Tuesday, November 05, 2019

Thoughts on Biodiversity Next

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It’s been a while since I’ve posted on iPhylo. Since returning from a fun and productive time in Australia there have been a bunch of profe...
Wednesday, August 21, 2019

Ozymandias in Canberra

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On Tuesday I was in Canberra to visit the Australian National Insect Collection at CSIRO and give a talk on knowledge graphs. David Yeates,...
Monday, July 15, 2019

Notes on collections, knowledge graphs, and Semantic Web browsers

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While working with linked data and ways to explore and visualise information, I keep coming back to the Haystack project , which is now over...
Friday, June 21, 2019

Messages from Melbourne: Towards linking all the things

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I'm doing some work with Nicole Kearney ( @nicolekearney ) at the Melbourne Museum on the general theme of "linking all the thin...
Tuesday, May 28, 2019

Frankenplace, geospatial search, and discrete global grid systems

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Quick note on Frankenplace , a cool search tool that displays the geographic distribution of documents that match the user's query as...

Ozymandias meets Wikipedia, with notes on natural language generation

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I've tweaked Ozymandias to now include short natural language summaries (snippets) for various taxa. This makes the output a little mor...
Wednesday, April 10, 2019

Ozymandias: A biodiversity knowledge graph published in PeerJ

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My paper "Ozymandias: A biodiversity knowledge graph" has been published in PeerJ https://doi.org/10.7717/peerj.6739 The pa...
Sunday, March 24, 2019

Where is the damned collection? Wikidata, GrBio, and a global list of all natural history collections

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One of the things the biodiversity informatics community has struggled to do is come up with a list of all natural history collections (Tayl...
Wednesday, December 05, 2018

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Glasgow University's Institute of Biodiversity, Animal Health & Comparative Medicine, where I'm based, hosts Naturally Speaking ...

Ozymandias: A biodiversity knowledge graph available as a preprint on Biorxiv

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I've written up my entry for the 2018 GBIF Challenge ("Ozymandias") and posted a preprint on Biorxiv ( https://www.biorxiv.org...
Thursday, November 15, 2018

Geocoding genomic databases using GBIF

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I've put a short note up on bioRxiv about ways to geocode nucleotide sequences in databases such as GenBank. The preprint is "Geoco...
Thursday, October 25, 2018

Taxonomic publications as patch files and the notion of taxonomic concepts

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There's a slow-burning discussion on taxonomic concepts on Github that I am half participating in. As seems inevitable in any discussio...
Wednesday, October 24, 2018

Specimens, collections, researchers, and publications: towards social and citation graphs for natural history collections

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Being in Ottawa last week for a hackathon meant I could catch up with David Shorthouse ( @dpsSpiders . David has been doing some neat wor...

Ottawa Ecobiomics hackathon: graph databases and Wikidata

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I spent last week in Ottawa at a "Ecobiomics" hackathon organised by Joel Sachs. Essentially we spent a week exploring the applic...

GBIF Ebbe Nielsen Challenge update

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🎉 🎉 CONGRATULATIONS to @UofGlasgow 's @rdmpage for winning joint first prize in the 2018 @GBIF Ebbe Nielsen Challenge, the annual in...
Tuesday, September 11, 2018

Guest post - Quality paralysis: a biodiversity data disease

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The following is a guest post by Bob Mesibov . In 2005, GBIF released Arthur Chapman's Principles of Data Quality and Principles and M...
Monday, August 20, 2018

GBIF Challenge Entry: Ozymandias

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I've submitted an entry for the 2018 GBIF Ebbe Nielsen Challenge . It's a couple of weeks before the deadline but I will be away the...