Pleiotrope
Welcome!
editHi. Great to have you aboard the Gene Wiki project! If I can help in any way in getting you started, don't hesitate to ask. Cheers. Boghog (talk) 18:34, 1 April 2011 (UTC)
Thanks for the warm welcome! Looking forward to contributing :) Pleiotrope (talk) 19:56, 1 April 2011 (UTC)
ProteinBoxBot edit summaries
editCould you please take a look at Wikipedia:Bot owners' noticeboard#General notice to bot owners about edit summaries and see if the suggestions might apply to your bot? Feel free to add your own suggestions and comments there too. Headbomb {talk / contribs / physics / books} 21:20, 21 August 2011 (UTC)
- Yes, they absolutely do apply- the current bot summaries are somewhat less than helpful. I'll expand it so that the next time the bot updates it'll use more expressive edit summaries. Thanks for giving me the heads up. Pleiotrope (talk) 16:28, 23 August 2011 (UTC)
Creation of new Gene Wiki articles
editHi. Thanks for your recent bot runs to create new Gene Wiki articles (10,000 down, 10,000 to go! ;-).
Before you make a new run, I do have a couple of requests:
Lead sentence – as discussed here and here, we have tried to make clear that these articles are not only about the human gene/protein, but also orthologs that exist in other species. The wording that was reached through consensus is perhaps a little awkward, but it is both accurate and concise:
- The "that" in the above sentence is non-limiting implying that the protein (and gene) exists in other species besides human. Since much of the text in these articles focus on the properties of the protein (structure, function, interactions with other proteins), I think it is appropriate that emphasis in the lead is on the protein. Hence I would appreciate if you would reword the lead sentence according to the above suggestion.
Citations – the following should be removed:
- There are a lot of "'" stray characters imbedded in the citations
- Empty citations – {{cite journal |author= |title= |journal= |volume= |issue= |pages= |year= |pmid= |doi= }}
- Large scale sequencing projects that list many genes. These should be "black listed" (e.g., PMID 15489334, PMID 12477932, PMID 17207965, and PMID 14702039).
Stub template – it would be appropriate to add a {{gene}} stub template to the end, for example, if the human gene is located on chromsome 4, please add {{gene-4-stub}} to the end.
See diff for an example.
Talk page – Finally it would be helpful if the following were added to the talk page:
{{WikiProjectBannerShell| {{Wikiproject MCB|class=stub|importance=Low}} {{WikiProject Gene Wiki|class=stub|importance=Low}} }}
Cheers. Boghog (talk) 18:22, 8 September 2011 (UTC)
- Thanks for the pointers! I'm in the process of re-writing the stub generator now, so I'll be sure to incorporate these changes before any more stubs are created. Pleiotrope (talk) 18:42, 8 September 2011 (UTC)
- I'm setting the filter to omit any projects that reference more than 100 genes. Would you agree with this filter level? Pleiotrope (talk) 00:48, 13 September 2011 (UTC)
- This seems like a reasonable number. There may be a few relevant citations that might be filtered out using this cutoff (false positives), but this is likely to be far exceeded by the number of low relevance citations (true negatives). Boghog (talk) 01:24, 13 September 2011 (UTC)
- I'm setting the filter to omit any projects that reference more than 100 genes. Would you agree with this filter level? Pleiotrope (talk) 00:48, 13 September 2011 (UTC)
ProteinBoxBot edit request
editHi,
I've placed a request on the Gene Wiki portal discussion page for ProteinBoxBot to fill in the name parameter of the infoboxes it updates as part of an enhancement of the {{PBB}} template. Any help you can provide would be much appreciated. Thanks! Chris Cunningham (user:thumperward) - talk 09:27, 15 September 2011 (UTC)
Your message
editThank you for answering my request here. I dropped you a quick answer. Thanks. Anthere (talk) 14:14, 29 September 2011 (UTC)
A barnstar for you!
edit
|
The Technical Barnstar |
| Thanks for improving thousands of pages about human genes with the gene wiki bot updates! Benjamin Good (talk) 15:48, 18 October 2011 (UTC) |
IUPHAR parameter
editHi. The Protein Box Bot has done a great job in maintaining the PBB templates. I do have one additional request. There is a parameter called IUPHAR that if set to yes generates an external link to the IUPHAR database of receptors, ion channels, and nuclear receptors. BogBot had added these parameters to a number of templates, but unfortunately these were overwritten by the Protein Box Bot. I still had a copy of the bot script that added these parameters, so I reran the script to add back the parameter to the appropriate templates (see for example diff).
I would appreciate if Protein Box Bot would check for the presence of this parameter, and if found, preserve it. This parameter that was previously undocumented, but I have just documented it (see Template:GNF_Protein_box#IUPHAR). Cheers. Boghog (talk) 07:37, 17 November 2011 (UTC)
- Hi Boghog, I'll add that behavior into ProteinBoxBot today. Thanks for pointing that out and documenting it. Pleiotrope (talk) 16:14, 17 November 2011 (UTC)
Ping
edit
Message added Boghog (talk) 22:02, 28 January 2012 (UTC). You can remove this notice at any time by removing the {{Talkback}} or {{Tb}} template.
Message added Boghog (talk) 22:02, 28 January 2012 (UTC). You can remove this notice at any time by removing the {{Talkback}} or {{Tb}} template.
Invitation to events: bot, template, and Gadget makers wanted
editI thought you might want to know about some upcoming events where you can learn more about MediaWiki customization and development, extending functionality with JavaScript, the future of ResourceLoader and Gadgets, the new Lua templating system, how to best use the web API for bots, and various upcoming features and changes. We'd love to have power users, bot maintainers and writers, and template makers at these events so we can all learn from each other and chat about what needs doing.
Check out the Chennai event in March, the Berlin hackathon in June, the developers' days preceding Wikimania in July in Washington, DC, or any other of our events.
Best wishes! - Sumana Harihareswara, Wikimedia Foundation's Volunteer Development Coordinator. Please reply on my talk page, here or at mediawiki.org. Sumanah (talk) 15:25, 16 February 2012 (UTC)
- You might especially be interested in coming to the Berlin event, as it will have a strong emphasis on structured/semantic data. Hope to see you there! Sumanah (talk) 15:26, 16 February 2012 (UTC)
PBB/28
editHi Pleiotrope, The ProteinBoxBot is replacing Uniprot P16442 with C3VA45 (an unreviewed fragment) for the human protein in PBB/28. As a result the PDBs are stripped out as the structures are mapped to P16422 not C3VA45. Can anything be done about this? Thanks A2-33 (talk) 19:31, 3 April 2012 (UTC)
- Hi A2-33, thanks for bringing this to my attention. PBB should check for reviewed entries before updating, so I'll fix this bug before the bot updates again. Please let me know if there are any other issues you notice. Cheers, Pleiotrope (talk) 19:40, 3 April 2012 (UTC)
- Following up: I've fixed the issue you've referred to. The bot now checks with Uniprot directly if it can't find a reviewed accn number from its primary source. In the future, if you notice an edit you make getting overwritten, you can add the {{nobots}} template until the bug gets fixed. Cheers, Pleiotrope (talk) 04:40, 4 April 2012 (UTC)
GeneWikiGenerator not creating pages
editHi. For quite some time, the GeneWikiGenerator no longer is able to create new Gene Wiki articles and templates. The Generator still creates the template and article code, but when one clicks the "create page" button, nothing happens. Is the Wikipedia bot that creates these pages still logged on? I would appreciate if you would check this when you get a chance. There is a growing list of requests. Thanks. Boghog (talk) 04:26, 11 April 2012 (UTC)
- Hi Boghog, I've fixed the bug. Thank you for letting me know, and don't hesitate to ping me asap if you notice it not working in the future. Note: it's currently working but will not display a confirmation message when the article is created. Refreshing the page should show the updated results. I'll have a fix for that soon, but feel free to use it in the meantime. Pleiotrope (talk) 04:57, 11 April 2012 (UTC)
ChEMBL links
editPer this discussion, I have started adding ChEMBL links to GNF_Protein_box templates. I would appreciate if you would modify the Protein box bot so this parameter is not over written. Thanks. Boghog (talk) 04:47, 4 May 2012 (UTC)
- Fixed, thanks for letting me know. Pleiotrope (talk) 21:51, 7 May 2012 (UTC)
Collaboration with NCBI?
editHi, I would appreciate your opinion on opportunities to collaborate with NCBI. Thanks, -- Daniel Mietchen - WiR/OS (talk) 02:20, 19 July 2012 (UTC)
ProteinBoxBot
editYour bot, ProteinBoxBot, uploaded a bundle of images a few years ago (eg. File:PBB Protein INDO image.jpg) with no description. There looks to be about 50 or so that are populating in Category:Wikipedia files lacking a description. I was wondering if there would be a way for you or your fellow bot owner to get the bot to go and add a description to the files. (I will also be posting on your bot co-owner's talk page) Thanks in advance. -- ТимофейЛееСуда. 21:57, 4 September 2012 (UTC)
I've asked a question at Template talk:PBB#Just a hardcoding? but not received a response. As one of ProteinBoxBot's operators, I'm wondering if you can shed a light on it for me. VanIsaacWS Vexcontribs 07:59, 30 July 2013 (UTC)
Please see my comment at User talk:Andrew Su#PBB templates.—Anomalocaris (talk) 19:00, 26 September 2013 (UTC)
ProteinBoxBot updates to UniProt links
editHi. ProteinBoxBot is making a large number updates that seem to be in error. See for example diff. Regards Boghog (talk) 10:41, 15 November 2013 (UTC)
In the meantime, I have requested a temporary emergency shutdown of the bot. Boghog (talk) 11:04, 15 November 2013 (UTC)
Bot being discussed
edithere Best Doc James (talk · contribs · email) 20:38, 11 December 2016 (UTC)
Bots Newsletter, April 2017
edit| Bots Newsletter, April 2017 | |
|---|---|
 Greetings! The BAG Newsletter is now the Bots Newsletter, per discussion. As such, we've subscribed all bot operators to the newsletter. You can subscribe/unsubscribe from future newsletters by adding/removing your name from this list. Highlights for this newsletter include:
Magioladitis ARBCOM case has closed. The remedies of the case include:
We currently have 27 open bot requests at Wikipedia:Bots/Requests for approval, and could use your help processing!
There are multiple ongoing discussions surrounding bot-related matters. In particular:
Several new things are around:
Wikimania 2017 is happening in Montreal, during 9–13 August. If you plan to attend, or give a talk, let us know! Thank you! edited by:Headbomb 11:35, 12 April 2017 (UTC) (You can unsubscribe from future newsletters by removing your name from this list.) | |
Since you've been inactive for a while, I've removed you from the subscription list. Feel free to re-add yourself to the newsletter if you become active again though. Headbomb {t · c · p · b} 00:06, 13 April 2017 (UTC)
Facto Post – Issue 1 – 14 June 2017
editFacto Post – Issue 1 – 14 June 2017
This newsletter starts with the motto "common endeavour for 21st century content". To unpack that slogan somewhat, we are particularly interested in the new, post-Wikidata collection of techniques that are flourishing under the Wikimedia collaborative umbrella. To linked data, SPARQL queries and WikiCite, add gamified participation, text mining and new holding areas, with bots, tech and humans working harmoniously. Scientists, librarians and Wikimedians are coming together and providing a more unified view of an emerging area. Further integration of both its community and its technical aspects can be anticipated. While Wikipedia will remain the discursive heart of Wikimedia, data-rich and semantic content will support it. We'll aim to be both broad and selective in our coverage. This publication Facto Post (the very opposite of retroactive) and call to action are brought to you monthly by ContentMine.
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Facto Post – Issue 2 – 13 July 2017
editFacto Post – Issue 2 – 13 July 2017
Editorial: Core models and topicseditWikimedians 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. Linksedit
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Facto Post – Issue 3 – 11 August 2017
editFacto Post – Issue 3 – 11 August 2017
Wikimania reporteditInterviewed 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 T Arrow talk at 3 pm today in Drummond West, Level 3. Linkedit
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MediaWiki message delivery (talk) 10:55, 12 August 2017 (UTC)
Facto Post – Issue 4 – 18 September 2017
editFacto Post – Issue 4 – 18 September 2017
Editorial: Conservation dataeditThe 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 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. Linksedit
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MediaWiki message delivery (talk) 14:46, 18 September 2017 (UTC)
Facto Post – Issue 5 – 17 October 2017
editFacto Post – Issue 5 – 17 October 2017
Editorial: AnnotationseditAnnotation 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. Linksedit
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MediaWiki message delivery (talk) 08:46, 17 October 2017 (UTC)
Facto Post – Issue 6 – 15 November 2017
editFacto Post – Issue 6 – 15 November 2017
WikidataCon Berlin 28–9 October 2017edit 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. Linksedit
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MediaWiki message delivery (talk) 10:02, 15 November 2017 (UTC)
Facto Post – Issue 7 – 15 December 2017
editFacto Post – Issue 7 – 15 December 2017
A new bibliographical landscapeeditAt 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!  Linksedit
Editor Charles Matthews, 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.
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MediaWiki message delivery (talk) 14:54, 15 December 2017 (UTC)
Facto Post – Issue 8 – 15 January 2018
editFacto Post – Issue 8 – 15 January 2018
Metadata on the MarcheditFrom 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 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. Linksedit
Editor Charles Matthews, 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.
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MediaWiki message delivery (talk) 12:38, 15 January 2018 (UTC)
Facto Post – Issue 9 – 5 February 2018
editFacto Post – Issue 9 – 5 February 2018
Wikidata as HubeditOne 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. 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. Linksedit
Editor Charles Matthews, 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.
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MediaWiki message delivery (talk) 11:50, 5 February 2018 (UTC)
Facto Post – Issue 10 – 12 March 2018
editFacto Post – Issue 10 – 12 March 2018
Milestone for mix'n'matcheditAround 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 Stakhanovite! Linksedit
Editor Charles Matthews, 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.
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MediaWiki message delivery (talk) 12:26, 12 March 2018 (UTC)
Facto Post – Issue 11 – 9 April 2018
editFacto Post – Issue 11 – 9 April 2018
The 100 Skins of the OnioneditOpen 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. Linksedit
Editor Charles Matthews, 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.
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Facto Post – Issue 12 – 28 May 2018
editFacto Post – Issue 12 – 28 May 2018
ScienceSource fundededitThe 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. 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. Linksedit
Editor Charles Matthews, 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.
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Facto Post – Issue 13 – 29 May 2018
editFacto Post – Issue 13 – 29 May 2018
 The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page.
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Facto Post enters its second year, with a Cambridge Blue (OK, Aquamarine) background, a new logo, but no Cambridge blues. On-topic for the ScienceSource project is a project page here. It contains some case studies on how the WP:MEDRS guideline, for the referencing of articles at all related to human health, is applied in typical discussions. Close to home also, a template, called {{medrs}} for short, is used to express dissatisfaction with particular references. Technology can help with patrolling, and this Petscan query finds over 450 articles where there is at least one use of the template. Of course the template is merely suggesting there is a possible issue with the reliability of a reference. Deciding the truth of the allegation is another matter. This maintenance issue is one example of where ScienceSource aims to help. Where the reference is to a scientific paper, its type of algorithm could give a pass/fail opinion on such references. It could assist patrollers of medical articles, therefore, with the templated references and more generally. There may be more to proper referencing than that, indeed: context, quite what the statement supported by the reference expresses, prominence and weight. For that kind of consideration, case studies can help. But an algorithm might help to clear the backlog. 
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Facto Post – Issue 14 – 21 July 2018
edit| Facto Post – Issue 14 – 21 July 2018
The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page.
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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". 
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Facto Post – Issue 15 – 21 August 2018
edit| Facto Post – Issue 15 – 21 August 2018
The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page.
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.jpg) To grasp the nettle, there are rare diseases, there are tropical diseases and then there are "neglected diseases". Evidently a rare enough disease is likely to be neglected, but neglected disease these days means a disease not rare, but tropical, and most often infectious or parasitic. Rare diseases as a group are dominated, in contrast, by genetic diseases. A major aspect of neglect is found in tracking drug discovery. Orphan drugs are those developed to treat rare diseases (rare enough not to have market-driven research), but there is some overlap in practice with the WHO's neglected diseases, where snakebite, a "neglected public health issue", is on the list. 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.
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MediaWiki message delivery (talk) 13:23, 21 August 2018 (UTC)
Facto Post – Issue 16 – 30 September 2018
edit| Facto Post – Issue 16 – 30 September 2018
The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page.
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 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 SI units are for the content. Likewise cataloguing publications would not be onerous, because part of the process would be to generate uniform metadata. Without claiming it could be the mythical free lunch, it might be reasonably be argued that sandwiches can be packaged much alike and have barcodes, whatever the fillings. The best on offer, to stretch the metaphor, is the meal kit option, in the form of XML. Where scientific papers are delivered as XML downloads, you get all the ingredients ready to cook. But have to prepare the actual meal of slow food yourself. See Scholarly HTML for a recent pass at heading off XML with HTML, in other words in the native language of the Web. The argument from real life is a traditional mixture of frictional forces, vested interests, and the classic irony of the principle of unripe time. On the other hand, discoverability actually diminishes with the prolific progress of science publishing. No, it really doesn't scale. Wikimedia as movement can do something in such cases. We know from open access, we grok the Web, we have our own horse in the HTML race, we have Wikidata and WikiJournal, and we have the chops to act. 
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MediaWiki message delivery (talk) 17:57, 30 September 2018 (UTC)
Facto Post – Issue 17 – 29 October 2018
edit| Facto Post – Issue 17 – 29 October 2018
The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page.
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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. 
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MediaWiki message delivery (talk) 15:01, 29 October 2018 (UTC)
Facto Post – Issue 18 – 30 November 2018
edit| Facto Post – Issue 18 – 30 November 2018
The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page.
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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 library science is coming Wikidata's way. That poses the question about the other direction: is more Wikimedia technology advancing on libraries? Good point. 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.
Account creation is now open on the ScienceSource wiki, where you can see SPARQL visualisations of text mining.
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MediaWiki message delivery (talk) 11:20, 30 November 2018 (UTC)
Facto Post – Issue 19 – 27 December 2018
edit| Facto Post – Issue 19 – 27 December 2018
The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page.
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Zotero is free software for reference management by the Center for History and New Media: see Wikipedia:Citing sources with Zotero. It is also an active user community, and has broad-based language support.  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.
Diversitech, the latest ContentMine grant application to the Wikimedia Foundation, is in its community review stage until January 2.
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MediaWiki message delivery (talk) 19:08, 27 December 2018 (UTC)
Facto Post – Issue 20 – 31 January 2019
edit| Facto Post – Issue 20 – 31 January 2019
The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page.
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Recently Jimmy Wales has made the point that computer home assistants take much of their data from Wikipedia, one way or another. So as well as getting Spotify to play Frosty the Snowman for you, they may be able to answer the question "is the Pope Catholic?" Possibly by asking for disambiguation (Coptic?). 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 Tim Berners-Lee. If the Knowledge Graph by Google exemplifies Heraclitean Web technology gaining authority, contra GIGO, Wikimedians still have a role in its critique. But not just with the teenage skill of detecting phoniness. There is more to beating Gresham than exposing the factoid and urban myth, where WP:V does do a great job. Placeholders must be detected, and working with Wikidata is a good way to understand how having one statement as data can blind us to replacing it by a more accurate one. An example that is important to open access is that, firstly, the term itself needs considerable unpacking, because just being able to read material online is a poor relation of "open"; and secondly, trying to get Creative Commons license information into Wikidata shows up issues with classes of license (such as CC-BY) standing for the actual license in major repositories. Detailed investigation shows that "everything flows" exacerbates the issue. But Wikidata can solve it.
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MediaWiki message delivery (talk) 10:53, 31 January 2019 (UTC)
Facto Post – Issue 21 – 28 February 2019
edit| Facto Post – Issue 21 – 28 February 2019
The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page.
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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.  Ben Goldacre in 2014 wrote (link below) "[...] : the "information architecture" of evidence based medicine (if you can tolerate such a phrase) is a chaotic, ad hoc, poorly connected ecosystem of legacy projects. In some respects the whole show is still run on paper, like it's the 19th century." Is there a Wikidatan in the house? Wouldn't some machine-readable content that is structured data help? Most likely it would, but the arcana of systematic reviews and how they add value would still need formal handling. The PRISMA standard dates from 2009, with an update started in 2018. The concerns there include the corpus of papers used: how selected and filtered? Now that Wikidata has a 20.9 million item bibliography, one can at least pose questions. Each systematic review is a tagging opportunity for a bibliography. Could that tagging be reproduced by a query, in principle? Can it even be second-guessed by a query (i.e. simulated by a protocol which translates into SPARQL)? Homing in on the arcana, do the inclusion and filtering criteria translate into metadata? At some level they must, but are these metadata explicitly expressed in the articles themselves? The answer to that is surely "no" at this point, but can TDM find them? Again "no", right now. Automatic identification doesn't just happen. Actually these questions lack originality. It should be noted though that WP:MEDRS, the reliable sources guideline used here for health information, hinges on the assumption that the usefully systematic reviews of biomedical literature can be recognised. Its nutshell summary, normally the part of a guideline with the highest density of common sense, allows literature reviews in general validity, but WP:MEDASSESS qualifies that indication heavily. Process wonkery about systematic reviews definitely has merit.
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MediaWiki message delivery (talk) 10:02, 28 February 2019 (UTC)
Facto Post – Issue 22 – 28 March 2019
edit| Facto Post – Issue 22 – 28 March 2019
The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page.
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Half a century ago, it was the era of the mainframe computer, with its air-conditioned room, twitching tape-drives, and appearance in the title of a spy novel Billion-Dollar Brain then made into a Hollywood film. Now we have the cloud, with server farms and the client–server model as quotidian: this text is being typed on a Chromebook. The term Applications Programming Interface or API is 50 years old, and refers to a type of software library as well as the interface to its use. While a compiler is what you need to get high-level code executed by a mainframe, an API out in the cloud somewhere offers a chance to perform operations on a remote server. For example, the multifarious bots active on Wikipedia have owners who exploit the MediaWiki API. APIs (called RESTful) that allow for the GET HTTP request are fundamental for what could colloquially be called "moving data around the Web"; from which Wikidata benefits 24/7. So the fact that the Wikidata SPARQL endpoint at query.wikidata.org has a RESTful API means that, in lay terms, Wikidata content can be GOT from it. The programming involved, besides the SPARQL language, could be in Python, younger by a few months than the Web. Magic words, such as occur in fantasy stories, are wishful (rather than RESTful) solutions to gaining access. You may need to be a linguist to enter Ali Baba's cave or the western door of Moria (French in the case of "Open Sesame", in fact, and Sindarin being the respective languages). Talking to an API requires a bigger toolkit, which first means you have to recognise the tools in terms of what they can do. On the way to the wikt:impactful or polymathic modern handling of facts, one must perhaps take only tactful notice of tech's endemic problem with documentation, and absorb the insightful point that the code in APIs does articulate the customary procedures now in place on the cloud for getting information. As Owl explained to Winnie-the-Pooh, it tells you The Thing to Do.
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MediaWiki message delivery (talk) 11:45, 28 March 2019 (UTC)
Facto Post – Issue 23 – 30 April 2019
edit| Facto Post – Issue 23 – 30 April 2019
The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page.
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 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 ad fontes, so prevalent here on Wikipedia as "can you give me a source for that?", and being prepared to deal with complicated analyses into specified subcases. Impatience expressed as a disdain for such pedantry is quite understandable, but neither dirty data nor false dichotomies are at all good to have around. Issue 13 and Issue 21, respectively on WP:MEDRS and systematic reviews, talk about biomedical literature and computing tasks that would be of higher quality if they could be made more "administrative". For example, it is desirable that the decisions involved be consistent, explicable, and reproducible by non-experts from specified inputs. What gets clouded out is not impossibly hard to understand. You do need to put together the insights of functional programming, which is a doctrinaire and purist but clearcut approach, with the practicality of office software. Loopless computation can be conceived of as a seamless forward march of spreadsheet columns, each determined by the content of previous ones. Very well: to do a backward audit, when now we are talking about Wikidata, we rely on integrity of data and its scrupulous sourcing: and clearcut case analyses. The MEDRS example forces attention on purge attempts such as Beall's list.
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MediaWiki message delivery (talk) 11:27, 30 April 2019 (UTC)
Facto Post – Issue 24 – 17 May 2019
editFacto Post – Issue 24 – 17 May 2019 The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page.
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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 (text and data mining). 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 ScienceSource project innovates in TDM, by storing its text mining results in a Wikibase site. It strives for compliance of its fact mining, on drug treatments of diseases, with an automated form of the relevant Wikipedia referencing guideline MEDRS. Where WikiFactMine set up an API for reuse of its results, ScienceSource has a SPARQL query service, with look-and-feel exactly that of Wikidata's at query.wikidata.org. It also now has a custom front end, and its content can be federated, in other words used in data mashups: it is one of over 50 sites that can federate with Wikidata. The human factor comes to bear through the front end, which combines a link to the HTML version of a paper, text mining results organised in drug and disease columns, and a SPARQL display of nearby drug and disease terms. Much software to develop and explain, so little time! Rather than telling the tale, Facto Post brings you ScienceSource links, starting from the how-to video, lower right.
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. 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.
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