User talk:Metacladistics

A new bibliographical landscape

At the beginning of December, Wikidata items on individual scientific articles passed the 10 million mark. This figure contrasts with the state of play in early summer, when there were around half a million. In the big picture, Wikidata is now documenting the scientific literature at a rate that is about eight times as fast as papers are published. As 2017 ends, progress is quite evident.

Behind this achievement are a technical advance (fatameh), and bots that do the lifting. Much more than dry migration of metadata is potentially involved, however. If paper A cites paper B, both papers having an item, a link can be created on Wikidata, and the information presented to both human readers, and machines. This cross-linking is one of the most significant aspects of the scientific literature, and now a long-sought open version is rapidly being built up.

The effort for the lifting of copyright restrictions on citation data of this kind has had real momentum behind it during 2017.

But all that is just the beginning. Topics of papers are identified, authors disambiguated, with significant progress on the use of the four million

More is on the way. OABot applies the unpaywall principle to Wikipedia referencing. It has been proposed that Wikidata could assist WorldCat in compiling the global history of book translation. Watch this space.

And make promoting #1lib1ref one of your New Year's resolutions. Happy holidays, all!

Links

• WikidataCon: Giving more people more access to more knowledge, report by Peter Kraker of Open Knowledge Maps
• This is a story of my knowledge adventure in New Zealand moths via Wikicommons, Wikipedia and Wikidata, @SiobhanLeachman
• Wikidata and Arabic dialects, research paper, DOI: 10.1109/AICCSA.2017.115
• c:Commons:British Library/Mechanical Curator collection/georeferencing status, Mechanical Curator project on Commons hits 50K maps milestone
• Historical dataset on the provenance of Wikipedia text: Who wrote this?, by Tilman Bayer, WMF blogpost
• "Anyone can edit", not everyone does: Wikipedia and the gender gap (PDF), journal paper, Heather Ford and Judy Wajcman
• Alpha Zero’s "Alien" Chess Shows the Power, and the Peculiarity, of AI, MIT Technology Review, by Will Knight, December 8, 2017

Metadata on the March

From the days of hard-copy

Today Wikipedia turns 17, with worlds still to conquer. Zooming out from the individual GLAM object to the ontology in which it is set, one such world becomes apparent: GLAMs use custom ontologies, and those introduce massive incompatibilities. From a recent article by sadads, we quote the observation that "vocabularies needed for many collections, topics and intellectual spaces defy the expectations of the larger professional communities." A job for the encyclopedist, certainly. But the data-minded Wikimedian has the advantages of Wikidata, starting with its multilingual data, and facility with aliases. The controlled vocabulary — sometimes referred to as a "thesaurus" as term of art — simplifies search: if a "spade" must be called that, rather than "shovel", it is easier to find all spade references. That control comes at a cost.

Case studies in that article show what can lie ahead. The schema crosswalk, in jargon, is a potential answer to the GLAM Babel of proliferating and expanding vocabularies. Even if you have no interest in Wikidata as such, simply vocabularies V and W, if both V and W are matched to Wikidata, then a "crosswalk" arises from term v in V to w in W, whenever v and w both match to the same item d in Wikidata.

For metadata mobility, match to Wikidata. It's apparently that simple: infrastructure requirements have turned out, so far, to be challenges that can be met.

Links

• 1lib1ref campaign starts today, see m:The Wikipedia Library/1Lib1Ref: also #1lib1ref introductory video by Felix Nartey
• Funders should mandate open citations, article 9 January 2018 in Nature by David Shotton
• From snowflake to avalanche: Possibilities of using free citation data in libraries, translation from the German original of Annette Klein, Mannheim University Library
• outreach:GLAM/Newsletter/December 2017/Contents/WMF GLAM report
• Why Mickey Mouse’s 1998 copyright extension probably won't happen again: Copyrights from the 1920s will start expiring next year if Congress doesn't act, Timothy B. Lee, 8 January 2018, Arstechnica

Wikidata as Hub

One way of looking at Wikidata relates it to the

Another perspective might be likened to a photographic negative of that one: Wikidata as an already-functioning Web hub. Over half of its properties are identifiers on other websites. These are Wikidata's "external links", to use Wikipedia terminology: one type for the DOI of a publication, another for the VIAF page of an author, with thousands more such. Wikidata links out to sites that are not nominally part of the semantic web, effectively drawing them into a larger system. The crosswalk possibilities of the systematic construction of these links was covered in Issue 8.

Wikipedia:External links speaks of them as kept "minimal, meritable, and directly relevant to the article." Here Wikidata finds more of a function. On viaf.org one can type a VIAF author identifier into the search box, and find the author page. The Wikidata Resolver tool, these days including Open Street Map, Scholia etc., allows this kind of lookup. The hub tool by maxlath takes a major step further, allowing both lookup and crosswalk to be encoded in a single URL.

Links

• What galleries, libraries, archives, and museums can teach us about multimedia metadata on Wikimedia Commons, Wikimedia Foundation blogpost, 29 January 2018, by Jonathan Morgan and Sandra Fauconnier
• m:The Wikipedia Library/1Lib1Ref/Connect, 2018 institutional participation in the #1lib1ref campaign
• Newspeak House queries, created at 3 February 2018 event in London led by Magnus Manske
• Cochrane–Wikipedia Initiative, Wikipedia Signpost special report 5 February 2018, by JenOttowa
• What is the Last Question?, 5 February 2018

Milestone for mix'n'match

Around the time in February when Wikidata clicked past item Q50000000, another milestone was reached: the mix'n'match tool uploaded its 1000th dataset. Concisely defined by its author, Magnus Manske, it works "to match entries in external catalogs to Wikidata". The total number of entries is now well into eight figures, and more are constantly being added: a couple of new catalogs each day is normal.

Since the end of 2013, mix'n'match has gradually come to play a significant part in adding statements to Wikidata. Particularly in areas with the flavour of digital humanities, but datasets can of course be about practically anything. There is a catalog on skyscrapers, and two on spiders.

These days mix'n'match can be used in numerous modes, from the relaxed gamified click through a catalog looking for matches, with prompts, to the fantastically useful and often demanding search across all catalogs. I'll type that again: you can search 1000+ datasets from the simple box at the top right. The drop-down menu top left offers "creation candidates", Magnus's personal favourite. m:Mix'n'match/Manual for more.

For the Wikidatan, a key point is that these matches, however carried out, add statements to Wikidata if, and naturally only if, there is a Wikidata property associated with the catalog. For everyone, however, the hands-on experience of deciding of what is a good match is an education, in a scholarly area, biographical catalogs being particularly fraught. Underpinning recent rapid progress is an open infrastructure for scraping and uploading.

Congratulations to Magnus, our data

Links

• Wikipedia goes 3D allowing users to upload .STLs for digital reference, Beau Jackson for 3dprintingindustry.com, February 22 2018
• WikiCite report (video)
• Formal publication and announcement of ISBN citation dataset, see Twitter post, February 23 2018
• Plotting the Course Through Charted Waters, workshop on data visualization literacy from Mikhail Popov, Wikimedia Foundation
• Using Wikidata to build an authority list of Holocaust-era ghettos, Nancy Cooey, United States Holocaust Memorial Museum, February 12 2018
• Why Should You Learn SPARQL? Wikidata! Mark Longair, blogpost November 29 2017
• Back to the future: Does graph database success hang on query language?, George Anadiotis for Big on Data, March 5 2018

The 100 Skins of the Onion

Open Citations Month, with its eminently guessable hashtag, is upon us. We should be utterly grateful that in the past 12 months, so much data on which papers cite which other papers has been made open, and that Wikidata is playing its part in hosting it as "cites" statements. At the time of writing, there are 15.3M Wikidata items that can do that.

Pulling back to look at open access papers in the large, though, there is is less reason for celebration. Access in theory does not yet equate to practical access. A recent LSE IMPACT blogpost puts that issue down to "heterogeneity". A useful euphemism to save us from thinking that the whole concept doesn't fall into the realm of the oxymoron.

Some home truths: aggregation is not content management, if it falls short on reusability. The PDF file format is wedded to how humans read documents, not how machines ingest them. The salami-slicer is our friend in the current downloading of open access papers, but for a better metaphor, think about skinning an onion, laboriously, 100 times with diminishing returns. There are of the order of 100 major publisher sites hosting open access papers, and the predominant offer there is still a PDF.

From the discoverability angle, Wikidata's bibliographic resources combined with the

• Crossref as a new source of citation data: A comparison with Web of Science and Scopus, CWTS blogpost 17 January 2018, Nees Jan van Eck, Ludo Waltman, Vincent Larivière, Cassidy Sugimoto
• Citations with identifiers in Wikipedia, figshare dataset
• Making women more visible online—with Wikidata tools!, Wikimedia blogpost 29 March 2018 by Sandra Fauconnier
• Village pump discussion, Turn on mapframe? We’re ready if you are reaches conclusions
• The Power of the Wikimedia Movement beyond Wikimedia, Forbes 28 March 2018, Michael Bernick
• Tracing stolen bitcoin, blogpost 26 March 2018 by Ross J. Anderson

ScienceSource funded

The Wikimedia Foundation announced full funding of the ScienceSource grant proposal from ContentMine on May 18. See the ScienceSource Twitter announcement and 60 second video.

A medical canon?

The proposal includes downloading 30,000 open access papers, aiming (roughly speaking) to create a baseline for medical referencing on Wikipedia. It leaves open the question of how these are to be chosen.

The basic criteria of

Two well-known but rather different areas where such considerations apply are tropical diseases and alternative medicine. There are also a number of potential downloading troubles, and these were mentioned in Issue 11. There is likely to be a gap, even with the guideline, between conditions taken to be necessary but not sufficient, and conditions sufficient but not necessary, for candidate papers to be included. With around 10,000 recognised medical conditions in standard lists, being comprehensive is demanding. With all of these aspects of the task, ScienceSource will seek community help.

Links

• d:Wikidata:Lexicographical data, Wikidata's multi-lingual dictionary project gets going
• Ordia tool, a basic search interface for Wikidata lexemes and forms
• OpenRefine tool 3.0, May update allows wrangling of tabular information into Wikidata
• d:Wikidata:WikiProject British Politicians pushes ahead with data modelling and imports
• #1Lib1Ref Returns for a Second Time in 2018, IFLA blogpost 25 May 2018, second chance this year to participate in referencing Wikipedia

Respecting MEDRS

Facto Post enters its second year, with a Cambridge Blue (OK, Aquamarine) background, a new logo, but no Cambridge blues. On-topic for the

Close to home also, a template, called {{

• World Cup scorers bubble chart, by the league in which they play, query run on Wikidata
• Timeline of discoveries of natural satellites in the solar system, query run on Wikidata
• 4800 Welsh portraits added to Wikimedia Commons and Wikidata, National Library of Wales blogpost 27 June 2018, by Jason.nlw
• The "deaditors" of Wikipedia, Hay Kranen blogpost, 15 June 2018
• Six dimensions of open access, polemical tweet, 17 June 2018

Plugging the gaps – Wikimania report

Officially it is "bridging the gaps in knowledge", with Wikimania 2018 in Cape Town paying tribute to the southern African concept of ubuntu to implement it. Besides face-to-face interactions, Wikimedians do need their power sources.

Facto Post interviewed Jdforrester, who has attended every Wikimania, and now works as Senior Product Manager for the Wikimedia Foundation. His take on tackling the gaps in the Wikimedia movement is that "if we were an army, we could march in a column and close up all the gaps". In his view though, that is a faulty metaphor, and it leads to a completely false misunderstanding of the movement, its diversity and different aspirations, and the nature of the work as "fighting" to be done in the open sector. There are many fronts, and as an eventualist he feels the gaps experienced both by editors and by users of Wikimedia content are inevitable. He would like to see a greater emphasis on reuse of content, not simply its volume.

If that may not sound like radicalism, the Decolonizing the Internet conference here organized jointly with Whose Knowledge? can redress the picture. It comes with the claim to be "the first ever conference about centering marginalized knowledge online".

Links

• ScienceSource focus list (shortcut WD:SSFL on Wikidata), project to tag a first-pass open access medical bibliography on Wikidata, and also overcome the systematic biases in the medical literature by curation.
• Wikimedia Foundation and Kiwix partner to grow offline access to Wikipedia, Wikimedia Foundation blogpost 18 July 2018.
• Wikipedia's upcoming Cape Town conference will tackle the issue of diversity, Jamie Matroos, 2 July 2018.
• VideoWiki, a video version of Wikipedia.
• Search Full-Text within 4M+ Books, by MEK, The Open Library Blog, 14 July 2018
• More than 5,000 German scientists have published papers in pseudo-scientific journals, NDR, 19 July 2018.

Neglected diseases

To grasp the nettle, there are

A major aspect of neglect is found in tracking

From an encyclopedic point of view, lack of research also may mean lack of high-quality references: the core medical literature differs from primary research, since it operates by aggregating trials. This bibliographic deficit clearly hinders Wikipedia's mission. The ScienceSource project is currently addressing this issue, on Wikidata. Its Wikidata focus list at WD:SSFL is trying to ensure that neglect does not turn into bias in its selection of science papers.

Links

• Wikipedia, Wikidata, and citations, a census, August 2 2018, blogpost by Magnus Manske
• The rise of Wikidata as a linked data source August 6, 2018, by Karen Smith-Yoshimura on OCLC Research blog
• Where do Mayors Come From: Querying Wikidata with Python and SPARQL, August 1 2018, Parametric Thoughts blog
• Newspapers On Wikipedia Update: Initial Wikidata Pass 9 August 2018, Mike Caulfield
• Google Scholar, Web of Science, and Scopus: a systematic comparison of citations in 252 subject categories Alberto Martín-Martín, Enrique Orduna-Malea, Mike Thelwall, Emilio Delgado López-Cózar, arxiv.org, submitted on 15 August 2018

The science publishing landscape

In an ideal world ... no, bear with your editor for just a minute ... there would be a format for scientific publishing online that was as much a standard as

Links

• ImageGrid SPARQL query for the Art+Feminism focus list on Wikidata. Run and then scroll ...
• The TABernacle tool for Wikidata editing, by Magnus Manske, has been upgraded. Demo with the ScienceSource focus list and main subjects: with a WiDar login you can edit directly in the table cells.
• Enslaved: People of the Historic Slave Trade, Michigan State University project for a
  linked open data
  platform. Quote: "Disambiguating and merging individuals across multiple datasets is nearly impossible given their current, siloed nature."
• As the Linked Data for Production (LD4P) project finishes its initial two-year cycle and moves into LD4P2, a list of its BIBFRAME and other RDF tools.
• Machine Learning with and for Semantic Web Knowledge Graphs, detailed slide pack by Heiko Paulheim, University of Mannheim.
• In Europe, Scientists Need to Share Their Research for Free if They Want Government Funding, Futurism, by Kristin House, 5 September 2018.

Wikidata imaged

Around 2.7 million Wikidata items have an illustrative image. These files, you might say, are Wikimedia's stock images, and if the number is large, it is still only 5% or so of items that have one. All such images are taken from Wikimedia Commons, which has 50 million media files. One key issue is how to expand the stock.

Indeed, there is a tool. WD-FIST exploits the fact that each Wikipedia is differently illustrated, mostly with images from Commons but also with fair use images. An item that has sitelinks but no illustrative image can be tested to see if the linked wikis have a suitable one. This works well for a volunteer who wants to add images at a reasonable scale, and a small amount of SPARQL knowledge goes a long way in producing checklists.

It should be noted, though, that there are currently 53 Wikidata properties that link to Commons, of which P18 for the basic image is just one. WD-FIST prompts the user to add signatures, plaques, pictures of graves and so on. There are a couple of hundred monograms, mostly of historical figures, and this query allows you to view all of them. commons:Category:Monograms and its subcategories provide rich scope for adding more.

And so it is generally. The list of properties linking to Commons does contain a few that concern video and audio files, and rather more for maps. But it contains gems such as P3451 for "nighttime view". Over 1000 of those on Wikidata, but as for so much else, there could be yet more.

Go on. Today is Wikidata's birthday. An illustrative image is always an acceptable gift, so why not add one? You can follow these easy steps: (i) log in at https://tools.wmflabs.org/widar/, (ii) paste the Petscan ID 6263583 into https://tools.wmflabs.org/fist/wdfist/ and click run, and (iii) just add cake.

Links

• Now Wikidata is six, Signpost Special Report
• Find out how @TheContentMine are attempting to mine scientific and medical literature to improve the accuracy of Wikipedia., Wikimedia UK tweet and video ScienceSource and the Semantic Web
• sciencesource-pmc-licenses tool by Oravrattas to extract Creative Commons license information from PubMed Central pages, created at the Cambridge Wikidata Workshop
• Whizzy use of SPARQL to map the London Underground system, whizzed past on Twitter.
• Wikidata birthday events mapped by SPARQL, too
• d:Wikidata:Sixth Birthday/Message from dev team

WikiCite issue

GLAM ♥ data — what is a gallery, library, archive or museum without a catalogue? It follows that Wikidata must love librarians. Bibliography supports students and researchers in any topic, but open and machine-readable bibliographic data even more so, outside the silo. Cue the WikiCite initiative, which was meeting in conference this week, in the Bay Area of California.

In fact there is a broad scope: "Open Knowledge Maps via SPARQL" and the "Sum of All Welsh Literature", identification of research outputs, Library.Link Network and Bibframe 2.0, OSCAR and LUCINDA (who they?), OCLC and Scholia, all these co-exist on the agenda. Certainly more

Wikimedians generally are not aware of the tech background that can be assumed, unless they are close to current training for librarians. A baseline definition is useful here: "bash, git and OpenRefine". Compare and contrast with pywikibot, GitHub and mix'n'match. Translation: scripting for automation, version control, data set matching and wrangling in the large, are on the agenda also for contemporary library work. Certainly there is some possible common ground here. Time to understand rather more about the motivations that operate in the library sector.

Links

• Wikidata and Libraries: Facilitating Open Knowledge, book chapter by Mairelys Lemus-Rojas, metadata librarian and Lydia Pintscher, Wikidata Product Manager, from Leveraging Wikipedia: Connecting Communities of Knowledge (2018)
• LD4P and WikiCite: Opportunities for collaboration, WikiCite 2018 program abstract, Christine Fernsebner Eslao of Harvard Library Information and Technical Services and Michelle Futornick, Linked Data for Production Program Manager at Stanford University
• Shell Lessons for Librarians, Library Carpentry lesson
• At-risk content on Flickr, blogpost 3 November 2018, Andrew Gray
• Toward an Abstract Wikipedia, recent white paper by Wikidata founder Denny Vrandečić (Google)

Learning from Zotero

Besides the handiness of Zotero's warehousing of personal citation collections, the Zotero translator underlies the citoid service, at work behind the VisualEditor. Metadata from Wikidata can be imported into Zotero; and in the other direction the zotkat tool from the University of Mannheim allows Zotero bibliographies to be exported to Wikidata, by item creation. With an extra feature to add statements, that route could lead to much development of the focus list (P5008) tagging on Wikidata, by WikiProjects.

There is also a large-scale encyclopedic dimension here. The construction of Zotero translators is one facet of Web scraping that has a strong community and open source basis. In that it resembles the less formal mix'n'match import community, and growing networks around other approaches that can integrate datasets into Wikidata, such as the use of OpenRefine.

Looking ahead, the thirtieth birthday of the World Wide Web falls in 2019, and yet the ambition to make webpages routinely readable by machines can still seem an ever-retreating mirage. Wikidata should not only be helping Wikimedia integrate its projects, an ongoing process represented by Structured Data on Commons and lexemes. It should also be acting as a catalyst to bring scraping in from the cold, with institutional strengths as well as resourceful code.

Links

• Zotero Comes to Google Docs, Zotero blogpost by Dan Stillman, 19 October 2018.
• Category:Wikipedians who use Zotero
• T115158 Write a Zotero translator and document process for creating new Zotero translator and getting it live in production, long Phabricator thread 2015–17.
• Zotero Translators, documentation from zotero.org.
• Home page on GitHub for Zotero translator Javascript
• Example translator, for Wikisource.
• m:Structured Data on Commons/Newsletter/2018-12-07

Everything flows (and certainly data does)

Recently Jimmy Wales has made the point that

Headlines about data breaches are now familiar, but the unannounced circulation of information raises other issues. One of those is Gresham's law stated as "bad data drives out good". Wikipedia and now Wikidata have been criticised on related grounds: what if their content, unattributed, is taken to have a higher standing than Wikimedians themselves would grant it? See Wikiquote on a misattribution to Bismarck for the usual quip about "law and sausages", and why one shouldn't watch them in the making.

Wikipedia has now turned 18, so should act like as adult, as well as being treated like one. The Web itself turns 30 some time between March and November this year, per

• Wikipedia:Wikipedia Day for 18th birthday celebrations
• WMUK video page, with "fake news", Jimmy Wales, Wikidata and more (health warning for those with tune allergy)
• Why Wikipedia’s Medical Content Is Superior, Stephen Harrison, 28 January 2019, Slate
• Olivia Colman reveals struggle with Wikipedia over age, Naomi Gordon, 28 January 2019, harpersbazaar.com
• Making Wikidata visible, Martin Poulter blogpost, 24 January 2019, Bodleian Digital Library
• Inventory, Magnus Manske blogpost, 24 January 2019, on Wikidata tech support for an image donation by Cleveland Museum of Art

What is a systematic review?

Systematic reviews are basic building blocks of evidence-based medicine, surveys of existing literature devoted typically to a definite question that aim to bring out scientific conclusions. They are principled in a way Wikipedians can appreciate, taking a critical view of their sources.

Most likely it would, but the arcana of systematic reviews and how they add value would still need formal handling. The

Actually these questions lack originality. It should be noted though that

Links

• Evidence-Based Practice: Appraise, resources page from Duke University Medical Library & Archives.
• What should Cochrane do next?, Bad Science blogpost 5 November 2014, Ben Goldacre.
• Cambridge (UK) Science Festival event, How do scientific discoveries become clinical medicine?, ScienceSource workshop for ContentMine 23 March 2019, with systematic review process diagram. Also on Eventbrite for tickets, taking place in Makespace, 16 Mill Lane.
• PROSPERO database of PRISMA, for registration of systematic review protocols.
• Process wonkery thread, wikien-l mailing list, September 2006.
• Meta-Analysis, xkcd cartoon.

When in the cloud, do as the APIs do

Half a century ago, it was the era of the

The term

• Wikidata as a semantic framework for the Gene Wiki initiative, 2016 paper by Andrawaag and others, commenting inter alia on the role of the API on Wikidata
• Working With Wikibase From Go, Digital Flapjack blogpost 26 November 2018, Michael Dales, developer for ScienceSource using
  golang
  , with a software engineer's view on Wikibase and the MediaWiki API
• Dealing with the Rust, Magnus Manske blogpost 12 March 2019, on the Rust language and the MediaWiki API
• mw:API:RecentChanges, mediawiki.org page on the API for access to "recent changes" on a wiki
• wikitech:Analytics/AQS/Pageviews, wikitech.wikimedia.org for the Pageview API, giving Wikimedia traffic information
• xkcd cartoon, API Guide

Completely clouded?

Talk of cloud computing draws a veil over hardware, but also, less obviously but more importantly, obscures such intellectual distinction as matters most in its use. Wikidata begins to allow tasks to be undertaken that were out of easy reach. The facility should not be taken as the real point.

Coming in from another angle, the "executive decision" is more glamorous; but the "administrative decision" should be admired for its command of facts. Think of the attitudes

Semantic Web and TDM – a ContentMine view

Two dozen issues, and this may be the last, a valediction at least for a while.

It's time for a two-year summation of ContentMine projects involving TDM (

Wikidata and now Structured Data on Commons represent the overlap of Wikimedia with the Semantic Web. This common ground is helping to convert an engineering concept into a movement. TDM generally has little enough connection with the Semantic Web, being instead in the orbit of machine learning which is no respecter of the semantic. Don't break a taboo by asking bots "and what do you mean by that?"

The

Links for participation

• http://sciencesource-review.wmflabs.org/, review tool link in the left-hand sidebar at http://sciencesource.wmflabs.org/wiki/Main_Page

The review tool requires a log in on sciencesource.wmflabs.org, and an OAuth permission (bottom of a review page) to operate. It can be used in simple and more advanced workflows. Examples of queries for the latter are at d:Wikidata_talk:ScienceSource project/Queries#SS_disease_list and d:Wikidata_talk:ScienceSource_project/Queries#NDF-RT issue.

Please be aware that this is a research project in development, and may have outages for planned maintenance. That will apply for the next few days, at least. The ScienceSource wiki main page carries information on practical matters. Email is not enabled on the wiki: use site mail here to Charles Matthews in case of difficulty, or if you need support. Further explanatory videos will be put into commons:Category:ContentMine videos.