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Archive 40 | ← | Archive 42 | Archive 43 | Archive 44 | Archive 45 | Archive 46 | → | Archive 50 |
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)
I've made some taxonomic suggestions to cygnis insignis ( I would have made them myself, but the editor and I sometimes conflict, so I thought that it would be a better way to make changes), namely subfamily Antrozoinae should now be changed to tribe Antrozoini somewhere under the Vespertilioninae as that is how the article is referenced now....Miniopterinae should now be changed to family Miniopteridae.....Vespertilioninae article taxonomy can be changed as well...it looks like the higher and lower taxa for these conflict. Cygnus cites Mammal Species of the World as the reference, and states the higher taxa is correct. Cistugidae also seems to follow this way as well. I thought somewhere along the line MSW was out of date. Any experts on bats out there who can determine if MSW is out of date for these groups? Which should Wikipedia follow, the higher or lower taxa?.I've also posted this on the bats task force talk page....feel free to leave your comments there... Pvmoutside ( talk) 16:45, 7 March 2019 (UTC)
I have started a discussion at Wikipedia talk:Notability (academics)#Notability of taxonomists about an issue that has been bothering me lately when wearing my NPP hat: does being a recognized taxonomic authority make you notable? Please pop over and comment; I suspect for some of you this may not be a new topic, and I think some codification would be useful. -- Elmidae ( talk · contribs) 22:09, 8 March 2019 (UTC)
Does anyone know anything about the status of Home of Ichneumonoidea (Taxapad), run by Dicky Sick Ki Yu? The web address (www.taxapad.com) has returned nothing for the last week or so. It's used as a reference on Wikipedia almost 4,000 times. I've sent an email to Yu and have received no response. Internet Archive's Wayback Machine usually seems to have copies, so the information is recoverable. What do we do next? SchreiberBike | ⌨ 00:57, 8 February 2019 (UTC)
A discussion on my talk page was started by Cygnis insignis. I thought I'd bring it here for a more comprehensive discussion if people feel like talking about it. I'll continue doing my thing unless a concensus develops to do something different..... Pvmoutside ( talk) 17:16, 14 March 2019 (UTC)
See Wikipedia talk:Template namespace#RfC on templates storing data. The automated taxobox system currently relies on storing the taxonomic hierarchy in taxonomy templates, which one outcome of this RfC would forbid. Peter coxhead ( talk) 10:13, 16 March 2019 (UTC)
I am getting completely fed up by what is currently going on with cygnis insignis and the formatting of the first sentence in articles on species with common names. To whit: for whatever reason, they insist on phrasing the first sentence as "Common name, species scientific name, is ...". Whereas the vast majority of articles (at a guess, 90%+ - didn't want to work up a regex for it) use "Common name (scientific name) is ...". They will happily edit war over it (e.g., [1] [2]), and appear to consider this short exchange as a justification for continuing to do so [3]. I'm not the only one who has blown a tyre on that particular pile of caltrops.
Now I'm aware that we are generally handicapped by the fact that our nominal topic-specific MOS, which contains the latter usage, still has this big rider on top that says "feel free to ignore me". I've also seen that there have been a couple of discussions in the past already ( [4]; [5]) that touched on the issue and went nowhere fast. However, I think the current state of affairs is quite counter-productive. I see no benefit in scattering around a small minority of articles that have divergent formatting and are enforced to remain in that state by ownership behaviour, for no practical gain. All the more since, when you as a reader are used to the C(S) format, encountering these articles looks just as if no-one had cleaned them up yet. To top it off, "Common name, species scientific name" is plain misleading - both names are the species name; the usual phrasing does make that clear.
I don't want to drag this to AN/I as disruptive behaviour (although it is getting there) and I don't want to get into one of these easily-provoked spats with cygnis insignis. Instead, I want to suggest that editors currently active in this area arrive at a consensus about preferred usage, and come to some decision about how to handle these instances. Do we treat this particular formatting issue as free-for-all, article creator gets to determine their version (the WP:ENGVAR/ WP:REFVAR approach)? Or do we promote a uniform approach that keeps articles in step with the majority? Then there would be something to point to, and we can ask people to stick to it.
(As an addendum, I would be very keen to get Wikipedia:Manual_of_Style/Organisms to functional status, and I'm not sure as to the reasons why it is still lingering in draft mode at this point?) -- Elmidae ( talk · contribs) 22:08, 4 March 2019 (UTC)
Two points:
Peter coxhead ( talk) 08:34, 5 March 2019 (UTC)
The {{TemplateName|foo|or=phoo|sci=Genus species|sci2=G. s. subspecies|aka=barbaz}} in South Africa, is ...
might output "The foo or phoo (Genus species, or G. s. subspecies), also known as the barbaz in South Africa, is ...)" on the browser side (see wikisource for example class output). At any rate, we need not concern ourselves with what Google or other tools outside our control are doing because we can't control them and they could change tomorrow. —
SMcCandlish
☏
¢ 😼 12:45, 7 March 2019 (UTC)Since the discussion seems to have about run its course, I'll try to sum up my overall impression:
{{organism name|lion|panthera leo}}
could change the preview behaviour or be a flag for it to not strip the name, although I generally don't like these types of template as they impair readability.
Jts1882 |
talk 09:17, 20 March 2019 (UTC)For anyone interested, there is a discussion on Wikidata regarding taxa and their names, and whether they should be separated into two items. The decision will not affect how we treat taxonomic articles on Wikipedia, but people with nomenclatural and/or data-management expertise may have good insight. --Animalparty! ( talk) 00:23, 19 March 2019 (UTC)
the name, the author(s), the publication and the datedo not specify a taxon in the sense of a particular group of organisms. These four define the taxon name, not its scope (circumscription), other than the need to include the type. The IPNI entry "Asparagaceae Juss. -- Gen. Pl. [Jussieu] 40. 1789 [4 Aug 1789] ; nom. cons." does not distinguish between the APG's Asparagaceae s.l. and the Asparagaceae s.s. of those who do not accept APG's lumping. As per my comments at the Wikidata discussion, Hyacinthaceae is the same taxon as Scilloideae in the two currently used alternative systems (which is why we rightly have a redirect from the former to the latter), although not one of the "four parts" is the same. Peter coxhead ( talk) 22:42, 20 March 2019 (UTC)
A variety of hypotheses about that nameisn't right, I think. The hypotheses (i.e. the choices that can be made by taxonomists) are (1) the circumscription of the taxon (2) its position (rank, placement) relative to other taxa. Once (1) and (2) are settled, the name follows algorithmically – (ignoring conservation of names) by finding the oldest name used for a type that falls into the taxon thus established. Applying the slightly different algorithms in the different codes isn't easy, partly because they are complicated, and partly because the research needed to find the oldest (highest priority) name is difficult. However, the
variety of hypothesesapply to the taxon, not the name. The circumscription, rank and placement determine the name uniquely. You can't hypothesize what the name for a family in which Felis is placed should be called; it has to be "Felidae", unless the family includes a genus with a higher priority family name formed from it.
@ Guettarda: it would seem so, and my first assumption was that Wikidata should have a data model that included such information. The key issue seems to be that, yes, you need entities in the model with the same name but the equivalent of "sensu" qualifiers (just as we less formally have Template:Taxonomy/Spermatophyta and Template:Taxonomy/Spermatophytes/Plantae to capture two different approaches to classification) but you also need to be able to choose which paths to follow. In the figure opposite, which I posted to a Wikidata discussion, there are three names (rounded boxes) and three taxa (square boxes). You must either follow the green arrows (sensu Stace, 2010, for example) or the red arrows (sensu APG, for example). Crucially, if you arrive at Taxon 3 (which is Lemnaceae sensu Stace and Lemnoideae sensu APG), by following the green arrow from Lemnaceae, you must not follow the red arrow and say that its parent is the taxon which is Araceae sensu APG. Now this can be handled via special purpose code (as we can write here in Module:Autotaxobox), but no-one seems to be able to say how to handle it in Wikidata, which is a relational database. As the Scholia example I gave above shows, without special handling, the classifications get merged and make no sense. Hopefully, it's just a failure to work out how to do it, rather than a total block. Peter coxhead ( talk) 15:41, 21 March 2019 (UTC)
Please see Talk:Monkey/Archive 1#Changed without discussion re this reversion I made. Peter coxhead ( talk) 16:30, 27 March 2019 (UTC)
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) 11:46, 28 March 2019 (UTC)
I would like to use qBugbot to resolve some self-redirects in Animal articles. For clarity, and because it confuses me, when page A links to page B, and page B is a redirect page pointing back to page A, I am saying that page A contains a self-redirect link to page B.
About 1181 animal articles contain self-redirect links pointing to 7622 redirect pages.
Pages with self-redirect links:
(These numbers could be a little low -- I may not have caught everything.)
Here is what I am considering:
Creation Exceptions:
The only case a self-redirect link would be left intact is when it goes to a subheading in the article. In total, 1181 pages would have the self-redirect links de-linked, and something less than 5400 redirect pages would be replaced with stub articles.
List of Tachinidae genera is a good example of a page with lots of self-redirects. I started fixing these manually a while back, and decided it was taking too long.
For context, qBugbot was used to create about 18,000 arthropod stubs last year, and is currently awaiting authorization to make an editing/update pass over these articles.
I'm looking for comments, criticism, and suggestions.
Thanks! Bob Webster ( talk) 00:16, 6 April 2019 (UTC)
A new Newsletter directory has been created to replace the old, out-of-date one. If your WikiProject and its taskforces have newsletters (even inactive ones), or if you know of a missing newsletter (including from sister projects like WikiSpecies), please include it in the directory! The template can be a bit tricky, so if you need help, just post the newsletter on the template's talk page and someone will add it for you.
Just throwing an idea out, haven't really thought about how to make it work. Many species don't have images. I've previously thought about going through Commons somehow to find instances where Commons has an image, but our articles don't. The downside of Commons is that there is no guarantee that images are correctly identified (images of museum specimens are likely to be correctly identified, but are generally poor representations of how living organisms appear; biological illustrations are likely to be correct, but plates are often cluttered with illustrations of several species). However, it now strikes that iNaturalist would be an excellent resource for images. It's possible to filter iNaturalist images for high confidence identifications and Wikimedia compatible licensing. Plantdrew ( talk) 16:11, 19 April 2019 (UTC)
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
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
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MediaWiki message delivery ( talk) 18:52, 17 May 2019 (UTC)
Is there a difference between "Asthena" subditaria and 'Asthena' subditaria, and is one preferred over the other on Wikipedia? SchreiberBike| ⌨ 00:58, 18 May 2019 (UTC)
This is an archive of past discussions. Do not edit the contents of this page. If you wish to start a new discussion or revive an old one, please do so on the current talk page. |
Archive 40 | ← | Archive 42 | Archive 43 | Archive 44 | Archive 45 | Archive 46 | → | Archive 50 |
Facto Post – Issue 21 – 28 February 2019
The Editor is
Charles Matthews, for
ContentMine. Please leave feedback for him, on his User talk page.
To subscribe to Facto Post go to
Wikipedia:Facto Post mailing list. For the ways to unsubscribe, see the footer.
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)
I've made some taxonomic suggestions to cygnis insignis ( I would have made them myself, but the editor and I sometimes conflict, so I thought that it would be a better way to make changes), namely subfamily Antrozoinae should now be changed to tribe Antrozoini somewhere under the Vespertilioninae as that is how the article is referenced now....Miniopterinae should now be changed to family Miniopteridae.....Vespertilioninae article taxonomy can be changed as well...it looks like the higher and lower taxa for these conflict. Cygnus cites Mammal Species of the World as the reference, and states the higher taxa is correct. Cistugidae also seems to follow this way as well. I thought somewhere along the line MSW was out of date. Any experts on bats out there who can determine if MSW is out of date for these groups? Which should Wikipedia follow, the higher or lower taxa?.I've also posted this on the bats task force talk page....feel free to leave your comments there... Pvmoutside ( talk) 16:45, 7 March 2019 (UTC)
I have started a discussion at Wikipedia talk:Notability (academics)#Notability of taxonomists about an issue that has been bothering me lately when wearing my NPP hat: does being a recognized taxonomic authority make you notable? Please pop over and comment; I suspect for some of you this may not be a new topic, and I think some codification would be useful. -- Elmidae ( talk · contribs) 22:09, 8 March 2019 (UTC)
Does anyone know anything about the status of Home of Ichneumonoidea (Taxapad), run by Dicky Sick Ki Yu? The web address (www.taxapad.com) has returned nothing for the last week or so. It's used as a reference on Wikipedia almost 4,000 times. I've sent an email to Yu and have received no response. Internet Archive's Wayback Machine usually seems to have copies, so the information is recoverable. What do we do next? SchreiberBike | ⌨ 00:57, 8 February 2019 (UTC)
A discussion on my talk page was started by Cygnis insignis. I thought I'd bring it here for a more comprehensive discussion if people feel like talking about it. I'll continue doing my thing unless a concensus develops to do something different..... Pvmoutside ( talk) 17:16, 14 March 2019 (UTC)
See Wikipedia talk:Template namespace#RfC on templates storing data. The automated taxobox system currently relies on storing the taxonomic hierarchy in taxonomy templates, which one outcome of this RfC would forbid. Peter coxhead ( talk) 10:13, 16 March 2019 (UTC)
I am getting completely fed up by what is currently going on with cygnis insignis and the formatting of the first sentence in articles on species with common names. To whit: for whatever reason, they insist on phrasing the first sentence as "Common name, species scientific name, is ...". Whereas the vast majority of articles (at a guess, 90%+ - didn't want to work up a regex for it) use "Common name (scientific name) is ...". They will happily edit war over it (e.g., [1] [2]), and appear to consider this short exchange as a justification for continuing to do so [3]. I'm not the only one who has blown a tyre on that particular pile of caltrops.
Now I'm aware that we are generally handicapped by the fact that our nominal topic-specific MOS, which contains the latter usage, still has this big rider on top that says "feel free to ignore me". I've also seen that there have been a couple of discussions in the past already ( [4]; [5]) that touched on the issue and went nowhere fast. However, I think the current state of affairs is quite counter-productive. I see no benefit in scattering around a small minority of articles that have divergent formatting and are enforced to remain in that state by ownership behaviour, for no practical gain. All the more since, when you as a reader are used to the C(S) format, encountering these articles looks just as if no-one had cleaned them up yet. To top it off, "Common name, species scientific name" is plain misleading - both names are the species name; the usual phrasing does make that clear.
I don't want to drag this to AN/I as disruptive behaviour (although it is getting there) and I don't want to get into one of these easily-provoked spats with cygnis insignis. Instead, I want to suggest that editors currently active in this area arrive at a consensus about preferred usage, and come to some decision about how to handle these instances. Do we treat this particular formatting issue as free-for-all, article creator gets to determine their version (the WP:ENGVAR/ WP:REFVAR approach)? Or do we promote a uniform approach that keeps articles in step with the majority? Then there would be something to point to, and we can ask people to stick to it.
(As an addendum, I would be very keen to get Wikipedia:Manual_of_Style/Organisms to functional status, and I'm not sure as to the reasons why it is still lingering in draft mode at this point?) -- Elmidae ( talk · contribs) 22:08, 4 March 2019 (UTC)
Two points:
Peter coxhead ( talk) 08:34, 5 March 2019 (UTC)
The {{TemplateName|foo|or=phoo|sci=Genus species|sci2=G. s. subspecies|aka=barbaz}} in South Africa, is ...
might output "The foo or phoo (Genus species, or G. s. subspecies), also known as the barbaz in South Africa, is ...)" on the browser side (see wikisource for example class output). At any rate, we need not concern ourselves with what Google or other tools outside our control are doing because we can't control them and they could change tomorrow. —
SMcCandlish
☏
¢ 😼 12:45, 7 March 2019 (UTC)Since the discussion seems to have about run its course, I'll try to sum up my overall impression:
{{organism name|lion|panthera leo}}
could change the preview behaviour or be a flag for it to not strip the name, although I generally don't like these types of template as they impair readability.
Jts1882 |
talk 09:17, 20 March 2019 (UTC)For anyone interested, there is a discussion on Wikidata regarding taxa and their names, and whether they should be separated into two items. The decision will not affect how we treat taxonomic articles on Wikipedia, but people with nomenclatural and/or data-management expertise may have good insight. --Animalparty! ( talk) 00:23, 19 March 2019 (UTC)
the name, the author(s), the publication and the datedo not specify a taxon in the sense of a particular group of organisms. These four define the taxon name, not its scope (circumscription), other than the need to include the type. The IPNI entry "Asparagaceae Juss. -- Gen. Pl. [Jussieu] 40. 1789 [4 Aug 1789] ; nom. cons." does not distinguish between the APG's Asparagaceae s.l. and the Asparagaceae s.s. of those who do not accept APG's lumping. As per my comments at the Wikidata discussion, Hyacinthaceae is the same taxon as Scilloideae in the two currently used alternative systems (which is why we rightly have a redirect from the former to the latter), although not one of the "four parts" is the same. Peter coxhead ( talk) 22:42, 20 March 2019 (UTC)
A variety of hypotheses about that nameisn't right, I think. The hypotheses (i.e. the choices that can be made by taxonomists) are (1) the circumscription of the taxon (2) its position (rank, placement) relative to other taxa. Once (1) and (2) are settled, the name follows algorithmically – (ignoring conservation of names) by finding the oldest name used for a type that falls into the taxon thus established. Applying the slightly different algorithms in the different codes isn't easy, partly because they are complicated, and partly because the research needed to find the oldest (highest priority) name is difficult. However, the
variety of hypothesesapply to the taxon, not the name. The circumscription, rank and placement determine the name uniquely. You can't hypothesize what the name for a family in which Felis is placed should be called; it has to be "Felidae", unless the family includes a genus with a higher priority family name formed from it.
@ Guettarda: it would seem so, and my first assumption was that Wikidata should have a data model that included such information. The key issue seems to be that, yes, you need entities in the model with the same name but the equivalent of "sensu" qualifiers (just as we less formally have Template:Taxonomy/Spermatophyta and Template:Taxonomy/Spermatophytes/Plantae to capture two different approaches to classification) but you also need to be able to choose which paths to follow. In the figure opposite, which I posted to a Wikidata discussion, there are three names (rounded boxes) and three taxa (square boxes). You must either follow the green arrows (sensu Stace, 2010, for example) or the red arrows (sensu APG, for example). Crucially, if you arrive at Taxon 3 (which is Lemnaceae sensu Stace and Lemnoideae sensu APG), by following the green arrow from Lemnaceae, you must not follow the red arrow and say that its parent is the taxon which is Araceae sensu APG. Now this can be handled via special purpose code (as we can write here in Module:Autotaxobox), but no-one seems to be able to say how to handle it in Wikidata, which is a relational database. As the Scholia example I gave above shows, without special handling, the classifications get merged and make no sense. Hopefully, it's just a failure to work out how to do it, rather than a total block. Peter coxhead ( talk) 15:41, 21 March 2019 (UTC)
Please see Talk:Monkey/Archive 1#Changed without discussion re this reversion I made. Peter coxhead ( talk) 16:30, 27 March 2019 (UTC)
Facto Post – Issue 22 – 28 March 2019
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Charles Matthews, for
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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) 11:46, 28 March 2019 (UTC)
I would like to use qBugbot to resolve some self-redirects in Animal articles. For clarity, and because it confuses me, when page A links to page B, and page B is a redirect page pointing back to page A, I am saying that page A contains a self-redirect link to page B.
About 1181 animal articles contain self-redirect links pointing to 7622 redirect pages.
Pages with self-redirect links:
(These numbers could be a little low -- I may not have caught everything.)
Here is what I am considering:
Creation Exceptions:
The only case a self-redirect link would be left intact is when it goes to a subheading in the article. In total, 1181 pages would have the self-redirect links de-linked, and something less than 5400 redirect pages would be replaced with stub articles.
List of Tachinidae genera is a good example of a page with lots of self-redirects. I started fixing these manually a while back, and decided it was taking too long.
For context, qBugbot was used to create about 18,000 arthropod stubs last year, and is currently awaiting authorization to make an editing/update pass over these articles.
I'm looking for comments, criticism, and suggestions.
Thanks! Bob Webster ( talk) 00:16, 6 April 2019 (UTC)
A new Newsletter directory has been created to replace the old, out-of-date one. If your WikiProject and its taskforces have newsletters (even inactive ones), or if you know of a missing newsletter (including from sister projects like WikiSpecies), please include it in the directory! The template can be a bit tricky, so if you need help, just post the newsletter on the template's talk page and someone will add it for you.
Just throwing an idea out, haven't really thought about how to make it work. Many species don't have images. I've previously thought about going through Commons somehow to find instances where Commons has an image, but our articles don't. The downside of Commons is that there is no guarantee that images are correctly identified (images of museum specimens are likely to be correctly identified, but are generally poor representations of how living organisms appear; biological illustrations are likely to be correct, but plates are often cluttered with illustrations of several species). However, it now strikes that iNaturalist would be an excellent resource for images. It's possible to filter iNaturalist images for high confidence identifications and Wikimedia compatible licensing. Plantdrew ( talk) 16:11, 19 April 2019 (UTC)
Facto Post – Issue 23 – 30 April 2019
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Charles Matthews, for
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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
The Editor is
Charles Matthews, for
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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
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MediaWiki message delivery ( talk) 18:52, 17 May 2019 (UTC)
Is there a difference between "Asthena" subditaria and 'Asthena' subditaria, and is one preferred over the other on Wikipedia? SchreiberBike| ⌨ 00:58, 18 May 2019 (UTC)