0368-34..., they will be in @biodivlibrary.bsky.social in a day or so. Process is semi-automated, but those pesky plates will get you every time 😭

Rod Page@rdmpage· May 8

Exploring 218,567 pages of @bhl-au.bsky.social content using a "gilbert" curve. Just some of the content added by @nicolekearney.bsky.social and her team, HT to @cajunjoel.bsky.social for putting @biodivlibrary.bsky.social images on AWS which made this visualisation possible.

Rod Page@rdmpage· May 6

More tweaks to the Open Tree of Life viewer. It now distinguishes between taxa that are placed solely based on taxonomy rather than any phyklogenetic evidence. For example Goniurosaurus is mostly based on taxonomy iphylo.org/ott-viewer/?... has shown by a polytomy with lots of dashed lines.

Rod Page@rdmpage· May 4

I've released my experimental Open Tree of Life browser at iphylo.org/ott-viewer. You can navigate the Open Tree of Life synthesis tree in all its (complicated) glory. Single click on a node for information, double click to focus on that node, search for node by name.

Rod Page@rdmpage· May 4

And @rbgkew.bsky.social might be surprised that their journal "Bulletin of Miscellaneous Information (Royal Gardens Kew)" has over seven million records, mostly to do with "Magnetic confinement fusion research" openalex.org/works?filter...

Rod Page@rdmpage· May 4

Anybody here from #openalex because I am seeing some batshit crazy things on the web site. For example openalex.org/works?filter... is a record for @inaturalist.bsky.social which is apparently provided by "Open MIND" and the focus of iNaturalist is "Military Technology and Strategies" Huh?

Rod Page@rdmpage· Apr 21

Latest displacement activity is playing with an idea for showing the Open Tree of Life opentreeoflife.github.io using summary trees and animated transitions (with some help from Claude Code and OpenAI) #opentreeoflife #phylogeny

Rod Page@rdmpage· Apr 20

"Why funders shouldn’t withdraw money from open access publishing" www.samuelmoore.org/2026/04/14/w... by @samuelmoore.org

if your problem with open access is that commercial publishers are hoovering up all the money, design open access interventions that specifically prevent commercial publishers from receiving your money.

Rod Page@rdmpage· Apr 19

Here's another example, this time Queensland in Australia. bold-view-bf2dfe9b0db3.herokuapp.com/geo.php?coun... This time the polygon isn't a close match for the actual state of Queensland, suggesting that either some barcodes have the wrong coordinates, or they didn't come from Queensland.

Rod Page@rdmpage· Apr 19

Inspired by an old Flickr post code.flickr.net/author/flick... I built a tool to display a polygon around DNA barcode localities in the @boldsystems.bsky.social database. For example, here is Switzerland bold-view-bf2dfe9b0db3.herokuapp.com/geo.php?coun... as outlined by DNA barcodes.

Rod Page@rdmpage· Apr 13

Here's a screenshot of text in the PDF, I get different characters depending on whether I copy from the PDF, or from the PDF rendered in mozilla.github.io/pdf.js/.

Material examined. Hඈඅඈඍඒඉൾ: female, ‘MEXICO, Puebla, 19.911
-97.328, 1370m, 13.vi.2019, sift., J.Longino 10670’, ‘CNCCOL-
VG00010339’ (deposited in the Canadian Museum of Nature, Ottawa,
Canada). The holotype is missing both hind legs (one used for sequen-
cing), the right middle leg and right front tarsus

Rod Page@rdmpage· Apr 9

Ah, it looks like Android has the original app only, which is the same as “classic” on the iPhone, which also has a newer app, confusingly called iNaturalist, but with a different icon.

Rod Page@rdmpage· Apr 9

Creating a map of @biodivlibrary.bsky.social geographic coverage using www.metabase.com and because the colours are pale green and red, I can't see anything 😭 What fool chose these colours?! And no, there won't be any alt text because I can't see anything to describe 🤬

Rod Page@rdmpage· Apr 9

The bulk of @gbif.org data comes from citizen science... and people like birds... a lot

EOD - eBird Observation Dataset 1,775,781,186
Naturalist Research-grade Observations 145,085,789
Observation.org, Nature data from arou... 126,458,414
Artportalen 117,907,280
DOF/BirdLife Denmark - Observations fro... 37,456,027
Norwegian Species Observation Service 36,870,820
Australian Microbiome 16S (Bacteria) Da... 34,766,568
Macro-moth distribution records for the ... 30,822,537
Australian Microbiome 16S (Bacteria) Da... 28,715,556
Southern African Bird Atlas Project 2 25,687,526

Rod Page@rdmpage· Apr 9

Four years ago as @gbif.org passed 2 billion records, I tweeted that GBIF was, to a first approximation a database of birds x.com/rdmpage/stat.... Four years later we have nearly twice as many records (3.6 billion) and... it's still a mostly a database of birds www.gbif.org/occurrence/t...

Sunburst diagram of taxonomic distribution of occurrences in GBIF in March 2022, as tweeted here https://x.com/rdmpage/status/1501477098434744332?s=20

Sunburst diagram of taxonomic distribution of occurrences in GBIF https://www.gbif.org/occurrence/taxonomy?occurrence_status=PRESENT on 9 April 2026

Rod Page@rdmpage· Apr 3

Over in the @biodivlibrary.bsky.social forum forum.biodiversitylibrary.org/t/experiment... I’ve been experimenting with @latest.allmaps.org to georeference a BHL map. This looks like it has a lot of potential.