January 14, 2013 in Access to Information, Bibliographic, Campaigning, Featured, News, Open Access, Open Data, Open Government Data, Policy

Aaron Swartz, coder, writer, archivist and activist, took his own life in New York on Friday. Aaron worked tirelessly to open up and maximise the societal impact of information in three areas which are central to our work at the Foundation: public domain cultural works, public sector information, and open access to publicly funded research. He was one of the original architects behind the Internet Archive’s Open Library project, which aims to create ‘one web page for every book’. While he was there we compared notes about trying to automatically estimatewhich works are in the public domain in different countries around the world. This was part of a broader vision to enable public access to the public domain, and to ensure that digitisation initiatives result in open digital copies of public domain works that everyone is free to use and enjoy, not just copies owned and protected by large corporations who might sell or restrict access to the world’s heritage. Around this time Aaron and I met in San Francisco to co-draft a petition to the Library of Congress to encourage them to take a leading role in opening up data from the world’s libraries and memory institutions. This was several years before a wave of institutions started explicitly opening up data about their holdings. We remained in contact regarding his work on open government data in the US. Aaron was involved in drafting the highly influential 8 principles for open government data. We wanted to try to better coordinate developments on either side of the Atlantic. Later he was in the papers for downloading around a fifth of the US government’s huge Public Access to Court Records (PACER) system, around 780 gigabytes, and releasing it for free to the public (access was usually charged by the page) – which earned him an FBI file. In his 2008 Guerilla Open Access Manifesto Aaron argued that “the world’s entire scientific and cultural heritage, published over centuries in books and journals, is increasingly being digitized and locked up by a handful of private corporations” and, “in the grand tradition of civil disobedience”, urged internet users to “fight back”:

We need to take information, wherever it is stored, make our copies and share them with the world. We need to take stuff that’s out of copyright and add it to the archive. We need to buy secret databases and put them on the Web. We need to download scientific journals and upload them to file sharing networks. We need to fight for Guerilla Open Access.

In 2010 he founded Demand Progress, which helped to mobilise over a million people in response to proposed legislation like the Combating Online Infringement and Counterfeits Act (COICA). In 2011 he again hit the headlines when he was arrested for downloading roughly 4 million subscription-only academic articles from JSTOR by placing a laptop in a computer cupboard at MIT and using this to gain unauthorised access to the JSTOR service. The prosecution alleged that he intended to make these articles freely available on the web. Last September the US Federal Government raised the felony count from four to thirteen, which meant that Aaron was potentially facing a total of 50+ years and a fine in the area of $4 million for his actions. His familysuggested that the case was a factor in his death – and blamed the Massachusetts U.S. Attorney’s office for “intimidation and prosecutorial overreach” and MIT for “refus[ing] to stand up for Aaron and its own community’s most cherished principles”. The president of MIT has just announced that he has ordered an investigation into their role in Aaron’s prosecution. As Peter Eckersley from the Electronic Frontier Foundation commented on Saturday:

While his methods were provocative, the goal that Aaron died fighting for — freeing the publicly-funded scientific literature from a publishing system that makes it inaccessible to most of those who paid for it — is one that we should all support.

While Aaron was deeply involved in all kinds of technical, scholarly and organising activities to promote an open digital commons and an open internet – from helping to develop RSS 1.0 and Markdown, to early sketches of the semantic web with some of its pioneers and work on the first technical implementations of the Creative Commons licenses – he also never lost sight of the bigger picture, of what it was all for. He was a talented coder and knew how to take a principled stance, but he was never one to get lost in detail or dogma. From his writings about how data-driven transparency initiatives are not enough to effect change in themselves, to his guide to developing software that addresses real needs, he was always aware of the fact that using the information, technology and the internet to change the world is not easy, and requires graft, skill, scrutiny, critical reflection and taking risks. Aaron’s passing is a tremendously sad and significant loss. Long live his legacy.   To find out more about Aaron’s life and works, you can look at his writings and the memorial site set up by his family. You can also read tributes from Tim Berners-Lee, Cory Doctorow, Brewster Kahle, Lawrence Lessig, andErik Moeller, and read obituaries and news articles on the BBC, Forbes, Gigaom, the Guardian, the Huffington Post, the New York Times, Techdirt, the Telegraph and Wired. In tribute, hundreds of academics have startedtweeting links to their research papers using the hashtag #pdftribute. The Internet Archive has started an Aaron Swartz Collection.

Since January 2012, I have been posting a monthly summary of Open-Access-related activities pertaining to Wikimedia projects as part of the GLAM Newsletter on the Wikimedia Outreach wiki. I have also occasionally contributed Tool Testing reports to the same GLAM newsletter, usually taking OA-related materials as examples.

I am posting these reports also here on the blog in order to reach out to a wider audience. This breaks some of the formatting, so please go to the respective wiki page to see things in a proper setting, including proper attribution.

Links to all Open Access reports posted so far: January, February, March, April, May, June, July, August, September, October, November, December.

Links to all Tool Testing reports posted so far: January, February, December.

Text is available under the Creative Commons Attribution/Share-Alike License 3.0. Licenses of images and media files used in the reports may differ but are always compatible with reuse in a CC BY-SA 3.0 environment.

Open Access Report

< GLAM‎ | Newsletter‎ | December 2012‎ | Contents

This Month in GLAM – Volume II, Issue XII, December 2012 Normal version • Single page version

 

OPEN ACCESS REPORT

1 year Open Access File of the Day

A bat in flight at night. Open Access File of the Day on December 11, 2011.

1 year Open Access File of the Day

On December 1, the Open Access File of the Day initiative turned one year. Since December 2011, a file originating from an open access source has been posted on a daily basis, the only exception being January 18, 2012, when a copy of theResearch Works Act article served as Open Access File of the Day for the duration of the SOPA blackout. During the first year, the main prerequisite for a file to be featured this way was that it be used at least twice across Wikimedia projects outside user space, and on the occasion of the anniversary, that criterion was raised to a usage of three times or more. About 400 files have been posted so far, originating from some 40 journals, half of which are published by BioMed Central. The most frequent sources of the files were PLOS Biology (136 files), PLOS ONE (76) and ZooKeys (40). According to BaGLAMa (see also the Tool testing report), these 400 files gathered a total of 10 million page views in December 2012, which is almost half of the 23 million for the entire category Open access (publishing), home to about 15,000 files (two thirds of which have been uploaded over the last few months by the Open Access Media Importer. On the occasion of the anniversary, this issue of the Open Access report ends with a listing of not only the files featured in December 2012 but also those early ones featured in December 2011, when no Open Access Report was compiled that they could have been included in.

Articles started this month

Growth of the number of open access repositories indexed in ROAR.

According to TreeViews, 30 articles on OA topics have been started this month across languages, including

• cs:Autoarchivace
• cs:ROAR
• en:Molecular Brain
• nl:BMC Cancer
• nl:Biology Direct
• no:arXiv

Open Access Media Importer

Gallery

The following files represent a selection of what has been uploaded by the Open Access Media Importer this month. If you can think of wiki pages where these files could be useful, please put them in there or let us know.

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WikiProject Open Access

The following news from WikiProject Open Access have been posted this month:

 

• December 30: A video of a distal phalanx of a thumb of an ancient hominid, Orrorin tugenensis, is featured on the Main Page of Wikimedia Commons under Media of the Day. It was originally published in PLOS ONE in 2010 and uploaded to Commons by the Open Access Media Importer Bot. Traffic stats: Main Page, video, Distal phalanx article, Thumb article, Orrorin tugenensis article.

 

• December 27: A video of a Pocillopora meandrina coral in the fringing reef off Lizard Island, Australia, is featured on the Main Page of Wikimedia Commons under Media of the Day. It was originally published in PLOS ONE last week and uploaded to Commons by the Open Access Media Importer Bot. Traffic stats: Main Page, video, Pocillopora meandrina article, Fringing reef article, Lizard Island article.

 

• December 23: A video of a Maritime Pine demonstrating gravitropism is featured on the Main Page of Wikimedia Commons under Media of the Day. It was originally published in BMC Plant Biology in 2010 and recently uploaded to Commons by the Open Access Media Importer Bot. Traffic stats: Main Page, video, Maritime Pine article, Gravitropism article.

 

• December 10: A video of developing Xenopus laevis embryos (haploid, diploid and cybrid) is featured on the Main Page of Wikimedia Commonsunder Media of the Day. It was originally published in PLOS Biology in 2011 and recently uploaded to Commons by the Open Access Media Importer Bot. One of the authors of that paper was John Gurdon, who is to receive this year’s Nobel Prize in Physiology or Medicine today, along with Shinya Yamanaka, for their work on stem cell therapy. Traffic stats: Main Page, video, Xenopus laevis article, haploid article, diploid article, cybrid article, John Gurdon article, Nobel Prize in Physiology or Medicine article, Shinya Yamanaka article, stem cell therapy article.
• December 9: Open Access report in the November 2012 issue of This month in GLAM. Traffic stats.

 

• December 9: A video of a single cardiomyocyte beating, five days after purification from cell culture, is featured on the Main Page of Wikimedia Commonsunder Media of the Day. It was originally published in PLOS ONE in 2011 and recently uploaded to Commons by the Open Access Media Importer Bot. One of the authors of that paper was Shinya Yamanaka, who is to receive this year’s Nobel Prize in Physiology or Medicine tomorrow, along with John Gurdon, for their work on stem cell therapy. Traffic stats: Main Page, single cardiomyocyte beating, five days after purification from cell culture.ogv video, Cardiac muscle article, Shinya Yamanaka article, Nobel Prize in Physiology or Medicine article, John Gurdon article, stem cell therapy article.

 

• December 3: A video of a pregnant bull shark at the Shark Reef Marine Reserve, Fiji, is featured on the Main Page of Wikimedia Commonsunder Media of the Day. It was originally published in PLOS ONE in 2011 and recently uploaded to Commons by the Open Access Media Importer Bot. Traffic stats: Main Page, video, Bull shark article, Fiji article.
• December 1: The Open Access File of the Day turns one year.

Open Access File of the Day

The following files have been featured as Open Access File of the Day in December 2011 and December 2012:

2011

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  31 December:Salamanders are a model system for the study of limb regeneration.
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  30 December: Anatomy of the human ear – editable version.
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  29 December:Bradypodion taeniabronchum on the watch.
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  28 December: A lissencephalic human brain.
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  27 December:Tyrannosaurus with skin infection.
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  26 December: Leaf mines by Phyllocnistis hyperpersea larvae.
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  25 December:Chlorobalius leucoviridis mimicking the song of its prey.
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  24 December: The production and diffusion of nitric oxide (NO) (white) in the cytoplasm (green) of clusters of conifer cells one hour after mechanical agitation.
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  23 December: A male Oligoxystre diamantinensis.
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  22 December: Mimicry in Heliconius butterflies.
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  21 December: A sow with suckling pigs.
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  20 December: The chromosomes of a women.
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  19 Dec 2011: Rice terraces in the Philippines.
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  18 December:Baltimartyria rasnitsyni.
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  17 December: Pomacea canaliculata eggs.
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  16 December: Bee waggle dance.
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  15 December: Shimmering bees drive hornet away.
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  14 December: Northwest Crown Fire Experiments in Canada.
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  13 December: HIV on macrophage.
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  12 December: The sea slug Pleurobranchaea meckelii.
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  11 December: A bat in flight.
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  10 December: Samples in a seedbank.
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  9 December: Chalcolithic leather shoe from the Areni-1 cave.
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  8 December: Soft tissue reconstruction of the Longdan tiger.
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  7 December: Qualia of sound.
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  6 December: Burying behaviour of an adult sandfish (Scincus scincus).
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  5 December: Genetic subdivision in the giraffe based on mitochondrial DNA sequences.
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  4 December: Apertural view of the snail Rapana venosa.
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  3 December: Genome of Arthrobacter arilaitensis.
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  2 December: A Giant Haasts eagle attacking a New Zealand moa.
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  1 December: Actenoides concretus.

2012

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  December 31: Ocularfundus aspect ofretinoblastoma
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  December 30: spawningPocillopora meandrina
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  December 29: A silvery mole rat.
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  December 28:Achelousaurus nasal openings
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  December 27: Example of a Scan for quantitative trait loci on a single chromosome
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  December 26: AGalápagos tortoise.
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  December 25: Fruiting bodies of the slime bacterium Myxococcus xanthus.
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  December 24: Electron microscopy ofProchlorococcus
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  December 23: Kent distribution of three point sets representing bond angle relations in a protein backbone.
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  December 22: The tiger beetle Omus dejeanii.
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  December 21: expression of FABP7 in mouse brains
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  December 20:Mycosphaerella graminicola chromosomes
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  December 19:Diplodocoidea cladogram
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  December 18: Drawing ofRhinopithecus strykeri
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  December 17: Rostral migratory stream of amouse
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  December 16: Cataglyphis fortis experiencing head-wind on a slippery substrate
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  December 15: Clytus arietes
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  December 14:Atelopus franciscus male territorial call
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  December 13: The mushroom Boletopsis nothofagi.
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  December 12: Alec Jeffreys
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  December 11: The modernEmu (centre) and extinctKing Island Emu (right) with human outline shown approximately to scale.
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  December 10: Blenniella gibbifrons jumping
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  December 9: Ebolavirusparticles
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  December 8: Ankylosaurustail terminology
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  December 7: Structural organization of the heart of the mosquito Anopheles gambiae
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  December 6: A Magicicadachorus.
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  December 5: Adélie Penguins.
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  December 4: Anodonthyla(frog) feet
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  December 3: The animal with the longest valid scientific name: the soldier fly Parastratiosphecomyia sphecomyioides.
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  December 2: Burrunan Dolphin jumping
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  December 1: Larvae ofCulex mosquitoes.

 

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IN THIS ISSUE

DECEMBER 2012

• France report
• Italy report
• Netherlands report
• Spain report
• UK report
• USA report
• Open Access report
• Tool testing report
• Calendar

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Tool Testing Report 

< GLAM‎ | Newsletter‎ | December 2012‎ | Contents

This Month in GLAM – Volume II, Issue XII, December 2012 Normal version • Single page version

 

TOOL TESTING REPORT

BaGLAMa is back

By Daniel Mietchen

This photograph is used on en:Isaac Newton, as it depicts a descendant of the tree that supposedly yielded the apple that helped Newton develop his understanding ofgravity. Seen in the December 2012 BaGLAMa record for “Cambridge University Botanic Garden”.

One of the most important tools for tracking the usage of files uploaded to Wikimedia Commons is BaGLAMa, which provides a summary of pageviews of Wikimedia pages that contain images from specific categories on Commons (seeJanuary 2012 report). It also provides for an easy way to compare the stats for any two months on record (see February 2012 report). The tool has had trouble finishing its job in recent months, due to the stressed Toolserver. Magnus Manske, the developer behind BaGLAMa, has taken this as an occasion to review and rework his code, with the result that the tool can now be used again. He also re-calculated the stats for those earlier months where a record was missing, which resulted in an overestimation of the respective pageviews, since category membership was taken as of the time of running, not as of the month in question (which is difficult to implement and would drain even more sources from the Toolserver). The stats for December 2012 had been computed within a few days, and on the basis of the results for Category:Open access (publishing), it can be seen that the combined pageviews for images from that category rose from about 16.5 million last December (discounting an image featured on the Main Page of the Russian Wikipedia) to 23 million in December 2012. In the following, I would like to highlight another use case of BaGLAMa – that of helping to identify articles that use a relatively large number of images from the target category. As an example, articles are listed that use at least five files from Category:Open access (publishing).

• it:Dardo (malacologia)

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• de:Morbus Fabry

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• no:Ordensbånd (sommerfugler)

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• ca:Paedophryne/ de:Paedophryne/ en:Paedophryne/ et:Paedophryne/ id:Paedophryne/ zh:童蛙属

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• it:Open access

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• it:Lista delle specie di Theridiidae, A-D

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• Italy report
• Netherlands report
• Spain report
• UK report
• USA report
• Open Access report
• Tool testing report
• Calendar

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I am posting these reports also here on the blog in order to reach out to a wider audience. This breaks some of the formatting, so please go to the respective wiki page to see things in a proper setting.

Links to all Open Access reports posted so far: January, February, March, April, May,June, July, August, September, October, November.

Text is available under the Creative Commons Attribution/Share-Alike License 3.0. Licenses of images and media files used in the reports may differ but are always compatible with reuse in a CC BY-SA 3.0 environment.

< GLAM‎ | Newsletter‎ | November 2012‎ | Contents

This Month in GLAM – Volume II, Issue XI, November 2012 Normal version • Single page version

 

OPEN ACCESS REPORT

The Open Access Media Importer at full speed; Publishers deliver inconsistent XML to PubMed Central; Importing from other sources

Open Access Media Importer

While walking, an Eland antelope emits multiple signals related to its fighting ability, including click sounds caused by knee movements.

After having been approved as a bot on Commons late in October, the Open Access Media Importer ran almost continuously throughout November, scanning PubMed Central for suitably licensed scholarly articles with supplementary multimedia and importing these into Wikimedia Commons, to a current total of well over 9,000, raising the number of files under Category:Open access (publishing) and its subcategories to almost 14,000 by the end of the month. The bot attempts to provide the files with categories based on keywords, subject categories or MeSH terms supplied by the journal, by PubMed Central or by PubMed for the corresponding article. This sometimes leads to miscategorizations, often to overcategorization, and occasionally to no categories at all. At present, the files are spread over more than 20,000 categories, almost 10% of which had to be created on the occasion (e.g. for well over a hundred journals). Some of these categories (e.g. Caenorhabditis elegans or Green fluorescent proteins) are now filled with hundreds of files, which will eventually have to be distributed across more fine-grained categories. For many topics covered by PubMed Central (mostly biomedicine), there are thus now way more multimedia files available than the current Wikipedia entries (if they exist) can accommodate. For further examples, see actin cytoskeleton (on the English Wikipedia and on Commons), Gap junction (Wikipedia; Commons) or Woronin body (Wikipedia; Commons). The review of the categorization of the files and of these new categories themselves continues – a process that you can facilitate by checking out (thanks to the overburdened Toolserver) a few of them and adding or removing categories as appropriate. If you can think of wiki pages where these files could be useful, please put them in there. Bug fixes continued but shifted in focus from providing functionality to minimizing the effects of inconsistent and incorrect metadata available from PubMed Central.

Metadata at PubMed Central

The most prominent issue with the XML is that of incorrect or self-contradicting licensing statements. While this had been noticed already in spring (e.g. “licensed under a Creative Commons Attr0ibution 3.0 License (by-nc 3.0)” – yes, with a typo on top of it, in an article from Orthopedic Reviews, published by PagePress), actually deploying the bot to larger parts of the database made it clear that the phenomenon is rather common and not restricted to small and lesser known publishers. The Open Access Media Importer analyzes the XML of articles stored in PubMed Central’s Open Access subset. That XML is being delivered there by the individual journals or publishers, which provides the basis for a plethora of individual styles that may or may not be close to the actual specifications of the National Library of Medicine‘s Document Type Definition (now named JATS).

License mismatch in Stem Cells (Dayton, Ohio), published by Wiley-Blackwell: while the machine-readable license is CC BY, the human-readable version has a non-commercial clause (PMC3468739).

Similar license mismatch – with an added “Share Alike” component – in mBio, published by Oxford University Press (PMC3000542).

Besides the two journals highlighted in the figures, other journals affected by contradictory license statements include Evolutionary Applications (Wiley-Blackwell),Traffic (Copenhagen, Denmark) (Wiley-Blackwell), Cellular Microbiology (Wiley-Blackwell), Cytotheraphy (Informa), The American Journal of Tropical Medicine and Hygiene (American Society of Tropical Medicine and Hygiene), The Febs Journal‏‎ (Wiley-Blackwell), Hepatology (Baltimore, Md.) (Wiley-Blackwell), Journal of Cellular Physiology (Wiley-Blackwell) and Database: The Journal of Biological Databases and Curation (Oxford University Press). At the Journal of Neurochemistry (Wiley-Blackwell), the self-contradictory notice “Re-use of this article is permitted in accordance with the Creative Commons Deed, Attribution 2.5, which does not permit commercial exploitation.” is even displayed directly on the article’s page. The closest match to the term “Creative Commons Deed, Attribution 2.5″ would be theCreative Commons Attribution 2.5 Generic License (CC BY 2.5), which is indeed linked from the XML and does permit commercial exploitation. While contradictions between machine-readable and human-readable license statements are one sort of problem, many journals – including those published by PLOS, which account for the majority of the bot’s uploads so far – do not provide a license link at all or mix up the license and copyright tags in other ways. On a related note, even articles clearly and unambiguously labeled CC BY may occasionally contain materials incompatible with such licensing, and some articles in journals otherwise using Creative Commons licenses occasionally publish something under Crown copyright or similar conditions, causing the bot to skip the articles. Such licensing mess raises a number of questions: if the licensing for a given article agrees in its human- and machine-readable version on PubMed Central, can we then be sure that this information is correct? This is the case, for instance, with the journal Molecular Vision. What if the same article does not have any licensing statement at the journal’s site (or in the XML there), or if the journal’s copyright policy states CC BY-NC-ND as the only option? What if Google finds several articles from the same journal that are also labeled as CC BY? The mismatch between stated licenses and actual licensing conditions also makes it difficult to assess, in an automated fashion, what amount of audio, video or other materials is available from PubMed Central under Wikimedia-compatible licenses. For some plots on the matter, see this blog post, which also highlights another frequent issue: that of a mismatch between the actual MIME type and that stated in the XML, as in the following example:

The MIME type of this supplementary video file from a PLOS ONE article is indicated at PubMed Central to be audio/wav. For another video from the same article, the MIME type is given as application/msword. In both cases, the XML at the journal’s website states the MIME types correctly.

As a rough estimate, MIME type mismatches of this kind affect on the order of 10% of the supplementary files in the database. Since this translates to hundreds of multimedia files, the bot now attempts to determine the MIME type of all supplementary materials and chooses those that are, in fact, audio or video, irrespective of what the XML states about them, thereby even covering cases in which the XML makes no statement about the MIME types . The bot naturally fails, however, in cases when suitably licensed articles do have supplementary multimedia files but these are not mentioned in the XML available from PMC (another case: journal;PMC) Another reason preventing the import of some suitably licensed materials is that files are frequently hidden in zip archives, which the bot ignores for the time being. Once suitably licensed multimedia have been identified as such, they have to be converted to a format accepted at Wikimedia Commons, i.e. OGG. This does not always work, since some authors use rather unusual file formats, or the metadata about the files (e.g. the length of a video) is incorrect or not stated at all. Most journals have a disclaimer that proper functioning of supplementary materials is within the authors’ responsibility, but it would be nice to establish a standard for testing that supplementary files submitted to journals actually convert properly to common standard formats. Further issues arise when the files are converted and need to be associated with their metadata in Commons style: Sometimes, there is no description whatsoever of supplementary files, or the description of several files is lumped together in a way that the bot cannot parse. Some minor issues include line breaks in article titles ortypos in categories or keywords provided by the journal, which the bot uses for the initial categorization of the files. A problem not really solved so far is that of duplicate detection – while this works well for images, this is not the case for multimedia files, since multiple copies of a file will normally have different hashes.

Gallery

The following files represent a selection of what has been uploaded by the Open Access Media Importer this month. If you can think of wiki pages where these files could be useful, please put them in there or let us know. For metadata about the files, please click on the Menu button.

Videos

Can you guess the research question addressed in the corresponding scholarly article?

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Sound files

Can you guess what these sounds represent?

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Beyond PubMed Central

While PubMed Central is the only database currently spidered by the Open Access Media Importer, it is designed in a modular fashion, such that other sources could easily be plugged in. To lay the ground for such future work, a number of (manual) test uploads from such potential sources have been made this month.

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  The metamorphosis of the protochordateBranchiostoma japonicum- the first file on Wikimedia Commons originating from a data paper (published inDataset Papers in Biology).
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  A “singing” iceberg – the first file from a data repository (PANGAEA).
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  Bugula flabellata - another file from a data repository (Dryad).

 

WikiProject Open Access

The following news from WikiProject Open Access have been posted this month:

 

• November 2: A video of a juvenile tentacled snake attacking a fish (a fathead minnow) is featured on the Main Page of Wikimedia Commonsunder Media of the Day. It was originally published in PLOS ONE in 2010 and uploaded to Commons by the Open Access Media Importer Bot. Traffic stats: Main Page, video, Tentacled snake article, fathead minnow article.

 

• November 4: An X-ray video of an American alligator while breathing is featured on the Main Page of Wikimedia Commons under Media of the Day. It was originally published in PLOS ONE in 2009 and uploaded to Commons by the Open Access Media Importer Bot. Traffic stats: Main Page, video, American alligator article, X-ray article.

 

• November 6: A video of a raspy cricket fabricating silk is featured on the Main Page of Wikimedia Commons under Media of the Day. It was originally published in PLOS ONE in February and uploaded to Commons by the Open Access Media Importer Bot. Traffic stats: Main Page,video, Raspy cricket article, Silk article.

 

• November 8: A video of chimpanzees sharing a papaya fruit is featured on the Main Page of Wikimedia Commons under Media of the Day. It was originally published in PLOS ONE in 2007 and uploaded to Commons by the Open Access Media Importer Bot. Traffic stats: Main Page,video, Chimpanzee article, Papaya article.

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• November 10: An audio recording of the giggling call of a spotted hyena is featured on the Main Page of Wikimedia Commons under Media of the Day. It was originally published in BMC Ecology in 2010 and uploaded to Commons by the Open Access Media Importer Bot. Traffic stats:Main Page, sound file, Giggling article, Spotted hyena article.

 

• November 11: A video of Emperor Penguins producing traveling waves is featured on the Main Page of Wikimedia Commons under Media of the Day. It was originally published in PLOS ONE in 2011 and uploaded to Commons by the Open Access Media Importer Bot. Traffic stats: Main Page, video, Emperor penguin article, Traveling wave article.
• November 11: Open Access report in the October 2012 issue of This month in GLAM. Traffic stats.

 

• November 13: A video of a pelagic thresher shark and a giant manta ray interacting in the presence of cleaner fish is featured on the Main Pageof Wikimedia Commons under Media of the Day. It was originally published in PLOS ONE in 2011 and uploaded to Commons by the Open Access Media Importer Bot. Traffic stats: Main Page, video, Pelagic thresher shark article, Giant manta ray article, Cleaner fish article.

 

• November 15: A video of a moth caterpillar defending itself and parasitoid wasp pupae against a stink bug is featured on the Main Page of Wikimedia Commons under Media of the Day. It was originally published in PLOS ONE in 2008 and uploaded to Commons by the Open Access Media Importer Bot. Traffic stats: Main Page, video, Thyrinteina article, Glyptapanteles article, Pentatomoidea article.

 

• November 16: A video of a Meioglossus psammophilus acorn worm is featured on the Main Page of Wikimedia Commons under Media of the Day. It was originally published in PLOS ONE last week and uploaded to Commons by the Open Access Media Importer Bot. Traffic stats:Main Page, video, Acorn worm article.
• November 16: The Open Access Media Importer Bot passed the mark of 5000 imported files.

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• November 17: An audio recording of an iceberg is featured on the Main Page of Wikimedia Commons under Media of the Day. It was originallypublished in 2005 in PANGAEA as part of the supplement to a paper published in Science. Traffic stats: Main Page, sound file, iceberg article.

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• November 19: An audio recording of calling song of a 17-year periodic cicada Magicicada septendecula is featured on the Main Page of Wikimedia Commons under Media of the Day. It was originally published in 2007 in PLOS ONE and uploaded to Commons by the Open Access Media Importer Bot. Traffic stats: Main Page, sound file, Magicicada septendecula article.

 

• November 20: A video - recorded with an acoustic camera – of an African bush elephant rumbling with its nose is featured on the Main Page of Wikimedia Commons under Media of the Day. It was originally published in PLOS ONE last week and uploaded to Commons by the Open Access Media Importer Bot. Traffic stats: Main Page, video, African bush elephant article.

 

• November 22: A video of a Manduca sexta larva on Nicotiana attenuata, reacting to experimental stimulation, is featured on the Main Page of Wikimedia Commons under Media of the Day. It was originally published in eLife last month and uploaded to Commons by the Open Access Media Importer Bot. Traffic stats: Main Page, video, Manduca sexta article, Nicotiana attenuata article.

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• November 26: An audio recording of a territorial call of a male toad Atelopus franciscus is featured on the Main Page of Wikimedia Commonsunder Media of the Day. It was originally published in 2011 in PLOS ONE and uploaded to Commons by the Open Access Media Importer Bot. Traffic stats: Main Page, sound file, Atelopus franciscus article.

 

• November 27: A video of astronaut Charles Duke trying to recover a hammer he had dropped on the surface of the moon is featured on theMain Page of Wikimedia Commons under Media of the Day. It was originally recorded during the Apollo 16 mission, then republished in PLOS ONE in 2009 and recently uploaded to Commons by the Open Access Media Importer Bot. Traffic stats: Main Page, video, Charles Duke article, Apollo 16 article.

 

• November 28: A video of the solitary bee Colletes cunicularius pseudocopulating on the flower labellum of the orchid Ophrys lupercalis isfeatured on the Main Page of Wikimedia Commons under Media of the Day. It was originally published in BMC Evolutionary Biology in 2010 and recently uploaded to Commons by the Open Access Media Importer Bot. Traffic stats: Main Page, video, Colletes article, Pseudocopulation article, Ophrys article.
• November 30: The Open Access Media Importer is featured in the Wikimedia Highlights of October 2012.

Open Access File of the Day

The following files have been featured as Open Access File of the Day this month:

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  November 30: AMagicicada cassini female laying its eggs.
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  November 29: Ahydrophilic termite(Schedorhinotermes sp.) attached to the surface of a wetted citrus leaf
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  November 28: A range of putative disease-causing mechanisms for the case of the disease progeria
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  November 27: A large male Bolitotherus cornutusundergoing a grip strengthtrial.
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  November 26: A femaleEuglossa hyacinthinaworking on the construction of her nest envelope.
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  November 25: Reconstruction of aNimbadon lavarackorummother with a juvenile.
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  November 24: SEM image of the tardigradeMilnesium tardigradum in its active state.
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  November 23: The brown lacewing Micromus variegatus.
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  November 22: Carpodacus mexicanus (finch) vocalizations
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  November 21: The fishAlticus arnoldorumperforming a jump (slow motion).
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  November 20:Larsenianthus arunachalensis, a member of the ginger family.
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  November 19: An Atlantic Yellow-nosed Albatross.
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  November 18: A Xenopus laevis female with egg batch and Xenopus tropicalis male.
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  November 17: Acoustic display of the hummingbirdArchilochus alexandri.
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  November 16: Thyrinteinacaterpillar parasitized byGlyptapanteles pupae defends against Supputius cincticeps
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  November 15:Anodonthyla theoi, dorsolateral and ventral views
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  November 14: A femaleIllacme plenipes with 662 legs.
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  November 13: Aerosteon riocoloradensis
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  November 12: maxilla fromFruitadens
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  November 11: The Garden centipede Scutigerella immaculata.
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  November 10: A femaletarantula Acanthoscurria gomesiana.
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  November 9: drawing of female of Glomeris marginata
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  November 8: Centropyge bicolor feeding onPalaemonetes
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  November 7: Archerfishshooting at prey
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  November 6: The butterflyErebia calcaria.
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  November 5: gastrulationin cybrid embryos
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  November 4: The sea slugSpurilla major.
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  November 3: Majormetabolic interactionsbetwen astrocytes andneurons.
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  November 2: Venogramshowing cerebral venous sinus thrombosis in a patient with Behçet’s disease
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  November 1: MRI scans of a microcephalic patient (right) and a healthy control (left).

 

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NOVEMBER 2012

• Africa report
• Australia and New Zealand report
• France report
• Germany report
• Italy report
• Mexico report
• Netherlands report
• Sweden report
• UK report
• USA report
• Wiki Loves Monuments report
• Open Access report
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The plot helper script now can sort data by DOI prefix, displaying publisher names. This is useful to identify high-yield sources of free content: Regarding PMC, both the Public Library of Science and BioMed Central lead by a noticeable margin. Note that quite a few publishers frequently signal the licensing conditions incorrectly in the XML they deliver to PubMed Central (see below), which probably explains, for instance, Wiley being listed third here.

Plotting data can also reveal the extent of problems in the PMC Open Access Subset:

Also, oa-cache can now selectively “forget” conversion, download and upload of materials.

Since I have not found a good way to prevent the OAMI from stalling on conversion of certain files, oa-cache convert-media now exits when conversion has not progressed for some amount of time. I already tried to debug the GStreamer pipeline – for the story so far, see this bug report. Media conversion stalling is one of the major obstacles to running the converter unattended.

Suggested by Daniel Mietchen, a new OAMI source called pmc_pmcid can now be used to import content via its PMCID. Since PMCIDs – unlike DOIs – are sequential, the seq command line tool can be used to generate a list of papers to be examined: seq 3461993 1 3491993 | ./oami_pmc_pmcid_import

The check for existing content was refactored and now happens also before downloading original files for conversion. For reasons unknown, the MediaWiki API sometimes errors out when checking for duplicates – if this happens, the OAMI now retries until it gets an answer.

Licensing proves to be a perpetual source of problems: non-free materials labeled incorrectly may be recognized as free. An example of this is the paper Nestin- and Doublecortin-Positive Cells Reside in Adult Spinal Cord Meninges and Participate in Injury-Induced Parenchymal Reaction, which has self-contradictory licensing information in the metadata XML:

<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.5/"> <license-p>Re-use of this article is permitted in accordance with the Creative Commons Deed, Attribution 2.5, which does not permit commercial exploitation. </license-p> </license>

Allowing commercial use in the machine-readable version while disallowing it in human-readable text is asking for trouble. Incorrect metadata creates additional work for humans – this is contrary to the automation approach of the OAMI.

To reduce the impact of mis-labeling, I am working on a whitelisting functionality for known-good DOI prefixes. The list was created by Daniel Mietchen, who reasoned that publishers that have a blanket policy of free licensing will not mistakenly label content as non-free – and even if they do, it is preferable to miss some free content than to import non-free content. A plot of problematic licensing metadata by DOI prefix is available.

I am posting these reports also here on the blog in order to reach out to a wider audience. This breaks some of the formatting, so please go to the respective wiki page to see things in a proper setting.

Links to all Open Access reports posted so far: January, February, March, April, May, June, July, August, September, October.

Text is available under the Creative Commons Attribution/Share-Alike License 3.0. Licenses of images and media files used in the reports may differ but are always compatible with reuse in a CC BY-SA 3.0 environment.

< GLAM‎ | Newsletter‎ | October 2012/Contents

This Month in GLAM – Volume II, Issue X, October 2012 Normal version • Single page version

 

OPEN ACCESS REPORT

Videos from Noble laureates; Open Access Week; Open Access Wikipedia Challenge; Open Access Media Importer approved

Membrane proteins are notoriously difficult to crystallize, so Kobilka and colleagues fused an easily crystallizable protein (orange) to a membrane protein (cyan) in order to facilitate the crystallization of the latter.

Videos from Noble laureates

The Nobel Prize winners were announced this month, and at least three of them have published in journals whose Creative Commons Attribution License allows for import into Wikimedia Commons: Brian Kobilka ( Chemistry) as well as John Gurdon and Shinya Yamanaka (who shared the prize for Physiology or Medicine this year). Running the Open Access Media Importer over these articles brought the following videos onto Wikimedia Commons:

• Co-authored by Gurdon:

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• Co-authored by Yamanaka:

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Physics laureate Serge Haroche has 21 papers listed on arXiv, but none of them is under a Wikimedia-compatible license.

Open Access Week

A video by Jorge Cham (of PhD Comics) on the occasion of Open Access Week 2012

The last full week in October each year is Open Access Week - an occasion for librarians, researchers, publishers, journal editors, students and others to engage in discussions around the past, present and future of Open Access and to showcase their related activities. Some of the highlights from this year include

• a guideline “How Open Is It?” has been released by SPARC, PLOS and OASPA that differentiates between different levels of access to scholarly articles, with reusability being an important aspect. Such information could be used to indicate systematically the openness of references cited on Wikimedia pages, as per Template:Open Access.
• an announcement by the publisher Institute of Physics to license its freely available journal articles under a Creative Commons Attribution License from next year on, which would make these materials reusable at Wikimedia projects.
• Wikipedia entries on Open Access Week have been started in French and Japanese

Open Access Wikipedia Challenge

The Open Access Wikipedia Challenge is an online challenge in the MOOC realm, where accepting users attempt are asked to place Open Access content from Wikimedia Commons into Wikipedia. It’s built as a social lesson in Wikipedia editing requiring no previous experience. The challenge is filleted into 6 phases each with an accompanying YouTube screencast tutorial and mini-challenge totaling 2 hours of instruction. The challenge, hosted on Peer to Peer University, gave users the guided tasks of rating journals for openness, calculating how quickly it took Gangnam Style to get onto Wikipedia, writing Wikitext, categorizing on Commons with Hot Cat, and embedding media into Wikipedia.

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  Found a new home at en:Transponder: a bumblebee (Bombus terrestris) worker with a transponder attached to its back.
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  Found a new home at en:Mechanisms of schizophrenia: artistic view of how the world feels like with schizophrenia.
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  Found a new home at ta:டாக்சோட்டைடீ: Archer fish shooting at prey.
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  Found a new home in the taxobox at en:Dendrelaphis caudolineatus.
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  The barnstar awarded after successful completion of the Open Access Week Challenge.

P2PU’s online platform allows users to track progress, to discuss the challenges, and to offer peer support, which probably makes the OAWC the first MOOC-ified Wikipedia tutorial. A special edition barnstar has been created for those who complete the challenge. Originally, the course was a celebratory measure, part of Wikipedia Loves Libraries and Open Access Week. After 21 netizens joined the course, it was decided to extend the challenge indefinitely. New and expert users are invited to sign up.

The first video associated with a PLOSarticle, from December 2003.

Open Access Media Importer approved

The Open Access Media Importer continued to be tested and refined throughout the month, leading to its approval on October 29.

Gallery

The following files represent a selection of what has been uploaded by the Open Access Media Importer this month. If you can think of wiki pages where these files could be useful, please put them in there or let us know.

Videos

Before you watch a video, consider guessing at the research question addressed in the corresponding scholarly article.

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Sound files

Can you guess what these sounds represent?

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WikiProject Open Access

 

 

The following news from WikiProject Open Access have been posted this month:

• October 1: Open Access Files of the Day now have their own category on Commons.
• October 5: A video documenting how a water droplet is being cut using a superhydrophobic knive on superhydrophobic surfaces is featured on the Main Page of Wikimedia Commons under Media of the Day. It illustrates research originally published in PLOS ONE on September 24. Traffic stats: Main Page, video, Water droplet article, Superhydrophobe article.
• October 8: A video documenting pattern formation in a computational model of dendrite growth is featured on the Main Page of Wikimedia Commons under Media of the Day. It was original published in the supplement of an article in PLOS Computational Biology in 2007 and uploaded by the Open Access Media Importer Bot. Traffic stats: Main Page, video, Pattern formation article, Dendrite article.

 

• October 9: A video documenting how muscles, skin, scales and quills are added to a skull cast of the plant-eating dinosaur  Heterodontosaurus tucki is featured on the Main Page of Wikimedia Commons under Media of the Day. It illustrates an article in ZooKeys published earlier this month. Traffic stats: Main Page, video, Heterodontosaurus tucki article.
• October 9: Open Access report in the September 2012 issue of This month in GLAM. Traffic stats.

 

• October 11: A video of a simulation of auxin transport in a plant’s meristem is featured on the Main Page of Wikimedia Commons under Media of the Day. It was originally published in PLOS Computational Biology in 2008 and uploaded by the Open Access Media Importer Bot. Traffic stats: Main Page, video, Auxin article, Growing tip article, Cell article, Primordium article.

 

• October 16: A video of an illusory motion is featured on the Main Page of Wikimedia Commons under Media of the Day. It was originally published in PLOS ONE in 2008 and uploaded by the Open Access Media Importer Bot. Traffic stats: Main Page, video, Illusory motion article.

 

• October 18: A video of a  Nerodia fasciata snake flicking its tongue towards a parvalbumin-coated lure that “smells like prey” to it is featured on the Main Page of Wikimedia Commons under Media of the Day. It was originally published in PLOS ONE in June and since uploaded by the Open Access Media Importer Bot. Traffic stats: Main Page, video, Nerodia fasciata article, Parvalbumin article, Prey article.
• October 22: Open Access Week 2012 starts. Some ideas on how to contribute are linked from en:Wikipedia:WikiProject Open Access/Open Access Week.

 

• October 22: A video of a magpie turning aggressive in the presence of a mirror is featured on the Main Page of Wikimedia Commons under Media of the Day. It was originally published in PLOS Biology in 2008 and uploaded by the Open Access Media Importer Bot. Traffic stats: Main Page, video, Pica pica article, Mirror test article.
• October 22: The Wikipedia Challenge goes live on Peer-to-Peer University. See also blog post on the OCLC blog.

 

• October 23: A video of a mudskipper vocalizing in the presence of an intruder is featured on the Main Page of Wikimedia Commons under Media of the Day. It was originally published in PLOS ONE in 2011 and uploaded by the Open Access Media Importer Bot. Traffic stats: Main Page, video, Mudskipper article, Oscillogram article, Spectrogram article.
• October 23: Examples of reusing, revising, remixing and redistributing Open Access materials in the context of Wikimedia projects are being highlighted in a blog post on the PLOS blog on the occasion of Open Access Week.

 

• October 24: A 200 fps video of a Bicolor angelfish feeding on Ghost shrimp is featured on the Main Page of Wikimedia Commons under Media of the Day. It was originally published in PLOS ONE in 2011 and uploaded by the Open Access Media Importer Bot. Traffic stats: Main Page, video, Bicolor angelfish article, Acetes article, Frame rate article.

 

• October 25: A video showing a MRI scan of the sea urchin  Psammechinus miliaris is featured on the Main Page of Wikimedia Commons under Media of the Day. It was originally published in PLOS ONE in 2011 and uploaded by the Open Access Media Importer Bot. Traffic stats: Main Page, video, MRI article, Psammechinus miliaris article.
• October 29: The Bot request for the Open Access Media Importer has been approved. The bot will now routinely spider the biomedical literature deposited in PubMed Central for articles that are licensed compatibly with reuse on Wikimedia Commons and that have audio or video files in their supplementary materials. The videos featured under under Media of the Day on Commons this month have all been uploaded during the test phase of the bot.

 

• October 30: A video of an  Aedes aegypti mosquito infected with  Wolbachia pipientis unsuccessfully trying to penetrate skin is featured on the Main Page of Wikimedia Commons under Media of the Day. It was originally published in PLOS Neglected Tropical Diseases in 2009 and uploaded to Commons by the Open Access Media Importer Bot. Traffic stats: Main Page, video, Aedes aegypti article, Wolbachia pipientis article.

• October 30: The article Pegomastax is featured on the Main Page of the German Wikipedia as part of a Halloween special of Did You Know. The formal description of this heterodontosaur genus was published in ZooKeys earlier this month. Traffic stats: Main Page, image, Pegomastax article.
• October 30: Article alerts for pages in Category:WikiProject Open Access articles are now available via a dedicated subpage of WikiProject Open Access, which is linked from the header of the project’s landing page.

Open Access File of the Day

The following files have been featured as Open Access File of the Day this month:

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  October 31: The Insular cortex ( Japanese version).
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  October 30: The Neanderthal skull La Chapelle-aux-Saints 1.
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  October 29: A  Varanus timorensis from Loré, Lautém District, East Timor.
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  October 28: Skeletal reconstruction (top) and inferred body outline (bottom) of the Cretaceous lizard  Platecarpus.
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  October 27: map of European genetic structure based on single-nucleotide polymorphismanalysis
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  October 26: Comparison of Nautilus capture rates with trapping depth
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  October 25: A male Labeotropheus fuellebornifrom Lake Malawi.
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  October 24:  Agdistis linnaei
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  October 23: Interneuron- radial glialinteractions in the developing cerebral cortex.
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  October 22: drip irrigationon loamy soil
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  October 21: Lectotype of Elimia cahawbensis.
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  October 20: A  Lamprolepis smaragdina skink.
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  October 19: Nylanderia pubens, the crazy Rasberry ant
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  October 18: Basal body of T3SS needle complex. The black line indicates 10 nanometers.
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  October 17: 3D reconstruction of the general anatomy of the small marine slug Pseudunela cornuta, based on histologicalsections.
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  October 16: map of where to find  Amphicyclotulus in Dominica
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  October 15: comparison of furcula of (A) a dinosaurand (B) a goose
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  October 14: The wonder gecko  Teratoscincus scincus.
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  October 13: A Morgan horse with silver rather than black pigments, due to the silver dapple gene.
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  MENU

  October 12: booms by Cercopithecus hamlyni
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  October 11:  Ipsa childreni, the charismatic cowrie
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  October 10: Combat between two forked fungus beetle ( Bolitotherus cornutus) males.
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  October 9: A timelapse video of how muscles, skin, scales and quills are added to a skull cast of Heterodontosaurus tucki
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  October 8: Life restorations of  Darwinius masillae
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  October 7:  Melanargia arge.
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  October 6: Mary F. Lyon, discoverer of X-chromosome inactivation.
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  October 5: Drawing of the right valve external view of Pisidium moitessierianum
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  October 4: growth depictions for Archaeopteryx
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  October 3: MRI scan of an osteochondroma.
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  October 2: Inside krill one can see (A) pregnancy (B) phytoplankton
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  October 1: A Somali wild ass,  Equus africanus somaliensis.

 

IN THIS ISSUE

OCTOBER 2012

• From the team
• USA report
• UK report
• France report
• Italy report
• Germany report
• Sweden report
• Africa report
• Open Access report
• Calendar

+ Add a comment

Introduction

The initial purpose of Open Access is to enable researchers to make use of information already known to science as part of the published literature. One way to do that systematically is to publish scientific works under open licenses, in particular the Creative Commons Attribution License that is compatible with the stipulations of the Budapest Open Access Initiative and used by many Open Access journals. It allows for any form of sharing of the materials by anyone for any purpose, provided that the original source and the licensing terms are shared alongside. This opens the door for the incorporation of materials from Open Access sources into a multitude of contexts both within and outside traditional academic publishing, including blogs and wikis.

Amongst the most active reusers of Open Access content are Wikimedia projects like the over 280 Wikipedia, Wikispecies and their shared media repository, Wikimedia Commons. In the following, a few examples of reusing, revising, remixing and redistributing Open Access materials in the context of Wikimedia projects shall be highlighted.

Reuse

An example for intensive reuse is an article from BMC Evolutionary Biology that features a number of phylogenetic trees of gastropods, along with pictorial depictions of individual species contained therein. Over a dozen of these depictions have been cropped from the figures and uploaded to Wikimedia Commons, from where they are currently being served to over 7000 pages across Wikimedia projects.

While these numbers far exceed the reuse of the average figure in scientific manuscripts, the potential for reuse has not been fully exploited yet. For instance, these phylogenetic trees have been published in a scalable format but some of the shell drawings have been included in bitmapped formats, which limits the size range at which the images can be re-used in Wikipedia articles. Furthermore, the trees have not been provided in an editable format, nor with code that could be used to reconstruct and adapt them.

A phylogenetic tree of some gastropods. // One of the tree’s species, Fusiturris similis.

Composite images like this illustrated phylogenetic tree take a lot of effort to assemble. Typical reuse scenarios — e.g. in articles on the individual species — then require decomposition and are limited by the resolution of the original figures. Source: Cunha, R. L.; Grande, C.; Zardoya, R. (2009). “Neogastropod phylogenetic relationships based on entire mitochondrial genomes”. BMC Evolutionary Biology 9: 210. doi:10.1186/1471-2148-9-210. PMC 2741453.PMID 19698157. License: CC BY 2.0.

Of course, some images are genuinely created in bitmapped formats, e.g. photographs. But why then do publishers not preserve the EXIF information that could provide valuable context in interpreting images or sound files?

Revise

In January, a species of frog — Paedophryne amauensis — made headlines as the smallest known vertebrate. It belongs to a genus whose currently six species have all been described in Open Access articles, of which the two latest ones — published one month apart — both state that there are four species. So did a map provided in one of them, and a contributor to the Polish Wikipedia — Szczureq — took the initiative to update the map accordingly, which is currently in use in about 20 Wikipedia languages in articles related to the genus. The file has since been tagged for conversion into SVG, an editable vector graphics format, so as to facilitate future updates.

A map indicating the localities at which Paedophryne species have been found. On the left is the original map published in PLOS ONE with four species. On the right is a revision that takes into account the two additional species that had been published in ZooKeys a month earlier. Sources:

• Rittmeyer, E. N.; Allison, A.; Gründler, M. C.; Thompson, D. K.; Austin, C. C. (2012). Etges, William J.. ed. “Ecological Guild Evolution and the Discovery of the World’s Smallest Vertebrate”. PLoS ONE 7: e29797.doi:10.1371/journal.pone.0029797. PMC 3256195. PMID 22253785. License: CC BY 2.5.
• Kraus, F. (2011). “At the lower size limit for tetrapods, two new species of the miniaturized frog genus Paedophryne (Anura, Microhylidae)”. ZooKeys 154: 71–88. doi:10.3897/zookeys.154.1963. PMC 3238040.PMID 22287916. License: CC BY 3.0.

Remix

Scholarly communication nowadays takes place primarily in English. Open licenses allow for materials to be translated into other languages. This is particularly relevant for topics that are being taught in schools, such as the basic anatomy of the human ear and auditory cortex, as illustrated in the following figure originally published in PLOS Biology.

(A) The human ear and frequency mapping in the cochlea. (B) Lateral view of the human brain, with theauditory cortex exposed. Source: Chittka, L.; Brockmann, A. (2005). “Perception Space—The Final Frontier”. PLoS Biology 3 (4): e137.doi:10.1371/journal.pbio.0030137. PMC 1074815. PMID 15819608. License: CC BY 2.5.

Part A of the above figure has been converted to SVG and from there adapted to Czech (with a variant), German, Spanish, Indonesian, Japanese, Polish, Potuguese, Romanianand Ukrainian, with further versions being devoid of any descriptions, numbered descriptions or detailed frequency mapping.

Part B has also been converted to SVG and from there adapted for use in the Japanese Wikipedia‘s article on the insula.

Still in the auditory system and PLOS Biology, the next figure depicts some of the key processing steps involved in auditory perception:

Sound processing in the auditory system. Source: Gollisch, T.; Herz, A. M. V. (2005). “Disentangling Sub-Millisecond Processes within an Auditory Transduction Chain”. PLoS Biology 3 (1): e8. doi:10.1371/journal.pbio.0030008. PMC 539322. PMID 15660161.License: CC BY 2.5.

For this one, too, a SVG version has been created but the file has also been remixed in another way: User:Was a bee noticed that the depicted processing chain includes neither a sound source nor a mental representation of the perceived sound, and created a new version that does, which is used on both the Japanese and Italian Wikipedias.

Redistribute

Distribution of the published literature traditionally takes place on the level of individual articles, journals or publishers but open licenses allow it to be aggregated at a cross-publisher level. For instance, the Open Access Subset at PubMed Central is now being automatically spidered for articles that (1) are licensed compatibly with reuse on Wikimedia platforms and (2) contain audio or video files. If such files have been detected, they will be downloaded from PubMed Central, converted to the open format OGG and uploaded to Wikimedia Commons, along with the accompanying metadata and suggested categories based on the article’s XML and the corresponding MeSH terms. Of course, the naming of these article-derived categories does not map one to one to categories used at Wikimedia Commons, but for known correspondances, there is another bot to fix that in a way that makes it easy for writers of Wikipedia articles to find relevant materials for illustration. This way, supplementary files — that otherwise are often neglected and rarely accessed — can live a second life in a new context. One of them, for instance, is featured on the Main Page of Wikimedia Commons today. The most recently uploaded media files from Open Access supplements can be viewed in a dedicated gallery.

In the process of setting up the bot, it became very clear that the XML supplied to PubMed Central varies widely in terms of compliance with PubMed Central guidelines and general machine readability. For instance, the XML indicates the MIME type of the supplementary files, but for about ten percent of the files, this type is indicated wrongly (e.g. for all videos in this paper), and even the licensing and copyright statements of the articles themselves are sometimes contradictory in themselves, so work remains to be done to address these issues and to further standardize the exchange of metadata.

It is interesting to note that the only permission that had to be sought in order to run the import from PubMed Central into Wikimedia Commons was actually on the Commons end, since running a bot there requires approval, which is normally granted after the bot has demonstrated compliance with relevant policies and standards. There is a caveat to such large-scale import, however: it relies on proper assertion of copyright and correct indication of licensing back at the journals and, ultimately, by the authors of the corresponding articles. This is not a given, since many scholarly authors are still far from being familiar with these legal aspects of publishing. Raising awareness of such issues amongst the scholarly, librarian and publishing communities is one of the purposes of Open Access Week, and trying to get Open Access materials used on Wikipedia (or simply checking the provenance of an image or media file used there) is a good start to familiarize oneself with the subject.

Wikifying publications

Reusing, revising, remixing and redistributing openly licensed content is easier if the materials are created in an editable fashion right from the start. The journal RNA Biology has for several years required that authors of manuscripts describing new families of RNA submit a draft for a Wikipedia entry along with their manuscript, which will go through the same peer-review process. Earlier this year, PLOS Computational Biology has taken this approach a step further by introducing Topic Pages — review articles drafted according to the guidelines of the journal and of the English Wikipedia — that are published as traditional non-editable documents in the journal and additionally also posted to the English Wikipedia, where they can be expanded and updated as the need arises. It would be nice to see further experimentation in this area, so as to increasingly integrate scholarly workflows with the Web, for which Open Access provides the first step.

From now on, I will post these reports also here on the blog in order to reach out to a wider audience.

Links to all Open Access reports posted so far: January, February, March, April, May, June, July, August, September.

Text is available under the Creative Commons Attribution/Share-Alike License 3.0. Licenses of images and media files used in the reports may differ but are always compatible with reuse in a CC BY-SA 3.0 environment.

< GLAM‎ | Newsletter‎ | September 2012‎ | Contents

This Month in GLAM – Volume II, Issue IX, September 2012 Normal version • Single page version

 

OPEN ACCESS REPORT

Open Access per default; Open Access Media Importer tests finished; Preparations for Open Access Week

Contents [hide] 1 Open Access per default; Open Access Media Importer tests finished; Preparations for Open Access Week 1.1 BOAI-10 recommendations 1.2 How open is it? 1.3 Open Access Week 1.4 Open Access Media Importer 1.4.1 Test phase finished 1.4.2 Gallery 1.4.2.1 Videos 1.4.2.2 Sound files 1.5 WikiProject Open Access 1.6 Open Access File of the Day

BOAI-10 recommendations

In February, the 10th anniversary of the Budapest Open Access Initiative, a meeting was held to look back upon that decade of open access and to discuss scenarios on how to move things forward over the next decade. The recommendations from the meeting have been released on September 12. Important from a Wikimedia perspective is that they cover licensing and designate the Creative Commons Attribution License (which is compatible with reuse on Wikimedia projects) as the default model for Open Access publishing. This will hopefully discourage publishers and authors from using licensing terms like thenon-commercial condition that prevent reuse in most educational contexts, including on Wikimedia projects.

How open is it?

While the term “Open Access” has been clearly defined in the Budapest Open Access Initiative, it is often used in the context of open access publishing or open access archiving models incompatible with that definition. In order to provide a basis for more granular assessment of the extent to which a particular resource is open, PLOS, SPARC, and OASPA have collaborated on a draft for How Open Is it?, for which public feedback is invited until Monday, October 8, 5pm EST, so that a final version can be released in time for Open Access Week (see also next section).

Open Access Week

Open Access Week is a global event aimed at highlighting the ways in which Open Access can and does impact society, and research and education in particular. Around the world, researchers, students, librarians and many others get together to share their own experiences and to raise awareness amongst others. One way to contribute to the event is to have a look at the Wikipedia articles related to Open Access in your preferred languages and to see whether they can improved by adding or modifying a few lines, by inserting a reference or illustration, or by simply improving the narrative flow or checking the spelling. Another way is to check Wikimedia Commons for files from Open Access sources and providing them with a new home in a Wikipedia article, Wiktionary entry or Wikibooks chapter. For further information, see Wikipedia:WikiProject Open Access/Open Access Week.

Open Access Media Importer presentation given to Wikimedia Germany on September 28, 2012.

Open Access Media Importer

Test phase finished

Over the course of the month, tests and bug fixes for the Open Access Media Importer continued, with the result that almost all known bugs concerning materials uploaded by the Open Access Media Importer Bot have been fixed. Their remnants in earlier uploads are currently being corrected manually, while a number of problems leading to suitable materials not being uploaded remain to be addressed. These are mostly due to non-standard markup of the XML provided by the publishers, or to non-standard file formats used by the original authors. An interesting problem that occurred on the way was that the MIME type of image and media files was stated incorrectly in about 5-10% of cases. This could be fixed by implementing a routine that tests, based on the first 4kB of a file, whether the MIME type is indeed the one that is indicated in the XML. Once the Open Access Media Importer is operational, it is intended to be handed over to Wikimedia Germany, but it remains uncertain as to whether that would be via the Toolserver,Wikimedia Labs or some other way. A more detailed report is available from a blog post.

Gallery

The following files represent a selection of what has been uploaded by the Open Access Media Importer this month. If you can think of wiki pages where these files could be useful, please put them in there or let us know.

Videos

Before you watch a video, consider guessing at the research question addressed in the corresponding scholarly article.

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Sound files

Can you guess what these sounds represent?

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WikiProject Open Access

The following notes from WikiProject Open Access have been posted this month:

• September 2: Open Access report in the August 2012 issue of This month in GLAM. Traffic stats.
• September 3: The article Trogloraptor was featured under WP:DYK (nomination) after the new family-defining genus had been described inZooKeys. Traffic stats.
• September 10: The article on the green lacewing Semachrysa jade on the German Wikipedia was featured under WP:DYK, pointing out that the species had been described with the help of Flickr and Google Docs. Traffic stats. See also August 14 entry.
• September 18: The article Lesula was featured on the Main Page of the Swedish Wikipedia after this new species of monkey (scientific name:Cercopithecus lomamiensis) had been described in PLOS ONE. Traffic stats.

Open Access File of the Day

The following files have been featured as Open Access File of the Day this month:

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  September 30: AnOncomelania hupensis hupensis snail.
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  September 29: ATaiwanophodes minorbeetle. Scale: 1mm.
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  September 28: A Nerodia fasciata snake attacking aparvalbumin-coated lure.
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  September 27: Aphanius mesopotamicus
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  September 26: Diversity of ancestral rices
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  September 25: Maize cob from the Ocampo Caves in Mexico dated to 3,890 years ago.
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  September 24: Adult female and fetalMaiacetus.
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  September 23: Biogeographic distribution of chasmosaurineceratopsid dinosaurs on the western landmass,Laramidia, during the late Campanian (~76–73 Ma).
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  September 22: A fiber-optic array for detection ofbreast cancer by way ofDiffuse Optical Tomography.
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  September 21:Bradypodion atromontanum
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  September 20: Muscle biopsy from a girl with X-linked myotubular myopathy
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  September 19: Miamira magnifica
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  September 18: Carabusrumelicus
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  September 17: Gorilla tool use
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  September 16: New Jerseyamber containing specimens of Plumalexius rasnitsyni
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  September 15:Buforaniidaegrasshoppers from theAustralian National Insect Collection.
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  September 14: Tigerphylogenetic relationships.
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  September 13: Vocalizations of the newly described monkey speciesCercopithecus lomamiensis, known to science since yesterday.
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  September 12: The rotiferBrachionus calyciflorus
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  September 11: A Volucella bombylans hoverfly.
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  September 10: Haliclystus antarcticus in the field
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  September 9: A Conepatus semistriatus skunk.
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  September 8: Map of theCahaba River and some of its tributaries.
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  September 7: Cross-section through the tail ofCarnotaurus sastrei
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  September 6: Common anatomical types ofesophageal atresia
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  September 5: Metarhizium anisopliae fungus, capable of killing more than 200 insect species including the pictured cockroach
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  September 4: The diversity and containment of coral reef systems make them good sites for testing nicheand neutral theories intheoretical ecology
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  September 3: Genomedata from the opossumMonodelphis domesticaaids understanding of the evolution of the mammalian immune system.
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  September 2: Schematic illustration of differences in neuronal specification and migration patterns between the mammalian and avian pallium
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  September 1: Thuridilla carlsoni. Locality: Lizard Island, Great Barrier Reef. The length of the slug is about 2 cm.

 

IN THIS ISSUE

SEPTEMBER 2012

• From the team
• USA report
• UK report
• Spain report
• Italy report
• Germany report
• Sweden report
• Switzerland report
• India report
• Mexico report
• Africa report
• Open Access report
• Calendar

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The modular software architecture and resulting workflow, adapted from the original proposal was quickly grasped, possibly due to being inspired by the Debian package manager apt. When discussing details, however, I realized that the documentation should explicitly mention that despite the size of the PMC Open Access Subset the OAMI can also be run with access to modest computing resources, focusing on particular documents.

Where the software will be run after the initial bulk import is done is unclear. According to Daniel Kinzler, it is not particularly suited to run on the Wikimedia Toolserver: Extracting metadata from archives and conversion of media are both processing intensive tasks while downloading and uploading are I/O-bound; additionally, quite some storage is required. Since a demonstration was not part of the visit. Daniel Kinzler now has an account on our development server to test and possibly review parts of the OAMI as soon as he finds the time to do so.

On the feature side, many incremental improvements were made: Besides bugfixes, there is now support for audio (which is converted to Vorbis); the new oa-cache subcommand update-mimetypes downloads the first 4 kB of files to supplementary materials and detects their MIME type via magic. While slow, this step is useful because some of the files in the PMC Open Access Subset are listed with a wrong type. For example, in the machine-readable version of this paper all videos are reported as being plain text.

When Daniel Mietchen came to Berlin on September 23th, we corrected some subtle bugs regarding data extraction from XML and implemented a cheap heuristic for proper (not too broad) categories – to be used in the page template, a category has to contain a space. For getting the upload done in fewer API calls, I imported a patched version of python-wikitools into our repository. Since python-wikitools was the only dependency that is not in Debian, installation is now possible with a simple git clone https://github.com/erlehmann/open-access-media-importer.git.

Jonathan Gray over on the main OKFN blog has already covered some of the most interesting details (I have listed a few other ones here), and I am reposting his entry (licensed CC BY) in full below the fold.

The notion of open access – or making research freely usable by all, without cost or legal barriers – has been in the news quite a bit this year.

It received significant media coverage on the back on the so-called Academic Spring, and subsequent high profile activities and announcements in the UK, the US and the EU.

One of the most significant milestones for open access advocates in the recent past is the Budapest Open Access Initiative, an international conference which convened experts from around the world to build consensus around a shared definition of ‘open access’. It is widely referred to as one of the defining events in the history of open access advocacy.

Ten years after this event, a diverse group of academics, advocates, librarians, and legal and policy experts met in Budapest. Today the group has issued a series of new recommendations for the next ten years of open access.

Some of the prefatory remarks to the recommendations are worth quoting in full:

Today we’re no longer at the beginning of this worldwide campaign, and not yet at the end. We’re solidly in the middle, and draw upon a decade of experience in order to make new recommendations for the next ten years. We reaffirm the BOAI “statement of principle,…statement of strategy, and…statement of commitment.” We reaffirm the aspiration to achieve this “unprecedented public good” and to “accelerate research, enrich education, share the learning of the rich with the poor and the poor with the rich, make this literature as useful as it can be, and lay the foundation for uniting humanity in a common intellectual conversation and quest for knowledge.” We reaffirm our confidence that “the goal is attainable and not merely preferable or utopian.” Nothing from the last ten years has made the goal less attainable. On the contrary, OA is well-established and growing in every field. We have more than a decade’s worth of practical wisdom on how to implement OA. The technical, economic, and legal feasibility of OA are well-tested and well-documented. Nothing in the last ten years makes OA less necessary or less opportune. On the contrary, it remains the case that “scientists and scholars…publish the fruits of their research in scholarly journals without payment” and “without expectation of payment.” In addition, scholars typically participate in peer review as referees and editors without expectation of payment. Yet more often than not, access barriers to peer-reviewed research literature remain firmly in place, for the benefit of intermediaries rather than authors, referees, or editors, and at the expense of research, researchers, and research institutions. Finally, nothing from the last ten years suggests that the goal is less valuable or worth attaining. On the contrary, the imperative to make knowledge available to everyone who can make use of it, apply it, or build on it is more pressing than ever.

If you believe in open access, the following four sections are worth reading in detail – and contain lots of ideas on policy, licensing, infrastructure, sustainability, and advocacy.

Following are a couple of excerpts that might be of particular interest to readers of the OKFN’s blog.

Firstly, while there have been no shortage of debates about the legal and practical meaning of ‘open access’ and associated questions of licensing and strategy (resulting in various inflections: strong/weak, libre/gratis, green/gold, etc), the recommendations contain a clear endorsement of a strong conception of open access which only requires attribution with the CC-BY license (which is compliant with the Open Knowledge Foundation’s Open Definition):

2.1. We recommend CC-BY or an equivalent license as the optimal license for the publication, distribution, use, and reuse of scholarly work.

• OA repositories typically depend on permissions from others, such as authors or publishers, and are rarely in a position to require open licenses. However, policy makers in a position to direct deposits into repositories should require open licenses, preferably CC-BY, when they can.
• OA journals are always in a position to require open licenses, yet most of them do not yet take advantage of the opportunity. We recommend CC-BY for all OA journals.
• In developing strategy and setting priorities, we recognize that gratis access is better than priced access, libre access is better than gratis access, and libre under CC-BY or the equivalent is better than libre under more restrictive open licenses. We should achieve what we can when we can. We should not delay achieving gratis in order to achieve libre, and we should not stop with gratis when we can achieve libre.

Secondly, they explicitly suggest that open access advocates should more closely coordinate with advocacy for other forms of openness:

The worldwide campaign for OA to research articles should work more closely with the worldwide campaigns for OA to books, theses and dissertations, research data, government data, educational resources, and source code.

If you’re interested in finding out more about the Open Knowledge Foundation’s open access activities you can join our open-access mailing list.

On the interface side, found media are now shown grouped by media type count:

Daniel Mietchen proposed a shell script to automate importing media via the pmc_doi source. As pmc_doi reads DOIs from stdin, it can be used both interactively and programmatically (for example, echo 10.1371/journal.pone.0002365 | ./oami_pmc_doi_import). Since the script is rather short and illustrates the usual workflow of running the Open Access Media Importer, it is shown below:

#!/bin/sh

# clear database to get rid of old data
./oa-cache clear-database pmc_doi

# normal workflow for OAMI
./oa-get download-metadata pmc_doi
./oa-cache find-media pmc_doi
./oa-get download-media pmc_doi
./oa-cache convert-media pmc_doi
./oa-put upload-media pmc_doi

I rewrote the code that tries to make sense of plain text licensing statements, mapping them to proper licensing URLs like http://creativecommons.org/publicdomain/zero/1.0/, correcting several bugs in the process. I am now convinced that publishers providing only plain text licensing information are one of the biggest obstacles to identifying materials that are suitable for Wikimedia Commons.

Daniel Mietchen has identified a number of articles that cause the import to fail at various stages. While I am working on correcting issues arising from my own code, I do not think that GStreamer being unable to decode a particular quicktime file or producing pixelated output are issues I will be able to solve on my own.