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iPhylo

Rants, raves (and occasionally considered opinions) on phyloinformatics, taxonomy, and biodiversity informatics. For more ranty and less considered opinions, see my Twitter feed.ISSN 2051-8188. Written content on this site is licensed under a Creative Commons Attribution 4.0 International license.
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ChallengeElsevierVideoCiências da Computação e da InformaçãoInglês
Publicados

Elsevier have released this video about the challenge, featuring a few of the contestants. I couldn't get my act together in time to send anything useful, and having seen the 16 gigabytes song (full version here), I'm glad I didn't -- there's just no way I could compete with Michael Greenacre and Trevor Hastie.

BioguidDOIJACCOpenRefOpenURLCiências da Computação e da InformaçãoInglês
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One of the judges for the Elsevier Article 2.0 Contest is Andrew Perry, whose blog has some posts on Noel O'Boyle's OpenRef idea (see DOI or DOH? Proposal for a RESTful unique identifier for papers). Andrew discusses some implementations he has come up with, and compares OpenRef with OpenURL. This prompted me to add OpenRef-style identifiers to bioGUID's OpenURL resolver.

Article 2.0ContestElsevierMashupCiências da Computação e da InformaçãoInglês
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Chris Freeland's tweet alterted me to the Elsevier Article 2.0 Contest: Elsevier are clearly looking for ideas (they also have their Grand Challenge), and there's been some interesting commentary on the Article 2.0 contest.

EOLPressCiências da Computação e da InformaçãoInglês
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Watch CBS Videos Online CBS News Sunday Morning Segment on the EOL. All fun stuff (Paddy skewering the interviewer who fails to recognise an echidna), but still long on promises and short on actual product.

ApacheDOIMediawikiRewriteCiências da Computação e da InformaçãoInglês
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One problem with my cunning plan to use Mediawiki REDIRECTs to handle DOIs is that some DOIs, such as those that BioOne serves based on SICIs contain square brackets, [ ], which conflicts with wiki syntax.

Bibliographic CouplingBibliometricsChallengeCitationData CouplingCiências da Computação e da InformaçãoInglês
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Bibliographic coupling is a term coined by Kessler (doi:10.1002/asi.5090140103) in 1963 as a measure of similarity between documents. If two documents, A and B, cite a third, C, then A and B are coupled. I'm interested in extending this to data, such as DNA sequences and specimens. In part this is because within the challenge dataset I'm finding cases where authors cite data, but not the paper publishing the data.

Digital LibraryDOIIdentifiersLibraryCiências da Computação e da InformaçãoInglês
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Duncan Hull alerted me to his paper "Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web" ( PloS Computational Biology , doi:10.1371/journal.pcbi.1000204). Here's the abstract: It's an interesting read, and it also cites my bioGUID project.

GenbankJSONOpenURLCiências da Computação e da InformaçãoInglês
Publicados

Following on from adding specimens to my OpenURL resolver, I've added support for GenBank records. Either an OpenURL request such as http://bioguid.info/openurl?id=genbank:DQ502033, or the short URL http://bioguid.info/genbank/DQ502033 will resolve the GenBank record for accession number DQ502033.

DOIGUIDsMediawikiNamesSemantic WebCiências da Computação e da InformaçãoInglês
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Thinking more and more about using Mediawiki (or, more precisely, Semantic Mediawiki) as a platform for storing and querying information, rather than write my own tools completely from scratch. This means I need ways of modelling some relationships between identifiers and objects. The first is the relationship between document identifiers such as DOIs and metadata about the document itself.

CodeExtensionsGoogle BooksMediawikiCiências da Computação e da InformaçãoInglês
Publicados

Following on from the previous post, I wrote a simpe Mediawiki extension to insert a Google Book into a wiki page. Written in a few minutes, not tested much, etc. To use this, copy the code below and save in a file googlebook.php in the extensions directory of your Mediawiki installation.