Wikipedia talk:WikiProject Biology/Archive 9
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Facto Post – Issue 5 – 17 October 2017
Facto Post – Issue 5 – 17 October 2017
 Editorial: AnnotationsAnnotation is nothing new. The glossators of medieval Europe annotated between the lines, or in the margins of legal manuscripts of texts going back to Roman times, and created a new discipline. In the form of web annotation, the idea is back, with texts being marked up inline, or with a stand-off system. Where could it lead?  ContentMine operates in the field of text and data mining (TDM), where annotation, simply put, can add value to mined text. It now sees annotation as a possible advance in semi-automation, the use of human judgement assisted by bot editing, which now plays a large part in Wikidata tools. While a human judgement call of yes/no, on the addition of a statement to Wikidata, is usually taken as decisive, it need not be. The human assent may be passed into an annotation system, and stored: this idea is standard on Wikisource, for example, where text is considered "validated" only when two different accounts have stated that the proof-reading is correct. A typical application would be to require more than one person to agree that what is said in the reference translates correctly into the formal Wikidata statement. Rejections are also potentially useful to record, for machine learning.
As a contribution to data integrity on Wikidata, annotation has much to offer. Some "hard cases" on importing data are much more difficult than average. There are for example biographical puzzles: whether person A in one context is really identical with person B, of the same name, in another context. In science, clinical medicine require special attention to sourcing ( WP:MEDRS ), and is challenging in terms of connecting findings with the methodology employed. Currently decisions in areas such as these, on Wikipedia and Wikidata, are often made ad hoc. In particular there may be no audit trail for those who want to check what is decided.
Annotations are subject to a World Wide Web Consortium standard, and behind the terminology constitute a simple JSON data structure. What WikiFactMine proposes to do with them is to implement the MEDRS guideline, as a formal algorithm, on bibliographical and methodological data. The structure will integrate with those inputs the human decisions on the interpretation of scientific papers that underlie claims on Wikidata. What is added to Wikidata will therefore be supported by a transparent and rigorous system that documents decisions. An example of the possible future scope of annotation, for medical content, is in the first link below. That sort of detailed abstract of a publication can be a target for TDM, adds great value, and could be presented in machine-readable form. You are invited to discuss the detailed proposal on Wikidata, via its talk page. Links
Editor Charles Matthews. Please leave feedback for him.
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MediaWiki message delivery (talk) 08:46, 17 October 2017 (UTC)
Self-assembling peptide
Self-assembling peptide was tagged for copy editing when it needed content revisions and relevant figures. I didn't know who else to send this to. Hopefully, someone here can improve the article. HRouillier (talk) 17:13, 13 November 2017 (UTC)
Facto Post – Issue 6 – 15 November 2017
Facto Post – Issue 6 – 15 November 2017
WikidataCon Berlin 28–9 October 2017 Under the heading rerum causas cognescere, the first ever Wikidata conference got under way in the Tagesspiegel building with two keynotes, One was on YAGO, about how a knowledge base conceived ten years ago if you assume automatic compilation from Wikipedia. The other was from manager Lydia Pintscher, on the "state of the data". Interesting rumours flourished: the mix'n'match tool and its 600+ datasets, mostly in digital humanities, to be taken off the hands of its author Magnus Manske by the WMF; a Wikibase incubator site is on its way. Announcements came in talks: structured data on Wikimedia Commons is scheduled to make substantive progress by 2019. The lexeme development on Wikidata is now not expected to make the Wiktionary sites redundant, but may facilitate automated compilation of dictionaries.  And so it went, with five strands of talks and workshops, through to 11 pm on Saturday. Wikidata applies to GLAM work via metadata. It may be used in education, raises issues such as author disambiguation, and lends itself to different types of graphical display and reuse. Many millions of SPARQL queries are run on the site every day. Over the summer a large open science bibliography has come into existence there. Wikidata's fifth birthday party on the Sunday brought matters to a close. See a dozen and more reports by other hands. Links
Editor Charles Matthews. Please leave feedback for him.
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MediaWiki message delivery (talk) 10:02, 15 November 2017 (UTC)
Chondrogenesis page
I am planing to amplify the information related to the molecular biology behind chondrogenesis. Alejandrobc95 (talk) 03:15, 26 November 2017 (UTC)
Biology articles at GAN
Some biology articles have languished in the GAN queue for over 6 months now. If anyone would like to review one or two it would be greatly appreciated. Chiswick Chap (talk) 10:21, 30 November 2017 (UTC)
WP:AALERTS need some help on Community Wishlist Survey
Many of you use Article Alerts to get notified of discussions (PRODs and AfD in particular). However, due to our limit resources (one bot coder), not a whole lot of work can be done on Article Alerts to expand and maintain the bot. If the coder gets run over by a bus, then it's quite possible this tool would become unavailable in the future.
There's currently a proposal on the Community Wishlist Survey for the WMF to take over the project, and make it both more robust / less likely to crash / have better support for new features. But one of the main things is that with a full team behind Article Alerts, this could also be ported to other languages!
So if you make use of Article Alerts and want to keep using it and see it ported to other languages, please
Amitosis: urgent editor help needed
The term "amitosis" was introduced in the late 19th century to designate a type of cell division that was then supposed to exist, namely, division of the nucleus and the cell without condensation and accurate segregation of chromosomes. From the moment the term was introduced, doubts about its relevance and its very existence lingered. In the 20th century, it was shown that splitting of the cell and its nucleus in animal and human cells is not cell division but cell death (apoptosis). The division of unicellular eukaryotes, occasionally also called "amitosis" because of the preservation of nuclear envelope at all stages , has nevertheless perfectly accurate segregation of chromosomes and is known today as "closed mitosis", while the mitosis of animal and plant cells which includes nuclear envelope breakdown is called "open".
The term "amitosis" together with the underlying concept was quietly abandoned by cell biologists. Serious textbooks and other educational resources, such as Molecular Biology of the Cell by Alberts et al., do not mention it at all. Unfortunately, it is perpetuated to this day in low-quality textbooks and even in new low-quality "research" that occasionally gets published in journals with low or zero impact factor.
In this respect, Wikipedia has very important role to educate the community. Unfortunately, many Wikipedians - I suppose, well-intentioned lay people - are happy to dig outdated and plain wrong statements about amitosis and to include them in the article. As a cell biologist and educator, I repeatedly correct the article but every time my efforts turn out in vain because someone puts the wrong things back in place and cites junk science from low-quality sources as a proof that this non-existent phenomenon is real.
I call for urgent help from experts in cell biology among Wikipedia editors, because I find the situation intolerable. — Preceding unsigned comment added by Rhodospirillum (talk • contribs) 10:06, 13 December 2017 (UTC)
Facto Post – Issue 7 – 15 December 2017
Facto Post – Issue 7 – 15 December 2017
A new bibliographical landscapeAt 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. CrossRef over 50% of the citation data is open. Now the holdout publishers are being lobbied to release rights on citations.
But all that is just the beginning. Topics of papers are identified, authors disambiguated, with significant progress on the use of the four million ORCID IDs for researchers, and proposals formulated to identify methodology in a machine-readable way. P4510 on Wikidata has been introduced so that methodology can sit comfortably on items about papers.
More is on the way. OABot applies the unpaywall principle to Wikipedia referencing. It has been proposed that Wikidata could assist WorldCat in compiling the global history of book translation. Watch this space. And make promoting #1lib1ref one of your New Year's resolutions. Happy holidays, all!  Links
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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
Facto Post – Issue 8 – 15 January 2018
Metadata on the MarchFrom the days of hard-copy 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. Links
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MediaWiki message delivery (talk) 12:38, 15 January 2018 (UTC)
One of your project's articles has been selected for improvement!
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Facto Post – Issue 9 – 5 February 2018
| Facto Post – Issue 9 – 5 February 2018
m:Grants:Project/ScienceSource is the new ContentMine proposal: please take a look.
Wikidata as HubOne way of looking at Wikidata relates it to the 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. Links
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MediaWiki message delivery (talk) 11:50, 5 February 2018 (UTC)
WikiProject X Newsletter • Issue 11
Check out this month's issue of the WikiProject X newsletter, with plans to renew work with a followup grant proposal to support finalising the deployment of CollaborationKit!
-— Isarra ༆ 21:26, 14 February 2018 (UTC)
RfC: The lead sentence of the Sex article
Opinions are needed on the following matter:
Modification of "Life timeline" in "Timeline of the formation of the Universe"
Re: https://en.wikipedia.org/wiki/Timeline_of_the_formation_of_the_Universe
Consider a supplement to the life timeline diagram in this document. The timeline lacks an epoch or period between the epoch "Single-celled life" and the epoch "water." I suggest an intervening epoch titled, "Proto-life". We know that pre-life organic molecules, biochemical pathways and structures such as lipid bi-layered cells must have evolved prior to actual single-celled life. During the proto-life period, substances and processes like complex biomolecules (e.g., nucleotides, RNA), metabolic biochemical pathways and cycles and other elements of intermediate metabolism, etc. evolved.
The length of this period is little known but would likely range from tens to hundreds of millions of years as best as I can assess. — Preceding unsigned comment added by WeakAnthroPrinc (talk • contribs) 20:09, 19 February 2018 (UTC)
Overlaps of articles on ecological relationships
There is a merge discussion at
Facto Post – Issue 10 – 12 March 2018
Facto Post – Issue 10 – 12 March 2018
Milestone for mix'n'matchAround 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 !
Links
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MediaWiki message delivery (talk) 12:26, 12 March 2018 (UTC)
Facto Post – Issue 11 – 9 April 2018
Facto Post – Issue 11 – 9 April 2018
The 100 Skins of the OnionOpen 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 text and data mining purposes they highlight. The long tail, or in other words the onion heart when it has become fiddly beyond patience to skin, does call for a pis aller . But the real knack is to do more between the XML and the heart.
Links
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MediaWiki message delivery (talk) 16:25, 9 April 2018 (UTC)
i-motif DNA discovery (New Type of DNA)
Hello WP:BIOLOGY! This past weekend a new type of DNA was found inside the nucleii of human cells. This DNA is called i-motif DNA and is a 4-stranded (quadroplex) type of DNA. It is notable because of its peculiar cytosine-cytosine bonds, which normally don't occur in standard DNA. I'm just a layman who edits Wikipedia, and I will be creating the new article at i-motif DNA, but I just wanted to give those who might be experts in the DNA field a heads-up about this exciting new discovery. I think there is a lot of information out there to make this a good article, but I'm working on other projects so I don't want to get too involved. Thank you, Fritzmann2002 17:47, 30 April 2018 (UTC)
Elisa Izaurralde article
Hi everyone. I'm working on expanding the Wikipedia page for Elisa Izaurralde, a prominent Uruguayan RNA researcher who died last week. I would appreciate help if people want to contribute. Thanks Biochemlife (talk) 10:03, 5 May 2018 (UTC)
Merger discussion for Longitudinal study
An article which may be of interest to this project—Longitudinal study —has been proposed for merging with Long-term experiment. If you are interested, please participate in the merger discussion. Thank you. Mathglot (talk) 03:16, 12 May 2018 (UTC)
Facto Post – Issue 12 – 28 May 2018
Facto Post – Issue 12 – 28 May 2018
ScienceSource fundedThe 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 Prophylaxis misses the point that gate-keeping will be done by an algorithm.
Two well-known but rather different areas where such considerations apply are tropical diseases and alternative medicine. There are also a number of potential downloading troubles, and these were mentioned in Issue 11. There is likely to be a gap, even with the guideline, between conditions taken to be necessary but not sufficient, and conditions sufficient but not necessary, for candidate papers to be included. With around 10,000 recognised medical conditions in standard lists, being comprehensive is demanding. With all of these aspects of the task, ScienceSource will seek community help. Links
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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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MediaWiki message delivery (talk) 10:16, 28 May 2018 (UTC)
Please come and help...
A
WikiProject collaboration notice from the Portals WikiProject
The reason I am contacting you is because there are one or more portals that fall under this subject, and the Portals WikiProject is currently undertaking a major drive to automate portals that may affect them.
Portals are being redesigned.
The new design features are being applied to existing portals.
At present, we are gearing up for a maintenance pass of portals in which the introduction section will be upgraded to no longer need a subpage. In place of static copied and pasted excerpts will be self-updating excerpts displayed through selective transclusion, using the template {{Transclude lead excerpt}}.
The discussion about this can be found here.
Maintainers of specific portals are encouraged to sign up as project members here, noting the portals they maintain, so that those portals are skipped by the maintenance pass. Currently, we are interested in upgrading neglected and abandoned portals. There will be opportunity for maintained portals to opt-in later, or the portal maintainers can handle upgrading (the portals they maintain) personally at any time.
Background
On April 8th, 2018, an RfC ("Request for comment") proposal was made to eliminate all portals and the portal namespace. On April 17th, the Portals WikiProject was rebooted to handle the revitalization of the portal system. On May 12th, the RfC was closed with the result to keep portals, by a margin of about 2 to 1 in favor of keeping portals.
Since the reboot, the Portals WikiProject has been busy building tools and components to upgrade portals.
So far, 84 editors have joined.
If you would like to keep abreast of what is happening with portals, see the newsletter archive.
If you have any questions about what is happening with portals or the Portals WikiProject, please post them on the
Thank you. — The Transhumanist 07:27, 30 May 2018 (UTC)
Hello from WikiProject Computational Biology!
I hope you don't mind me adding our WikiProject to your list of related WikiProjects - if there's a better place to link this, just let me know. Thanks! Amkilpatrick (talk) 09:35, 8 June 2018 (UTC)
Various Biology drafts
Over on
Facto Post – Issue 13 – 29 May 2018
Facto 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 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. WP:MEDRS
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MediaWiki message delivery (talk) 18:19, 29 June 2018 (UTC)
Facto Post – Issue 14 – 21 July 2018
| 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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MediaWiki message delivery (talk) 06:10, 21 July 2018 (UTC)
Does anyone here know if International Code of Area Nomenclature is dead?
I am curious to see if anyone in this WP knows if the International Code of Area Nomenclature ever published the code, or if the code was adopted? -Furicorn (talk) 11:16, 24 July 2018 (UTC)
AFD Discussion - Modern Mars habitability
There is an article at AfD that may interest you. The article is here Modern Mars habitability. Please vote or comment at WP:Articles for deletion/Modern Mars habitability
Robert Walker (talk) 03:40, 18 August 2018 (UTC)
Please read Lucien Cuénot#A voice unheard? and then read my comments on the article's talk page. -- PBS (talk) 16:42, 19 August 2018 (UTC)
Facto Post – Issue 15 – 21 August 2018
| 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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Côte d'Ivoire To grasp the nettle, there are genetic diseases .
A major aspect of neglect is found in tracking 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)
Request for comments
This is a request for comments regarding the relevance of Denny (hybrid hominin) as it relates to human interspecies breeding. The link to the discussion is at: Talk:Human evolution#A curious discovery, but not really on-topic. Cheers, Rowan Forest (talk) 16:35, 26 August 2018 (UTC)
WikiProject X Newsletter • Issue 12
This month: WikiProject X: The resumption
Work has resumed on WikiProject X and CollaborationKit, backed by a successfully funded Project Grant. For more information on the current status and planned work, please see this month's issue of the newsletter!
-— Isarra ༆ 22:24, 30 August 2018 (UTC)
Sex determination material at the Sexual differentiation in humans article
Opinions are needed on the following: