Friday, November 10, 2017

Exploring images in the Biodiversity Literature Repository

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A post by on the Plaza blog Expanded access to images in the Biodiversity Literature Repository has prompted me to write up a little toy I ...
Friday, October 06, 2017

Notes on finding georeferenced sequences in GenBank

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Notes on how many georeferenced DNA sequences there are in GenBank, and how many could potentially be georeferenced. BCT Bacterial sequen...
Wednesday, October 04, 2017

TDWG 2017: thoughts on day 3

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Day three of TDWG 2017 highlighted some of the key obstacles facing biodiversity informatics. After a fun series of "wild ideas"...

Bitcoin, biodiversity, and micropayments for open data

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I gave a "wild ideas" talk at TDWG17 suggesting that the biodiversity community use Bitcoin to make micropayments to use data. ...
Tuesday, October 03, 2017

TDWG 2017: thoughts on day 1

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Some random notes on the first day of TDWG 2017. First off, great organisation with the first usable conference calendar app that I've s...
Monday, September 18, 2017

Guest post: Our taxonomy is not your taxonomy

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The following is a guest post by Bob Mesibov . Do you know the party game "Telephone", also known as "Chinese Whispers...
Monday, August 28, 2017

Let’s rise up to unite taxonomy and technology

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Let’s rise up to unite taxonomy and technology - I thought it already was? @rdmpage https://t.co/AkNz1GYGbw — Sjúrður Hammer 🐣 (@sjurdur) ...
Sunday, August 20, 2017

Notes on displaying big trees using Google Maps/Leaflet

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Notes to self on web map-style tree viewers. The basic idea is to use Google Maps or Leaflet to display a tree. Hence we need to compute til...
Tuesday, July 04, 2017

Apple's Knowledge Navigator concept video (1987): we are still a long way from this vision

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I've been viewing Apple's Knowledge Navigator concept video from 1987 and it's striking how much of this we have today, and yet ...
Friday, June 30, 2017

Response to To Increase Trust, Change the Social Design Behind Aggregated Biodiversity Data

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Nico Franz and Beckett W. Sterner recently published a preprint entitled "To Increase Trust, Change the Social Design Behind Aggregated...
Friday, June 16, 2017

GBIF Challenge 2017: Liberating species records from open data repositories for scientific discovery and reuse

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GBIF is running its Ebbe Nielsen Challenge for the third successive year. This year the title is Liberating species records from open data ...
Wednesday, May 31, 2017

Programming with Glitch: microservices and serverless computing

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Yes, this post is indeed an attempt to fit as many buzzwords that I don't really understand into the title. I've been playing around...

Querying Wikidata

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Over 7 million #SPARQL queries/day in @wikidata #WikiCite 👏🏻 pic.twitter.com/l2I6IcnGJj — WikiCite (@Wikicite) May 23, 2017 For my o...

Wikidata, WikiCite, and the "bibliography of life"

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Last week I was at WikiCite 2017 , a fascinating three day event in Vienna. Wikicite is "a proposal to build a bibliographic database ...
Friday, March 24, 2017

This is what phylodiversity looks like

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Following on from earlier posts exploring how to map DNA barcodes and putting barcodes into GBIF it's time to think about taking advan...

Notes for WikiCite 2017: Wikispecies reference parsing

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In preparation for WikiCite 2017 I'm looking more closely at extracting bibliographic information from Wikispecies. The WikiCite proj...
Wednesday, February 15, 2017

New feature for BioStor: extracting literature cited from OCR text

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At present BioStor provides a simple display of an article extracted from BHL. You get the page images, and sometimes a map and an altmetri...
Saturday, January 14, 2017

Displaying taxonomic classifications from Wikidata using d3js and SPARQL

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Following on from previous posts The Semantic Web made fun: d3sparql and The Biodiversity Heritage Library meets Wikidata via Wikispecies:...
Wednesday, January 11, 2017

The Biodiversity Heritage Library meets Wikidata via Wikispecies: adding author identifiers to BioStor

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I've added an experimental feature to BioStor that uses data from Wikidata and Wikispecies to augment what information BioStor displays ...