Friday, August 14, 2015

Possible project: NameStream - a stream of new taxonomic names

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Yet another barely thought out project, although this one has some crude code . If some 16,000 new taxonomic names are published each year, ...

Possible project: A PubMed Central for taxonomy

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I need more time to sketch this out fully, but I think a case can be made for a taxonomy-centric (or, perhaps more usefully, a biodiversity...
Monday, August 10, 2015

Demo of full-text indexing of BHL using CouchDB hosted by Cloudant

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One of the limitations of the Biodiversity Heritage Library (BHL) is that, unlike say Google Books, its search functions are limited to sea...

Possible project: mapping authors to Wikipedia entries using lists of published works

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One of the less glamorous but necessary tasks of data cleaning is mapping "strings to things", that is, taking strings such as ...
Sunday, August 09, 2015

More Neo4J tests of GBIF taxonomy: Using IPNI to find objective synonyms

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Following on from Testing the GBIF taxonomy with the graph database Neo4J I've added a more complex test that relies on linking taxa to...

Possible project: #itaxonomist, combining taxonomic names, DOIs, and ORCID to measure taxonomic impact

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Imagine a web site where researchers can go, log in (easily) and get a list of all the species they have described (with pretty pictures and...
Friday, August 07, 2015

Testing the GBIF taxonomy with the graph database Neo4J

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I've been playing with the graph database Neo4J to investigate aspects of the classification of taxa in GBIF's backbone classificat...
Tuesday, August 04, 2015

Possible project: extract taxonomic classification from tags (folksonomy)

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Note to self about a possible project. This PLoS ONE paper: Tibély, G., Pollner, P., Vicsek, T., & Palla, G. (2013, December 31). Extr...
Friday, July 31, 2015

Towards a new BioStor

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One of my pet projects is BioStor , which has been running since 2009 (gulp). BioStor extracts articles from the Biodiversity Heritage Libra...
Tuesday, July 28, 2015

Modelling taxonomic names in databases

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Quick notes on modelling taxonomic names in databases, as part of an ongoing discussion elsewhere about this topic. Simple model One mode...
Monday, July 27, 2015

The Biodiversity Data Journal is not machine readable

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In my ( previous post ) I discussed the potential for the Biodiversity Data Journal (BDJ) to be a venue for nano (or near-nano publications...

Nanopublications and annotation: a role for the Biodiversity Data Journal?

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I stumbled across this intriguing paper: Do, L., & Mobley, W. (2015, July 17). Single Figure Publications: Towards a novel alternative...
Thursday, July 23, 2015

Purposeful Games and the Biodiversity Heritage Library

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. @BioDivLibrary Had a quick play of the Beanstalk OCR correction game http://t.co/fjUAFssKQu , lack of context is off-putting #bhlib — Ro...
Wednesday, July 22, 2015

Altmetrics, Disqus, GBIF, JSTOR, and annotating biodiversity data

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Browsing JSTOR's Global Plants database I was struck by the number of comments people have made on individual plant specimens. For exa...

Steve Baskauf on RDF and the "Rod Page Challenge"

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Steve Baskauf has concluded a thoughtful series of blog posts on RDF and biodiversity informatics with http://baskauf.blogspot.co.uk/2015/07...
Thursday, June 25, 2015

Biodiversity Data Journal data lost on the way to GBIF and EOL

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Two ongoing challenges in biodiversity informatics are getting data into a form that is usable, and linking that data across different proje...
Wednesday, June 24, 2015

Thoughts on ReCon 15: DOIs, GitHub, ORCID, altmetric, and transitive credit

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I spent last Friday and Saturday at ( Research in the 21st Century: Data, Analytics and Impact , hashtag #ReCon_15 ) in Edinburgh. Friday 1...

Visualising Geophylogenies in Web Maps Using GeoJSON

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I've published a short note on my work on geophylogenies and GeoJSON in PLoS Currents Tree of Life : Page R. Visualising Geophylogenies...
Tuesday, May 19, 2015

Text mining for museum specimen identifiers

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Text mining for museum specimen identifiers #TDM http://t.co/BsFXSAZJpK cc @rdmpage @robgural thoughts? — Ross Mounce (@rmounce) May 19,...
Thursday, May 14, 2015

The value of ION to GBIF

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This a quick writeup of an analysis I did to make the case that the list of names held by the Index of Organism Names (ION) (part of Thomso...