User talk:Petermr

Welcome!

Hello, and welcome to Wikipedia! Thank you for your contributions. I hope you like the place and decide to stay. Here are a few good links for newcomers: I hope you enjoy editing here and being a Wikipedian! Please sign your name on talk pages using four tildes (~&#126;); this will automatically produce your name and the date. If you have any questions, check out Where to ask a question or ask me on my talk page. Again, welcome! - UtherSRG (talk) 13:02, 5 December 2005 (UTC)
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Serogroup
Hi. This article doesn't really say anything. Are you planning on expanding it with information on exactly what 'Serogroup' is? Otherwise it might be deleted.

This was done as part of a class activity. We found many references to 'serogroup' in Wikipedia and elsewhere but no explanation. I couldn't even find it in a dictionary on the Web. So this stub is really a call for help from anyone who can give even a semi-authoritative description.

Petermr 13:16, 25 February 2006 (UTC)

By the way, those templates are at Userboxes :-) --Malthusian (talk) 22:44, 23 February 2006 (UTC)

Category:Wikipedian chemist
Hi Peter, on the WikiProject page you have linked yourself to User:Peter Murray-Rust, not Petermr. As for the Category, I am not convinced we need it. We do not have a userbox that puts people into this category, so I doubt it will catch on. I think you should have discussed this on the talk page of the WikiProject before creating it. Regards, Brian Duke 12:12, 2 April 2006 (UTC)

Peter, lets keep the discussion here in one place. Your talk page is now on my watch list (suggestion - change your preferences so everything you edit automatically goes on your watchlist). Being the other side of the world, my message to you last night was the last thing I did before going to bed. I think the place to discuss the category is Wikipedia talk:WikiProject Chemistry. I suppose some people might want it as there are several sub-projects and it would list everybody. WP is trying to move from lists to categories, but some people do not like the Wikipedian categories - not central to writing an encyclpedia.

Take a look at Using Jmol to display molecular models. That is right up your street. It is my current project but I am having to rely on others who have root access to various wikis. Progress is slow. Nico, who is running the new Jmol wiki, got it working in a fashion on the Folding@Home wiki, but I have tried to repeat this in the CompChem wiki with no success. The last I heard from Nico, he was going to develop his approach further yesterday on the Jmol wiki. I hope he is successfull. WP needs Jmol on the chemicals pages. Brian, --Bduke 21:33, 2 April 2006 (UTC)

Image copyright problem with Image:2bix.jpg
Thanks for uploading Image:2bix.jpg. However, the image may soon be deleted unless we can determine the copyright holder and copyright status. The Wikimedia Foundation is very careful about the images included in Wikipedia because of copyright law (see Wikipedia's Copyright policy).

The copyright holder is usually the creator, the creator's employer, or the last person who was transferred ownership rights. Copyright information on images is signified using copyright templates. The three basic license types on Wikipedia are open content, public domain, and fair use. Find the appropriate template in Image copyright tags and place it on the image page like this:.

Please signify the copyright information on any other images you have uploaded or will upload. Remember that images without this important information can be deleted by an administrator. If you have any questions, feel free to contact me, or ask them at the Media copyright questions page. Thank you. --Hetar 04:54, 4 May 2006 (UTC)

Let me know, if you need help
Peter, good to have you here, too. Let me know if you need any help with Wikipedia since I have already edited some things;-) Best, Joerg JKW 22:51, 9 May 2006 (UTC)
 * O.k. and do not forget to sign you messages with the four tildes;-) I am pretty sure you can work the copyright thing out. Otherwise ask just students if they can create some new images or use talk pages on a higher level. JKW 23:04, 9 May 2006 (UTC)

Suppliers 'dispute'
Dear Peter, I still have the 'dispute' about the chemical suppliers in the back of my head. What do you think about the following suggestion (and the accompanying .. 'yes, but how?'): Would it be an idea to make a page comparable to the ISBN search engine (e.g. Special:Booksources&isbn=0002570122) working on the CAS number. Such a page could contain an infinite list with suppliers, making the data easily accessible, as well as (and probably more important) searches into many other search-engines. As announced, if the answer to this question is 'yes!' .. how are special pages made (I saw you are into cheminformatics .. hope I am asking the right person)? --Dirk Beetstra 07:23, 6 June 2006 (UTC)

Hi Peter,

The correct machine is at Special:Booksources, sometimes these links don't work (may be depending on browser). But that is the type of page I mean.

I read something about the InChI, seems like a good plan. But to implement it maybe less functional (YET!!). I mean, the functionality that I am thinking about is a page, that links into as many external sources as possible, based on one searchterm. E.g. with CAS-number, it is possible to make search-URL's into many suppliers, and a lot of other web-based engines (people really using the link will maybe have to pay when they want to get to the result, but that happens also with some results on the ISBN site). I don't have any objection against the use of InChI (just implement it in the chembox, and make sure that it shows advantages).

But .. the one does not exclude the other!! People can decide whether to search via InChI or CAS, and see for themselves which gives the best result.

It may be worth a thought, it would give the functionality that I (and some others) like to see, does not give an unfair advantage to certain suppliers (no bias from the writers side, suppliers that don't support deeplinking get 'punished'), does not give problems in linking to the wrong isomer when we choose to link to the wrong side of the ocean .. etc. etc. --Dirk Beetstra 21:39, 6 June 2006 (UTC)

P.S. you can answer here, I am watching this page for now. --Dirk Beetstra 21:39, 6 June 2006 (UTC)


 * greetings,

I understand this ... there are, however, already tools that search for CAS (remember there are > 10,000,000 compounds so there has to be a significant database and this is beyond Wikipedia). The purpose of WP, IMO, is to gather the most important information and add the sources. CAS is one source but I suspect that relatively few WP entries have actually used a paid CAS search, while I assume that many referenced ISBNs have actually been read by the WP editors.

and, as I have said, I wish to promote InChI...

Best

P. Petermr 23:00, 6 June 2006 (UTC)

¡Hola! You are right, there is a difference. Hmm .. I need to think more and better about this.

About InChI, my opinion, get it added it to the chembox template (or whichever template), implement it on the pages, and try to add functionality, within WP, but also to external sources (as in above example, linking to as many suppliers as possible). If people see it in work, you get your promotion, otherwise it is nothing more than a CAS number, or a poiling point .... --Dirk Beetstra 23:20, 6 June 2006 (UTC)

Another point is that PubChem - which is by far the largest public collection of molecular information - uses InChI and does not use CAS (deliberately, because of copyright concerns). PubChem is rapidly becoming the communal aggregation of chemical information this is one of a few verys sites I would publicly point to on a large-scale basis. Note also that PubChem welcomes contributions (unlike many other sources) and if WP sends a list of WP entries to PubChem I am almost certain they will be delighted to add these links and to publicise that WP has done this. PubChem's sole purpose is to collect and disseminate information, unlike almost all other organisations we have discussed. They are complemented by ChEBI and NIST - these are highly quality, but have many fewer entries.

Petermr 06:04, 7 June 2006 (UTC)

Yesyes, I now get the point of the advantages of the InChI, are you being paid by the number? ;-)

Still, I believe that we could use a centralised way that links directly into as many external sources as possible (suppliers, databases, &c). Even if people have to pay to get into some/most of those databases, the people that have payed, and those that are in a good IP-range (unis, companies) can get in anyway. And free databases can be grouped in front of the pay(-per-view)-databases. For now, I would do that with both InChI ánd CAS, if CAS starts nagging WP, these links are gone fast enough. --Dirk Beetstra 07:30, 7 June 2006 (UTC)

I get paid as much for each InChI as for WP entries...

PubChem already links into as many external sources as are required. And although I am not a WP expert, I got the sense from the correspondence. that it is important to avoid WP becoming a central supplier of *links*

Petermr 17:22, 7 June 2006 (UTC)

The ISBN searchpage is a centralised page to link to 'the outside world'. I think it is meant there that not every page should be flooded with external links (which may/will be biased), but that it is then better to have a central page, that links to as many as possible links based on a single input. And, if only PubChem is linked from the InChI (on every page), that would also be biased (however good PubChem is, what if I want to go to a supplier, do I really have to go through PubChem then .. hmmm .. PubChem might get money then for every link that goes through their page (now or in the future) .. so WP would then sponsor such an institution). --Dirk Beetstra 17:31, 7 June 2006 (UTC)

I am not quite sure where this discussion is going. Firstly it is between just 2 people and I suspect is neither informing or being informed by many others. I obviously haven't got across the main arguments:
 * suppliers supply chemicals for money. Some also supply information, but this is not their primary purpose. This information is neither verified nor universally correct.
 * chemical information aggregators such as Chmoogle or ChemExper aggregate chemical information on an unpredictable business model (i.e. this may be terminated at any time, or changed to a pay-per-view). As far as I know they do not check information.
 * PubChem is part of the US government's funding of public research, in a similar manner to the UK research councils or the Wellcome Trust. All information is free and they are funded to make it freely available. They are part of the US NCBI (National Centre of Biotechnology) which, for example, publishers MEDLINE, a public collection of abstracts in the biomoedical field. Medline is FREE, OPEN ACCESS, infinitely accessible and verified. NIST is another arm of the US goverment, like the Environmental Protection Agency, Food and Drug Administration and many others. They are required (with some minor qualifications) to make all their works copyright free. They are completely non-profit, open and completely different from the other suppliers of information.

Finally I see WP as a supplier of information, not a catalog of suppliers of goods. I am relatively new to WP, but I get the sense that this is a mainstream view. You write: " what if I want to go to a supplier, do I really have to go through PubChem then .. hmmm .. PubChem might get money then for every link that goes through their page (now or in the future) .. so WP would then sponsor such an institution). "
 * Pubchem is NOT a supplier.
 * It does not get money and never will get money (except from the US goverment for its core research - they are a research organisation; I am collaborating with them in medical research).

I hope this makes it clearer. It is important that the role of PubChem, Reseach Councils, Royal Society, National Science Foundation. etc. are recognised as resrach institutions without a commercial mandate. For example I have been funded to calculate the properties of 250,000 molecules provided by the National Cancer Institute. I have posted the results in DSpace at the University of Cambridge where they are freely available as Open Access for all time. The information is freely available for anyone, including WP editors. It is unbiased (in your terminology) and has been published in peer-reviewed scientific journals. This is entirely different from pointing to a commercial supplier of goods.

It hope we are moving to some convergence - I have a heavy program of student marking in the next few days and am limited in what can write.

Best wishes

Petermr 18:44, 7 June 2006 (UTC)

I don't think we are converging, don't mind. I will try a bit and see what I can come up with. See you around, thanks anyway. Good luck with the student marking! --Dirk Beetstra 18:50, 7 June 2006 (UTC)

Chemical publishing
Hi Peter,

I'm a chemist trying to get together thoughts on how chemical publishing may be going in the future, and I can't think of a better person to ask than your good self! I'm approaching it from two directions - one as a chemist who is keeping an eye on things like InChI and CML, and another as a Wikipedian interested in chemical information and assessment of articles. I'm also fresh from discussions on validation and article citations at Wikimania last weekend.


 * how exciting! I have been away for ca 10 days so don't take this as lack of interest! Your ideas are spot-on! Petermr 14:28, 20 August 2006 (UTC)

It seems that the best way to approach this is to consider what an ideal chemistry journal would look like given current (or soon-to-be-current) technology. I expect it would be easily updated and corrected, with a fast dynamic peer review process (maybe ongoing, as people run things in the lab) and interlinking of the sort any Wikipedian would be proud of. You should be able to draw in a structure with ChemDraw and search - maybe this is what WWMM will do. You should be able to link to a chemical compound by its structure (as its InChI?) rather than its name. You should be able to see the drawing on a page on a site like Wikipedia or JACS, but behind the image would be the machine-searchable representation of that structure. Would it use CML, and if so, how would that be handled? You should be able to fully interlink citations, perhaps using something along the lines of the DOI and possibly Wikicat.


 * Yes - this is all abolutely right, except that we are hoping to move away from ChemDraw as it is (a) not-semantic (b) proprietary and therefore non-extensible.Petermr 14:28, 20 August 2006 (UTC)

Of course any new style of journal would have to deal with some of the established features of traditional journals. How would you deal with authorship/attribution, so that an author can receive proper credit for their original research (for tenure & promotion, etc.)? This might be difficult if a paper becomes more fragmented, wiki-style, but it could be done. What would be the new system for peer review, and how would credentials be handled? How could a completely new style of journal establish itself and gain credibility/respect of the chemical community?


 * several publishers are starting to think along these lines. There is exceitement about both social publishing (e.g. Wikipedia) and the new technology. Of course they interact. Henry and I have been promoting the "Datument" idea - combined document and data.

So far I've been disappointed at what I've seen from the publishers - we essentially have paper journals scanned onto the web, with subscription requirements and little metadata available. The ACS Chemical Biology wiki is very hard to use, and seems more like a blog than a wiki. However, I think some in the publishing community are very open to ideas right now, and I'd like to try and develop a viable model. I'm not too strong with the heavy technical stuff - anything beyond simple HTML and BASIC tends to be beyond me, so please keep it simple! I'd love to hear some of your ideas on this, many thanks, Walkerma 00:56, 11 August 2006 (UTC)


 * There are things I can't say in public, but I am hoping to present much of this at the Sept meeting of the ACS in San Francisco. Essentially we want to show that a mixture of Blue Obelisk and Bioclipse has to be the way forward. As we are a volunteer community I am sure that your contributions - whether technical, content, evangelism, etc. would be highly welcomed.Petermr 14:28, 20 August 2006 (UTC)

If you want to do something in a non-WP context (or work towards tools which can be used in WP - which we really need) suggest you mail me at pm286 atsign cam dot ac dot uk

P.

special:chemicalsources
Hi! I just decided to spam some people directly, who I know are very active on chemicals. There is now a wiki running on http://chemistry.poolspares.com (a site created by Nickj from the wikimedia IRC channel, the site will be taken offline again in a couple of weeks), where I have now hosted a small wikipedia. It runs two extensions I have written to the wikipedia software, a special page (for chemical sources, see also chemical sources and a chemform tag (for easy input of chemical formulae). Could you have a look, and comment on it (if useful I would like to try to let Tim or Brion enable it on wikipedia, though I feel some resistance there).  Cheers!  --Dirk Beetstra T  C 17:52, 26 October 2006 (UTC)

Re: thanks for references
Petermr wrote:
 * Thanks for showing me how to do references. Petermr 19:59, 31 October 2006 (UTC)

No problem. I was reading your blog post here (I have a habit of reading Wikipedia-related blog posts just to get an idea of Wikipdia's reputation) and thought I'd check the article to see if anything else needed doing. I thought the post was very good, by the way; obviously I know how to edit Wikipedia myself, but I think it will be of use to first-time contributors – Gurch 20:08, 31 October 2006 (UTC)

Petermr wrote:
 * ''Thanks for your reply (how do I quote it here if I want to - as you quoted mine?). Yes, A blog has many of the aspects that are useful for a communal discussion on a new topic when coupled with a WP aricle. I actually run the Open Data mailing list and am trying to activate it by using WP as a catalyst to define our term. (There is no shortage of usage of "Open Data" now, so it's not a research project but an exercise in communal scholarship. I need additional input from the community.

Petermr 08:25, 1 November 2006 (UTC)''

Unfortunately there's no quick shortcut for quoting messages. Many people just reply to messages without quoting, but I find that makes the discussion hard to follow as it's split into two. I usually include the original message in my reply, by copying and pasting it into the edit window, and then formatting it like this:

(name) wrote:
 * (message)

Now that Open Data exists and is linked from other articles, it will inevitably be edited at some point, though how much attention articles will recieve is difficult to predict. If you haven't already done so, I suggest you add the page to your watchlist (click the "watch" tab at the top of the page); that way you can quickly see if there have been any changes – Gurch 11:23, 1 November 2006 (UTC)

Open Science
I see that you redirected "Open Science" to Open Access. My own feeling is that they are quite distinct and I am interested in creating material for Opwn Science. However I wanted to check whether they was a reason for this before.

Open Science is not yet widely used but I think it may develop. It certainly has aspects of Open Source and Open Data as well as open access.

But I am new to the rules of redirection :-) Petermr 08:19, 1 November 2006 (UTC)


 * There simply was nothing at the open science page. If you have something to put there, please go ahead. AaronSw 14:57, 1 November 2006 (UTC)

Your article
Oops. Sorry about the spelling of your name, Peter, Yours, Brian. --Bduke 23:08, 15 November 2006 (UTC)

Hello after MKM
Dear Peter, nice to meet you again here – hope you had a safe trip back home :-) Just for fun, I searched Wikipedia for you, and, for the sake of completeness, I added a reference to your homepage and blog to the article about you – until I realised that you also contribute to Wikipedia. So, if you should not like these links to be listed there, just let me know, or remove them again. BTW, have you seen the OMDoc article I once wrote? Maybe we should eventually add a comment about extending OMDoc towards chemistry there… Best, Langec 18:30, 1 July 2007 (UTC)

CSA Trust
Hi Peter, please take a look at this article which has just been written and now put up for deletion. Regards, Brian Duke. --Bduke 11:27, 19 August 2007 (UTC)

CrystalEye
Thanks for telling me about CrystalEye, it looks very useful!

Ben 06:56, 24 September 2007 (UTC)

Just looked at Bens talk page, and set up Crystaleye--great! ThanksAxiosaurus 15:23, 1 December 2007 (UTC)

Note that CrystalEye is OpenData so any or all of it could be used in WP without asking permission Petermr 23:44, 6 December 2007 (UTC)

Workshop
Hi, I have started a bit of a workshop on chembox new here, may I invite you to help discuss the different parts of the box? Thanks. --Dirk Beetstra T C 16:59, 16 January 2008 (UTC)

Barnstar
See new chem project proposal

http://en.wikipedia.org/wiki/Wikipedia_talk:WikiProject_Chemistry/Participants#Proposal_for_project.

See also my user page. My informatics mentor at Abbott was YC Martin. — Preceding unsigned comment added by Meduban (talk • contribs) 22:13, 22 July 2012 (UTC)

ArbCom elections are now open!
MediaWiki message delivery (talk) 13:36, 23 November 2015 (UTC)

Facto Post – Issue 1 – 14 June 2017
MediaWiki message delivery (talk) 09:33, 14 June 2017 (UTC)

Facto Post – Issue 2 – 13 July 2017
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 * Facto Post – Issue 2 – 13 July 2017

 

Editorial: Core models and topics
Wikimedians interest themselves in everything under the sun — and then some. Discussion on "core topics" may, oddly, be a fringe activity, and was popular here a decade ago.

The situation on Wikidata today does resemble the halcyon days of 2006 of the English Wikipedia. The growth is there, and the reliability and stylistic issues are not yet pressing in on the project. Its Berlin conference at the end of October will have five years of achievement to celebrate. Think Wikimania Frankfurt 2005.

Progress must be made, however, on referencing "core facts". This has two parts: replacing "imported from Wikipedia" in referencing by external authorities; and picking out statements, such as dates and family relationships, that must not only be reliable but be seen to be reliable.

In addition, there are many properties on Wikidata lacking a clear data model. An emerging consensus may push to the front key sourcing and biomedical properties as requiring urgent attention. Wikidata's "manual of style" is currently distributed over thousands of discussions. To make it coalesce, work on such a core is needed.

Links

 * WikiFactMine project pages on Wikidata, including a SPARQL library (in development).
 * Fatameh tool for adding items on scientific papers to Wikidata, by User: T Arrow. It has made a big recent impact. Offline for maintenance as we go to press, it is expected back soon.
 * As of July 2017, Zotero has a Wikidata translator. A personal Zotero library acts as an intermediary in managing and storing citation metadata.
 * GLAM Newsletter June 2017, Wikidata report. This is a good monthly round-up to follow, and welcomes contributions.
 * Exciting and Impressive! The Initiative for Open Citations (I4OC) was launched in April: Infodocket on the first three months.
 * Olivia Solon in San Francisco, the net neutrality protest matters, opinion piece in The Guardian'' on 11 July.

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Facto Post – Issue 3 – 11 August 2017
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 * Facto Post – Issue 3 – 11 August 2017

 

Wikimania report
Interviewed by Facto Post at the hackathon, Lydia Pintscher of Wikidata said that the most significant recent development is that Wikidata now accounts for one third of Wikimedia edits. And the essential growth of human editing. Impressive development work on Internet-in-a-Box featured in the WikiMedFoundation annual conference on Thursday. Hardware is Raspberry Pi, running Linux and the Kiwix browser. It can operate as a wifi hotspot and support a local intranet in parts of the world lacking phone signal. The medical use case is for those delivering care, who have smartphones but have to function in clinics in just such areas with few reference resources. Wikipedia medical content can be served to their phones, and power supplied by standard lithium battery packages.

Yesterday Katherine Maher unveiled the draft Wikimedia 2030 strategy, featuring a picturesque metaphor, "roads, bridges and villages". Here "bridges" could do with illustration. Perhaps it stands for engineering round or over the obstacles to progress down the obvious highways. Internet-in-a-Box would then do fine as an example.

"Bridging the gap" explains a take on that same metaphor, with its human component. If you are at Wikimania, come talk to WikiFactMine at its stall in the Community Village, just by the 3D-printed display for Bassel Khartabil; come hear talk at 3 pm today in Drummond West, Level 3.

Link

 * Plaudit for the Medical Wikipedia app, content that is loaded into Internet-In-A-Box with other material, such as per-country documentation.

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Facto Post – Issue 4 – 18 September 2017
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 * Facto Post – Issue 4 – 18 September 2017

 

Editorial: Conservation data
The IUCN Red List update of 14 September led with a threat to North American ash trees. The International Union for Conservation of Nature produces authoritative species listings that are peer-reviewed. Examples used as metonyms for loss of species and biodiversity, and |theoretical discussion of extinction rates, are the usual topics covered in the media to inform us about this area. But actual data matters. Clearly, conservation work depends on decisions about what should be done, and where. While animals, particularly mammals, are photogenic, species numbers run into millions. Plant species lie at the base of typical land-based food chains, and vegetation is key to the habitats of most animals.

ContentMine dictionaries, for example as tabulated at d:Wikidata:WikiFactMine/Dictionary list, enable detailed control of queries about endangered species, in their taxonomic context. To target conservation measures properly, species listings running into the thousands are not what is needed: range maps showing current distribution are. Between the will to act, and effective steps taken, the services of data handling are required. There is now no reason at all why Wikidata should not take up the burden.

Links

 * What Makes a Good Collaborative Knowledge Graph: Group Composition and Quality in Wikidata (paywall)
 * Wikimedia and the free knowledge ecosystem by Maria Cruz
 * Another Year Again: 2017 this time (long), blog by Joe Wass of CrossRef
 * Attack of the 50 Foot Blockchain, blog by User:David Gerard
 * WikiTribune in beta

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Facto Post – Issue 5 – 17 October 2017
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 * Facto Post – Issue 5 – 17 October 2017

 

Editorial: Annotations
Annotation is nothing new. The glossators of medieval Europe annotated between the lines, or in the margins of legal manuscripts of texts going back to Roman times, and created a new discipline. In the form of web annotation, the idea is back, with texts being marked up inline, or with a stand-off system. Where could it lead? ContentMine operates in the field of text and data mining (TDM), where annotation, simply put, can add value to mined text. It now sees annotation as a possible advance in semi-automation, the use of human judgement assisted by bot editing, which now plays a large part in Wikidata tools. While a human judgement call of yes/no, on the addition of a statement to Wikidata, is usually taken as decisive, it need not be. The human assent may be passed into an annotation system, and stored: this idea is standard on Wikisource, for example, where text is considered "validated" only when two different accounts have stated that the proof-reading is correct. A typical application would be to require more than one person to agree that what is said in the reference translates correctly into the formal Wikidata statement. Rejections are also potentially useful to record, for machine learning.

As a contribution to data integrity on Wikidata, annotation has much to offer. Some "hard cases" on importing data are much more difficult than average. There are for example biographical puzzles: whether person A in one context is really identical with person B, of the same name, in another context. In science, clinical medicine require special attention to sourcing (WP:MEDRS), and is challenging in terms of connecting findings with the methodology employed. Currently decisions in areas such as these, on Wikipedia and Wikidata, are often made ad hoc. In particular there may be no audit trail for those who want to check what is decided.

Annotations are subject to a World Wide Web Consortium standard, and behind the terminology constitute a simple JSON data structure. What WikiFactMine proposes to do with them is to implement the MEDRS guideline, as a formal algorithm, on bibliographical and methodological data. The structure will integrate with those inputs the human decisions on the interpretation of scientific papers that underlie claims on Wikidata. What is added to Wikidata will therefore be supported by a transparent and rigorous system that documents decisions.

An example of the possible future scope of annotation, for medical content, is in the first link below. That sort of detailed abstract of a publication can be a target for TDM, adds great value, and could be presented in machine-readable form. You are invited to discuss the detailed proposal on Wikidata, via its talk page.

Links

 * Jon Udell, blogpost Annotating to extract findings from scientific papers, 15 December 2015
 * TDM and Libraries, Virginia Tech report
 * Magnus Manske, The Whelming: Scaling up Wikidata editing
 * OCLC and Internet Archive collaborate to expand library access to digital collections, metadata and linking exchange
 * GLOW week in November: Wikidata workshops on politician info

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Facto Post – Issue 6 – 15 November 2017
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 * Facto Post – Issue 6 – 15 November 2017

 

WikidataCon Berlin 28–9 October 2017
Under the heading rerum causas cognescere, the first ever Wikidata conference got under way in the Tagesspiegel building with two keynotes, One was on YAGO, about how a knowledge base conceived ten years ago if you assume automatic compilation from Wikipedia. The other was from manager Lydia Pintscher, on the "state of the data". Interesting rumours flourished: the mix'n'match tool and its 600+ datasets, mostly in digital humanities, to be taken off the hands of its author Magnus Manske by the WMF; a Wikibase incubator site is on its way. Announcements came in talks: structured data on Wikimedia Commons is scheduled to make substantive progress by 2019. The lexeme development on Wikidata is now not expected to make the Wiktionary sites redundant, but may facilitate automated compilation of dictionaries. And so it went, with five strands of talks and workshops, through to 11 pm on Saturday. Wikidata applies to GLAM work via metadata. It may be used in education, raises issues such as author disambiguation, and lends itself to different types of graphical display and reuse. Many millions of SPARQL queries are run on the site every day. Over the summer a large open science bibliography has come into existence there.

Wikidata's fifth birthday party on the Sunday brought matters to a close. See a dozen and more reports by other hands.

Links

 * Wikidata statistics
 * I4OC progress in its first year, with 47% of scientific citation data now open (announced two days ago)
 * The flowering ORCID, Magnus Manske blogpost on identifying authors of scientific papers
 * @querybook, a Twitter feed devoted to SPARQL queries
 * Massive progress on Wikidata coverage of the UK parliament
 * Reminder: WikiFactMine pages on Wikidata are at WD:WFM

Editor. Please leave feedback for him. If you wish to receive no further issues of Facto Post, please remove your name from our mailing list. Alternatively, to opt out of all massmessage mailings, you may add Category:Wikipedians who opt out of message delivery to your user talk page. Newsletter delivered by MediaWiki message delivery MediaWiki message delivery (talk) 10:02, 15 November 2017 (UTC)
 * }

Facto Post – Issue 7 – 15 December 2017
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 * Facto Post – Issue 7 – 15 December 2017

 

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. WikiCite and the I4OC have been pushing hard, with the result that on CrossRef over 50% of the citation data is open. Now the holdout publishers are being lobbied to release rights on citations.

But all that is just the beginning. Topics of papers are identified, authors disambiguated, with significant progress on the use of the four million ORCID IDs for researchers, and proposals formulated to identify methodology in a machine-readable way. P4510 on Wikidata has been introduced so that methodology can sit comfortably on items about papers.

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
To subscribe to Facto Post go to Facto Post mailing list. For the ways to unsubscribe, see below. Editor, for ContentMine. Please leave feedback for him. Back numbers are here. Reminder: WikiFactMine pages on Wikidata are at WD:WFM. If you wish to receive no further issues of Facto Post, please remove your name from our mailing list. Alternatively, to opt out of all massmessage mailings, you may add Category:Wikipedians who opt out of message delivery to your user talk page. Newsletter delivered by MediaWiki message delivery MediaWiki message delivery (talk) 14:54, 15 December 2017 (UTC)
 * 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
 * }

Facto Post – Issue 8 – 15 January 2018
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 * Facto Post – Issue 8 – 15 January 2018

 

Metadata on the March
From the days of hard-copy liner notes on music albums, metadata have stood outside a piece or file, while adding to understanding of where it comes from, and some of what needs to be appreciated about its content. In the GLAM sector, the accumulation of accurate metadata for objects is key to the mission of an institution, and its presentation in cataloguing.

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, 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
To subscribe to Facto Post go to Facto Post mailing list. For the ways to unsubscribe, see below. Editor, for ContentMine. Please leave feedback for him. Back numbers are here. Reminder: WikiFactMine pages on Wikidata are at WD:WFM. If you wish to receive no further issues of Facto Post, please remove your name from our mailing list. Alternatively, to opt out of all massmessage mailings, you may add Category:Wikipedians who opt out of message delivery to your user talk page. Newsletter delivered by MediaWiki message delivery MediaWiki message delivery (talk) 12:38, 15 January 2018 (UTC)
 * 1lib1ref campaign starts today, see The Wikipedia Library/1Lib1Ref: also #1lib1ref introductory video by
 * 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
 * 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
 * }

Facto Post – Issue 9 – 5 February 2018
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 * Facto Post – Issue 9 – 5 February 2018

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m:Grants:Project/ScienceSource is the new ContentMine proposal: please take a look.

Wikidata as Hub
One way of looking at Wikidata relates it to the semantic web concept, around for about as long as Wikipedia, and realised in dozens of distributed Web institutions. It sees Wikidata as supplying central, encyclopedic coverage of linked structured data, and looks ahead to greater support for "federated queries" that draw together information from all parts of the emerging network of websites. 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.

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 takes a major step further, allowing both lookup and crosswalk to be encoded in a single URL.

Links
To subscribe to Facto Post go to Facto Post mailing list. For the ways to unsubscribe, see below. Editor, for ContentMine. Please leave feedback for him. Back numbers are here. Reminder: WikiFactMine pages on Wikidata are at WD:WFM. If you wish to receive no further issues of Facto Post, please remove your name from our mailing list. Alternatively, to opt out of all massmessage mailings, you may add Category:Wikipedians who opt out of message delivery to your user talk page. Newsletter delivered by MediaWiki message delivery MediaWiki message delivery (talk) 11:50, 5 February 2018 (UTC)
 * 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
 * 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
 * Cochrane–Wikipedia Initiative, Wikipedia Signpost special report 5 February 2018, by
 * What is the Last Question?, 5 February 2018
 * }

Facto Post – Issue 10 – 12 March 2018
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 * Facto Post – Issue 10 – 12 March 2018

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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,, 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. 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 Stakhanovite!

Links
To subscribe to Facto Post go to Facto Post mailing list. For the ways to unsubscribe, see below. Editor, for ContentMine. Please leave feedback for him. Back numbers are here. Reminder: WikiFactMine pages on Wikidata are at WD:WFM. If you wish to receive no further issues of Facto Post, please remove your name from our mailing list. Alternatively, to opt out of all massmessage mailings, you may add Category:Wikipedians who opt out of message delivery to your user talk page. Newsletter delivered by MediaWiki message delivery MediaWiki message delivery (talk) 12:26, 12 March 2018 (UTC)
 * 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
 * }

WikiProject Source MetaData
I don't know if anyone every told you, but you are a motivator behind WikiProject Source MetaData. There's a video of a talk of yours on that page. Thank you! HLHJ (talk) 02:50, 27 March 2018 (UTC)

Facto Post – Issue 11 – 9 April 2018
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 * Facto Post – Issue 11 – 9 April 2018

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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 SPARQL query are superior in principle, by far, to existing keyword searches run over papers. Open access content should be managed into consistent HTML, something that is currently strenuous. The good news, such as it is, would be that much of it is already in XML. The organisational problem of removing further skins from the onion, with sensible prioritisation, is certainly not insuperable. The CORE group (the bloggers in the LSE posting) has some answers, but actually not all that is needed for the text and data mining purposes they highlight. The long tail, or in other words the onion heart when it has become fiddly beyond patience to skin, does call for a pis aller. But the real knack is to do more between the XML and the heart.

Links
To subscribe to Facto Post go to Facto Post mailing list. For the ways to unsubscribe, see below. Editor, for ContentMine. Please leave feedback for him. Back numbers are here. Reminder: WikiFactMine pages on Wikidata are at WD:WFM. If you wish to receive no further issues of Facto Post, please remove your name from our mailing list. Alternatively, to opt out of all massmessage mailings, you may add Category:Wikipedians who opt out of message delivery to your user talk page. Newsletter delivered by MediaWiki message delivery MediaWiki message delivery (talk) 16:25, 9 April 2018 (UTC)
 * 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
 * }

Facto Post – Issue 12 – 28 May 2018
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 * Facto Post – Issue 12 – 28 May 2018

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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.

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.
 * A medical canon?

The basic criteria of WP:MEDRS include a concentration on secondary literature. Attention has to be given to the long tail of diseases that receive less current research. The MEDRS guideline supposes that edge cases will have to be handled, and the premature exclusion of publications that would be in those marginal positions would reduce the value of the collection. Prophylaxis misses the point that gate-keeping will be done by an algorithm.

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
To subscribe to Facto Post go to Facto Post mailing list. For the ways to unsubscribe, see below. Editor, for ContentMine. Please leave feedback for him. Back numbers are here. Reminder: WikiFactMine pages on Wikidata are at WD:WFM. ScienceSource pages will be announced there, and in this mass message. If you wish to receive no further issues of Facto Post, please remove your name from our mailing list. Alternatively, to opt out of all massmessage mailings, you may add Category:Wikipedians who opt out of message delivery to your user talk page. Newsletter delivered by MediaWiki message delivery MediaWiki message delivery (talk) 10:16, 28 May 2018 (UTC)
 * 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
 * }

Facto Post – Issue 13 – 29 May 2018
MediaWiki message delivery (talk) 18:19, 29 June 2018 (UTC)

Facto Post – Issue 14 – 21 July 2018
MediaWiki message delivery (talk) 06:10, 21 July 2018 (UTC)

Facto Post – Issue 15 – 21 August 2018
MediaWiki message delivery (talk) 13:23, 21 August 2018 (UTC)

Facto Post – Issue 16 – 30 September 2018
MediaWiki message delivery (talk) 17:57, 30 September 2018 (UTC)

Facto Post – Issue 17 – 29 October 2018
MediaWiki message delivery (talk) 15:01, 29 October 2018 (UTC)

Facto Post – Issue 18 – 30 November 2018
MediaWiki message delivery (talk) 11:20, 30 November 2018 (UTC)

IETF/ISOC
As discussed: IETF Newcomers Presentation (2016) Zazpot (talk) 18:13, 15 December 2018 (UTC)

Facto Post – Issue 19 – 27 December 2018
MediaWiki message delivery (talk) 19:08, 27 December 2018 (UTC)

Facto Post – Issue 20 – 31 January 2019
MediaWiki message delivery (talk) 10:53, 31 January 2019 (UTC)

Facto Post – Issue 21 – 28 February 2019
MediaWiki message delivery (talk) 10:02, 28 February 2019 (UTC)

Facto Post – Issue 22 – 28 March 2019
MediaWiki message delivery (talk) 11:45, 28 March 2019 (UTC)

Facto Post – Issue 23 – 30 April 2019
MediaWiki message delivery (talk) 11:27, 30 April 2019 (UTC)

Facto Post – Issue 24 – 17 May 2019
MediaWiki message delivery (talk) 18:52, 17 May 2019 (UTC)

Wikiversity Node Cambridge, 19-20 January, 2022
Following the success of the Decolonise Art History Wiki Jam in November 2021 our next step is the establishment of a pop-up Bricks and Clicks Wikiversity Node. Please see Wikiversity Node Cambridge.