Thursday, August 02, 2012

Google Knowledge Graph using data from BBC and Wikipedia

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Google's Knowledge Graph can enhance search results by display some structured information about a hit in your list of results. It'...
Tuesday, July 24, 2012

Dear GBIF, please stop changing occurrenceIDs!

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If we are ever going to link biodiversity data together we need to have some way of ensuring persistent links between digital records. This ...
Monday, July 23, 2012

Microbiome as climate, macrobiome as weather, and a global model of biodiversity

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Half-baked idea time. Thinking about projects such as the Earth Microbiome Project and Genomic Observatories , the recent GBIC2012 meeting...
Friday, July 20, 2012

Figshare and F1000 integrate data into publication: could TreeBASE do the same?

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Quick thoughts on the recent announcement by figshare and F1000 about the new journals being launched on the F1000 Research site. The arti...
Tuesday, July 17, 2012

Building a BHL Africa: BHL in a box

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Was going to post this as a comment on the BHL blog but they use Blogger's native comment system, which is horrible, and it refused to a...
Friday, July 13, 2012

Sometimes the mess taxonomy creates drives me nuts

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Playing with some sequence data I found numerous Plasmodium sequences from the following paper: Werner, E. B. ., Taylor, W. R., & Holde...
Thursday, July 12, 2012

Dimly lit taxa - guest post by Bob Mesibov

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The following is a first for iPhylo, a guest post by Bob Mesibov . Rod Page introduced 'dark taxa' here on iPhylo in April 2011. He...
Wednesday, July 11, 2012

Citations, Social Media & Science

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Quick note that Morgan Jackson ( @BioInFocus ) has written nice blog post Citations, Social Media & Science inspired by the fact that t...
Friday, July 06, 2012

Post GBIC2012 thoughts

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I'm back from Copenhagen and GBIC2012 . The meeting spanned three fairly intense days (with the days immediately before and after also w...
Sunday, July 01, 2012

Using orthographic projections to map organism distributions

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For a current project I'm currently working I show organism distributions using data from GBIF, and I display that data on a map that us...
Friday, June 29, 2012

Planet management, GBIF, and the future of biodiversity informatics

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Next week I'm in Copenhagen for GBIC , the Global Biodiversity Informatics Conference. The goal of the conference is to: ...convene expe...
Thursday, June 28, 2012

Where is the "crowd" in crowdsourcing? Mapping EOL Flickr photos

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In any discussion of data gathering or data cleaning the term "crowdsourcing" inevitably comes up. A example where this approach ...
Wednesday, June 27, 2012

UUIDs

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Just for future reference: @ rdmpage To make it more concise, help tracking etc — figshare (@figshare) June 22, 2012
Monday, June 25, 2012

More fictional taxa and the myth of the expert taxonomic database

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I know I'm starting to sound like a broken record, but the more I look, the more taxonomic databases seem to be full of garbage. Databas...
Tuesday, June 19, 2012

70,000 articles extracted from the Biodiversity Heritage Library

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Just noticed that BioStor now has just over 70,000 articles extracted from the Biodiversity Heritage Library . This number is a little ...
Monday, June 18, 2012

BHL and text-mining: some ideas

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Some quick notes on possibilities for text-mining BHL (in rough order of priority). Any text-mining would have to be robust to OCR errors. I...

Fictional taxa

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Anyone who works with taxonomic databases is aware of the fact that they have errors. Some taxonomic databases are restricted in scope to a ...
Friday, June 15, 2012

BHL to PDF workflow

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Just some random thoughts on creating searchable PDFs for article extracted from BHL.
Thursday, June 14, 2012

Taxonomy and the nine billion names of God

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In Arthur C. Clarke's short story The Nine Billion Names of God Tibetan monks hire two programmers to help them generate all the the po...
Wednesday, June 13, 2012

Visualising differences between classifications using cluster maps

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As part of a project to build a tool to navigate through taxonomic names and classifications I've become interested in quick ways to com...