Charting taxonomic knowledge through ontologies and ranking algorithms - Post-print at GFZ

For those who are interested in reading our paper on Taxonrank , feel free to download a post-print copy at: http://edoc.gfz-potsdam.de/gfz/get/13007/0/d8b09c133462792c99eb6a163a6c5601/13007.pdf

TaxonRank is a ranking algorithm based on bibliometric analysis and Internet page ranking algorithms. TaxonRank uses published synonymy list data stored in TaxonConcept, a taxonomic information system. The basic ranking algorithm has been modified to include a measure of confidence on species identification based on the Open Nomenclature notation used in synonymy list, as well as other synonymy specific criteria...

iPhylo: Patenting biodiversity tools

Software patents are a real pain!
Especially when claimed by members of a research community. I was quite shocked when I read Rod Page's post Patenting biodiversity tools .
Even worse to see that the same organizations - like uBio, which I was a big fan of - which make massive use of freely available information do apply for software patents!

By claiming a software patent they reserve the rights to prohibit others to use the same methods to handle biodiversity data and the uBio patent goes pretty far...

Biodiversity informatics is not the research area to earn the big money. So in this particular research context do we have to assume such patents aim to hinder scientific progress? Or what else can be the intention of such patents?

A preprint archive for the geosciences

Today two interesting blog posts about getting hold of geoscientific papers have been published: The Open Source Paleontologist lists several ways to find and retrieve pdfs on your own. Dave Hone picks this up and complains a bit about those people who are too lazy to use these resources but are asking copies directly from the authors-thus causing extra work.

Surely, there are a variety of possibilities to find relevant literature on the web. But the majority of geoscientific papers are still published in commercial, closed access journals. So even if you found your artcle on Google Scholar, you'll frequently end on a page asking you for your credit card, unless you work for an institution which can afford the necessary licenses or it was publishe in an Open Access journal.

Open Access is a fine thing and many interesting papers already appear in open access journals such as PLOS. The idea certainly will become even more popular in the future. But in my opinion it is unrealistic to assume that researchers will favor open access journals for their top results when they have the chance to get their 'Nature paper'.
Other disciplines have reacted on this dilemma and provide and maintain so called preprint archives such as Arxiv. A preprint is a draft of a scientific paper that has not yet been published in a scientific journal. Preprint archives enable authors to quickly circulate their results and most important: copies of archived preprints are freely available!

Unfortunately, there is no dedicated geoscientific preprint archive :(( You can find geoscientific preprints in some institutional repositories and postprints on some homepages etc.., but there is no common access point.

But it should be there! Could a geo preprint archive be a community effort? Of cource it had to include the community, but could a community driven archive work?
Alternatively, libraries could take on that responsibility. So... geolibrarians could you hear me? Give us a working geo preprint archive, ..please.. (maybe you could call it Geoxiv;) ).
Sure, motivating the geo community to contribute will not be an easy job, but maybe one just has to start?

Geosciences e-Journals

Bruno Granier just sent an interesting link to the paleonet newsgroup:
Geosciences e-Journals is a new portal for freely available (Open Access) geoscientific journals. It provides an impressive collection of links to open access journals and contains much more valuable information such as editorial board members, author instructions etc..

GPeerReview: Rumours about a new Google peer review tool

Some blogs, e.g. DigitalKoans or NeuroDojo have reported about a new "Google" peer review tool called GPeerreview. Despite the leading G in it's name it certainly is not a member of the Google family but simply is published at and hosted by "Google Code" which led to some confusion.

However, the concept of GPeerreview is very interesting and might influence the future of scientific publishing. GPeerreview is mainly a piece of software, "a command-line tool that makes it simple to write a review of someone's work and digitally".

But the review concept itself significantly differs from the traditional peer review process, as the author of a (electronic) publications would have much more influence on the whole procedure, and it would allow authors to use a peer review process outside the world of scientific journals, e.g on their homepages and -halleluja!- blogs!

This is a short summary of features from their homepage:

With GPeerReview, you can:

• Publish immediately (and get reviews later),
• Seek an unlimited number of reviews,
• Verify the integrity of the reviews,
• Verify the credibility of the reviewers,
• Publish without limitation on format, style, or number of pages,
• Maintain complete copyright ownership of your works, and
• Enhance the acclaim of your already-published works.