User talk:Andrew Su

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ProteinBoxBot[edit]

Your 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)

Yes, thanks for the note. We'll look into those ASAP. Ideally actually we'll just replace those older images with newer versions that are better looking (and have descriptions). Cheers, AndrewGNF (talk) 17:00, 5 September 2012 (UTC)

PBB/2232[edit]

Based on my comments EC commission changed the EC number from 1.8.1.2 to 1.8.1.6 I noted this on page: http://en.wikipedia.org/wiki/Template_talk:PBB/2232

I keep changing the number to the updated number and you reverse it to the old number. Please check EC 1.8.1.6 to verify that it is the correct number. Redactor271 (talk) 06:23, 25 March 2013 (UTC)

Portal:Gene Wiki/PDB listed at Redirects for discussion[edit]

Information.svg

An editor has asked for a discussion to address the redirect Portal:Gene Wiki/PDB. Since you had some involvement with the Portal:Gene Wiki/PDB redirect, you might want to participate in the redirect discussion (if you have not already done so). Chris Cunningham (user:thumperward) (talk) 12:15, 23 September 2012 (UTC)

Portal:Gene Wiki/SCOP listed at Redirects for discussion[edit]

Information.svg

An editor has asked for a discussion to address the redirect Portal:Gene Wiki/SCOP. Since you had some involvement with the Portal:Gene Wiki/SCOP redirect, you might want to participate in the redirect discussion (if you have not already done so). Chris Cunningham (user:thumperward) (talk) 12:15, 23 September 2012 (UTC)

Hi Andrew,

I've read that already but don't see any reference to TR2 so I wanted to know more about this- did you reanalyze this yourself?

Thanks,

Jen — Preceding unsigned comment added by 74.96.74.226 (talk) 15:38, 1 February 2013 (UTC)



Proper Citation Request[edit]

I would like to know the methods you used to get the testicular receptor 2 graph because I would like to cite your work correctly.

Can you provide me with a link to your original paper or something along those lines so I can read more?

Thank you,

Jennifer 74.96.74.226 (talk) 17:13, 24 January 2013 (UTC)

Hi Jennifer, those expression graphs came from this paper. Cheers, AndrewGNF (talk) 18:27, 24 January 2013 (UTC)

Welcome to the WP:MED/WP:PHARM[edit]

I really like these ideas and look forwards to discussing them more. How does your current bot work?Doc James (talk · contribs · email) (if I write on your page reply on mine) 01:22, 14 May 2013 (UTC)

A barnstar for you![edit]

Team Barnstar Hires.png The Teamwork Barnstar
For reaching out to new partners, charging ahead with new ventures, and taking Wikipedia's role in science and medicine so seriously, I award you this Teamwork Barnstar. Keep being awesome! Ocaasi t | c 01:20, 17 May 2013 (UTC)
Thank you, very kind! Cheers, Andrew Su (talk) 05:08, 17 May 2013 (UTC)

Hey Andrew Su

I'm sending you this because you've made quite a few edits to the template namespace in the past couple of months. If I've got this wrong, or if I haven't but you're not interested in my request, don't worry; this is the only notice I'm sending out on the subject :).

So, as you know (or should know - we sent out a centralnotice and several watchlist notices) we're planning to deploy the VisualEditor on Monday, 1 July, as the default editor. For those of us who prefer markup editing, fear not; we'll still be able to use the markup editor, which isn't going anywhere.

What's important here, though, is that the VisualEditor features an interactive template inspector; you click an icon on a template and it shows you the parameters, the contents of those fields, and human-readable parameter names, along with descriptions of what each parameter does. Personally, I find this pretty awesome, and from Monday it's going to be heavily used, since, as said, the VisualEditor will become the default.

The thing that generates the human-readable names and descriptions is a small JSON data structure, loaded through an extension called TemplateData. I'm reaching out to you in the hopes that you'd be willing and able to put some time into adding TemplateData to high-profile templates. It's pretty easy to understand (heck, if I can write it, anyone can) and you can find a guide here, along with a list of prominent templates, although I suspect we can all hazard a guess as to high-profile templates that would benefit from this. Hopefully you're willing to give it a try; the more TemplateData sections get added, the better the interface can be. If you run into any problems, drop a note on the Feedback page.

Thanks, Okeyes (WMF) (talk) 21:20, 28 June 2013 (UTC)

AANAT (gene)[edit]

Hello, Andrew Su, and thank you for your contributions!

An article you worked on AANAT (gene), appears to be directly copied from http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=736736. Please take a minute to make sure that the text is freely licensed and properly attributed as a reference, otherwise the article may be deleted.

It's entirely possible that this bot made a mistake, so please feel free to remove this notice and the tag it placed on AANAT (gene) if necessary. MadmanBot (talk) 23:28, 11 July 2013 (UTC)

Template:PBB[edit]

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 07:58, 30 July 2013 (UTC)

PBB templates[edit]

I have been editing the PBB templates in Category:Human protein templates making changes in the Name field:

  1. If the name includes a number kDa without a space, e.g. 30kDa, insert a nonbreaking space, e.g. 30 kDa
  2. If the name includes a genus, e.g. Drosophila, or a genus and species, italicize it, e.g. Drosophila
  3. If the name includes a plus sign that is superscripted in chemical notation, e.g. H+, superscript it, e.g. H+
  4. If the name includes a genus abbreviated to initial, e.g. S. cerevisiae, spell out the genus, e.g. Saccharomyces cerevisiae

These changes are consistent with Wikipedia style.

At the beginning of this project, for the fourth type of edit, I set the edit summary to: "italics; spell out genus name — if you don't like it put a note on my talk page". I used this summary for Template:PBB/10111, Template:PBB/10248, Template:PBB/10412, Template:PBB/10427, Template:PBB/10436, Template:PBB/10483, Template:PBB/10484.

When I got to the first one that included C. elegans, Template:PBB/10497, I used the edit summary "italics; spell out genus name — there are over 170 C. elegans species on C. elegans (disambiguation), not counting synonyms!"

By this time I had put the request to put a note on my talk page in 7 edit summaries, so I thought that was enough. But now I see that your ProteinboxBot has been systematically removing all of the edits I have been making.

I request that you modify ProteinBoxBot to automatically make at least the first 3 of my four changes, if not all four, consistent with WP:MOS. —Anomalocaris (talk) 18:56, 26 September 2013 (UTC)

Sorry for butting in here. Concerning gene names in {{PBB}} templates, these are based on the official Human Genome Organisation names (see HGNC Guidelines and PMID 11944974). The bot is acting to make sure that the gene names in the PBB templates match the current official HUGO gene names. While your changes have merit, they do differ from the approved names. By HUGO convention gene names, in part or in whole, are never italicized (gene symbols are italicized but not names) nor do they contain sub- or superscripts. In addition, "... molecular weights may be specified in kilodaltons using the SI unit: kDa with no space after the molecular weight". Finally the genus is abbreviated to keep the gene names from becoming too long. Boghog (talk) 05:27, 27 September 2013 (UTC)
One additional note. The gene names in PBB articles were systematically created by an approved bot. Hence changing these names is very likely to be controversial. As a general rule, it is wise to first seek consensus before making potentially controversial edits to a large number of articles or templates. Boghog (talk) 05:50, 27 September 2013 (UTC)
Thank you, Boghog, for this information. I didn't purchase "Guidelines for Human Gene Nomenclature" in Genomics, but I read HGNC's "Guidelines for Human Gene Nomenclature" section 3: Gene names, and here, it shows Drosophila italicized in the example "lunatic fringe homolog (Drosophila)" and the example "anillin, actin binding protein (scraps homolog, Drosophila)". But the same guideline in section 5: Homologies with other species, includes the example "BarH-like 1 (Drosophila)". [without italics!]
I began to insert the space before kDA because I found some templates had spaces, e.g. Template:PBB/10621, with name "Polymerase (RNA) III (DNA directed) polypeptide F, 39 kDa". I suspect that ProteinBoxBot removes nonbreaking spaces but not ordinary spaces before kDa. According to NGNC, there is not supposed to be a space between the number and kDa. Why isn't ProteinBoxBot taking out regular spaces between the number and kDa? —Anomalocaris (talk) 08:28, 27 September 2013 (UTC)
Since this discussion began, HGNC's "Guidelines for Human Gene Nomenclature" section 3: Gene names has been updated. The example with a genus or species name is now ASXL1 "additional sex combs like 1 (Drosophila)", without italics. As I said on 27 September, I suggest modifying ProteinBoxBot to take out regular spaces between the number and kDa. —Anomalocaris (talk) 15:47, 3 October 2013 (UTC)
Sorry for joining late. And thanks Boghog for chiming in -- as usual, I have very little to add. I'll just mention that PBB does not do anything to the gene symbols and titles as they come from HGNC (through NCBI) -- neither italicization nor adding/removing whitespaces. While technically it's possible to add logic to do as you suggest, I think we'd want to make sure we had consensus first (please post at WP:MCB). Cheers, Andrew Su (talk) 05:10, 10 October 2013 (UTC)

ProteinBoxBot updates to UniProt links[edit]

Hi Andrew. ProteinBoxBot is making a large number updates that seem to be in error. See for example diff. In the meantime, I have requested a temporary emergency shutdown of the bot. Cheers. Boghog (talk) 11:03, 15 November 2013 (UTC)

Thanks for the note, Boghog. We're on it now and will report back here soon... Cheers, Andrew Su (talk) 17:24, 15 November 2013 (UTC)
All should be fixed now thanks to User:X0xMaximus. Thanks for reporting this! Cheers, Andrew Su (talk) 21:21, 16 November 2013 (UTC)

User pages in Category:Human proteins[edit]

Hello, Andrew. I was perusing "Category:Human proteins" and saw that two of your user pages are in the category. I do not know how to remove them from the category because it seems like a template is putting them in there. You are probably more capable than I am with templates, so I will leave it to you. You do not need to reply to this message, unless you want to.

Warmest regards, Kjkolb (talk) 01:39, 6 March 2014 (UTC)

Fixed, thank you! Cheers, Andrew Su (talk) 05:39, 6 March 2014 (UTC)

PBB Bot at Czech wikik[edit]

Hi,

our community at Czech wikipedia is interested in enriching our articles on proteins with PBB templates (as seen on en.wikipedia) which are being filled by the bot you operate. I would like to know, if you or someone from your co-operators could operate the bot in Czech mutation of wikipedia or if we need to do it ourselves (and if you can provide guidance). Thank you very much! --Hypothalamus (talk) 12:38, 24 March 2014 (UTC)

Hi there. We unfortunately don't have the bandwidth to take on the Czech pages. (Having enough trouble keeping up to date on English WP!) You are welcome to use/adapt the code base here: https://bitbucket.org/sulab/pygenewiki. Cheers, Andrew Su (talk) 17:37, 24 March 2014 (UTC)
We really need to focus on Wikidata. A single lua-infobox and a single bot could keep all languages of Wikipedia up-to-date. I directed the discussion here: d:Wikidata_talk:WikiProject_Molecular_biology#Wikidata_Infobox_on_Czech_Wikipedia. --Tobias1984 (talk) 11:28, 25 March 2014 (UTC)
I agree completely of course. Wikidata to me is the long-term solution. I suggested the pygenewiki code base only if you wanted to do a short-term hack, but in retrospect, any effort you would have put into that would be much better directed to Wikidata... Cheers, Andrew Su (talk) 18:29, 25 March 2014 (UTC)

WikiHack in DC on April 5-6[edit]

It's a long shot, but if you were going to be in DC for the weekend after next, you might consider going to this event, Open Government WikiHack. Klortho (talk) 05:01, 26 March 2014 (UTC)

Looks awesome, but yeah, unfortunately not possible for me to attend... Thanks for the heads up! Cheers, Andrew Su (talk) 21:39, 26 March 2014 (UTC)

ProteinBoxBot Errors[edit]

As documented here, the ProteinBoxBot appears to have made a large number of erroneous edits from July 2 to 4. Please recheck the bot script before running the bot again. Thanks. Boghog (talk) 08:19, 5 July 2014 (UTC)

Aaack, sincere apologies. The bot was dormant for a few months for an unknown reason. We did a first pass of debugging to work through some changes in the mwclient library, and assumed all would be good for a small run. Obviously we were wrong. We'll clearly apply much more scrutiny and caution as we move forward. Thank you for being our second set of eyes and fixing those errors! Cheers, Andrew Su (talk) 14:06, 5 July 2014 (UTC)
... and doing more spot checking, it's clear that the error rate is unacceptably high. I'm going to just manually revert all edits from PBB made on 3 July 2014. If you have an easy mechanism to programmatically do that, feel free... Cheers, Andrew Su (talk) 14:27, 5 July 2014 (UTC)
No problem. It appears only the edits marked as Minor aesthetic updates have problems. I have been manually reverting these and leaving the other edits which appear to be OK alone. Cheers. Boghog (talk) 14:33, 5 July 2014 (UTC)
But there are hundreds of minor revisions that we made, right? Ugh... Andrew Su (talk) 14:36, 5 July 2014 (UTC)
Plus I've noticed several minor removals of correct content (EC number, chromosome). Certainly not as egregious as the others, but that also makes me not opposed to a wholesale reversion of all edits... Andrew Su (talk) 14:39, 5 July 2014 (UTC)
222 to be exact. And most, but not all of these edits are faulty. So far, I have reverted about 1/3 of them. Boghog (talk) 14:40, 5 July 2014 (UTC)
Okay, all done now... Thanks for the eagle eyes. Spotting that problem after a couple hundred edits is a lot easier to fix than after a couple thousand edits. As always, let me know if you see any other problems! Cheers, Andrew Su (talk) 23:28, 5 July 2014 (UTC)
Great! Thanks for your diligence in fixing this. Cheers. Boghog (talk) 09:19, 6 July 2014 (UTC)

New bot run with same errors[edit]

Hi Andrew. Just a friendly alert. An apparently new bot run but with the same types of errors. Cheers. Boghog (talk) 15:02, 9 July 2014 (UTC)

Thanks! Our enthusiastic new programmer gets in earlier than I do (hadn't yet had a chance to debrief on last week's run). A quick email and chat later, we're back on track. Those new edits are now being reverted... Cheers, Andrew Su (talk) 15:31, 9 July 2014 (UTC)

Proposed GNF Protein box name change[edit]

Hi Andrew. Just a heads up to the above proposed name change. Cheers. Boghog (talk) 18:29, 21 July 2014 (UTC)

Thank you, much appreciated! Cheers, Andrew Su (talk) 18:36, 21 July 2014 (UTC)

GeneWikiGenerator[edit]

Hi Andrew. The BioGPS GeneWikiGenerator no longer seems to work. For quite awhile, it would create template code and article text, but would not directly create GeneWiki articles. One had to manually copy and paste the code and text into Wikipedia. Now the GeneWikiGenerator will not even create code or text. After selecting a gene, all that is returned is an empty "Gene Wiki Code Creator" window. I would appreciate if you or someone in your group would look into this when you get a chance. Thanks. Boghog (talk) 10:40, 3 August 2015 (UTC)

Thanks Boghog. Yes, we know some things fell into disrepair on our end, my apologies. Since about a month ago we have a new programmer working on getting things back to stable ground, and I hope we have that complete soon. Fixing the GeneWikiGenerator is definitely on the to-do list. More soon hopefully... Best, Andrew Su (talk) 04:11, 4 August 2015 (UTC)
Actually @Boghog:, it was even a more dumb error than that. We had updated the generator code to a new code base that operates directly within the Gene Wiki plugin on BioGPS (instead of a dedicated Code Generator plugin). But I forgot to update the link when using http://biogps.org/GeneWikiGenerator/. Apologies, done now. (For example: http://biogps.org/GeneWikiGenerator/#goto=genereport&id=11275 -- if the page exists then it redirects, and if not then it displays the creation interface.) Anyway, I noticed that the tool does return an error for "Invalid or missing Entrez Identifier" for some valid Entrez Gene IDs -- looking into that one... Best, Andrew Su (talk) 04:36, 4 August 2015 (UTC)
Thanks Andrew. The generator now works for creating new pages. As you say, if the article already exists, but the template is missing, the GeneWikiGenerator layout shows only the Wikipedia article and does not generate a template (see for example ELF1). I would appreciate if you would also fix that when you get a chance. Cheers. Boghog (talk) 07:28, 4 August 2015 (UTC)
Thanks Boghog, yes, we'll check that one out too... Best, Andrew Su (talk) 22:00, 4 August 2015 (UTC)
@Boghog: We just moved things to a more stable server and fixed all the bugs we were aware of. So things should be in good working order at the moment. Also, the "GeneWikiGenerator" links will now always display the interface to create a new page (e.g., [1]). Obviously, let us know if you find any issues big or small! Best, Andrew Su (talk) 22:46, 16 September 2015 (UTC)
Hi Andrew. Thanks for the fixes. Things have improved, but there still are some problems:
  • There is no article text code toggle similar to the template code toggle. The reason this is useful is to add bot generated text to pre-existing articles.
  • The Gene Wiki generator is creating blank pages (see for example diff, diff, diff), at least when the article already exists under a different name.
  • Mouse data is missing (see for example diff).
When you get a chance, I would appreciate if you would take a look at this. Thanks. Boghog (talk) 05:08, 4 October 2015 (UTC)
Thanks Boghog, checking on those issues now... Best, Andrew Su (talk) 15:30, 5 October 2015 (UTC)

ProteinBoxBot creates blank page?[edit]

So, like, 20 minutes ago, ProteinBoxBot has created a blank page named "IFITM5". Is this accidental? TVShowFan122 (talk) 13:32, 5 September 2015 (UTC)

@TVShowFan122: sorry, I don't see evidence of such an edit in the bot's user contribution history? Can you clarify or send a diff? Best, Andrew Su (talk) 20:45, 9 September 2015 (UTC)
It seems the edit has disappeared. The deletion log states the page was deleted 3 hours after I informed you. It's been recreated since then, as a redirect. TVShowFan122 (talk) 13:28, 10 September 2015 (UTC)
@TVShowFan122: Great, thanks for the recap! We obviously don't intend to create blank pages and haven't seen widespread evidence of this, but we'll keep our eye out... Best, Andrew Su (talk)

ArbCom elections are now open![edit]

Hi,
You appear to be eligible to vote in the current Arbitration Committee election. The Arbitration Committee is the panel of editors responsible for conducting the Wikipedia arbitration process. It has the authority to enact binding solutions for disputes between editors, primarily related to serious behavioural issues that the community has been unable to resolve. This includes the ability to impose site bans, topic bans, editing restrictions, and other measures needed to maintain our editing environment. The arbitration policy describes the Committee's roles and responsibilities in greater detail. If you wish to participate, you are welcome to review the candidates' statements and submit your choices on the voting page. For the Election committee, MediaWiki message delivery (talk) 16:32, 23 November 2015 (UTC)

Protein stubs[edit]

Lots of your articles are in the list of long stubs which I work through when I have nothing more exciting to do. I think they are mostly created by your bot. I've been removing the stub tag because the articles look quite substantial to me, but I don't understand much of them, and I certainly don't feel competent to decide how complete they are in relation to what could be written. Am I doing the right thing? do you regard them as stubs? could the process of deciding whether they are stubs be automated?Rathfelder (talk) 19:25, 16 December 2015 (UTC)

Hi @Rathfelder: Thanks for checking in! I'm not sure I'm the best person to say what is or isn't a stub. Definitely read Wikipedia:Stub if you haven't already, and post on the talk page if you have questions. In general though for gene and protein pages, I would say that you can look at the edit history. If it has only been touched by bots, then probably best to leave the stub tag. For example, KCNA2 should remain a stub IMHO. Best, Andrew Su (talk) 19:38, 16 December 2015 (UTC)
Wikipedia:Stub isn't much help because it talks about comparing the the content of the article with that which could be written - You would expect more in an article about London than about a small village. But I have no idea at all what could be written. Most of these articles incorporate extensive further reading, and I think that should be taken into account. I also look at the history. If an article like KCNA2 has been largely untouched for many years I'm inclined to think that nobody has found much more to say on the subject. Rathfelder (talk) 19:46, 16 December 2015 (UTC)
@Rathfelder: Got it. However, I think your assumption that "if it's untouched then it's probably finished" does not apply for genes and proteins. We're still drawing the molecular biology community here, so there is lots known that isn't reflected in these articles. (Not to mention that more is continually being discovered.) So for these articles, I would err on the side of having a higher bar than your "untouched" rule of thumb. As examples, I think FLT3LG and OS9_(gene) actually are still a stubs, whereas RAD51C and FERMT3 are not (IMO). Also, I would note that sections on "function", "interactions", and "model organisms" are for the most part automatically added, so their presence does NOT support removing the stub tags. Other sections like "clinical significance", "structure", "regulation", "isoforms", "discovery" would be better evidence that an expert has visited and perhaps updated the article to the current state of knowledge... Best, Andrew Su (talk) 19:56, 16 December 2015 (UTC)
thank you very much. I'll be more cautious in removing the tag. Rathfelder (talk) 20:04, 16 December 2015 (UTC)

ArbCom Elections 2016: Voting now open![edit]

Scale of justice 2.svg Hello, Andrew Su. Voting in the 2016 Arbitration Committee elections is open from Monday, 00:00, 21 November through Sunday, 23:59, 4 December to all unblocked users who have registered an account before Wednesday, 00:00, 28 October 2016 and have made at least 150 mainspace edits before Sunday, 00:00, 1 November 2016.

The Arbitration Committee is the panel of editors responsible for conducting the Wikipedia arbitration process. It has the authority to impose binding solutions to disputes between editors, primarily for serious conduct disputes the community has been unable to resolve. This includes the authority to impose site bans, topic bans, editing restrictions, and other measures needed to maintain our editing environment. The arbitration policy describes the Committee's roles and responsibilities in greater detail.

If you wish to participate in the 2016 election, please review the candidates' statements and submit your choices on the voting page. MediaWiki message delivery (talk) 22:08, 21 November 2016 (UTC)

Bot being discussed[edit]

here Best Doc James (talk · contribs · email) 20:38, 11 December 2016 (UTC)

Presentation at Wikimania, eventually?[edit]

Hello. Wikimania is the international Wikipedia / Wikimedia conference. I think that Gene Wiki has never presented at this conference, but that it would be a good venue for claiming community support that your project merits.

When the year is right and other projects align, could someone from Gene Wiki consider proposing a presentation and attending? This is a general interest gathering of all Wikimedia contributors from all language backgrounds, so it is a layman event. Gene Wiki is a major success story in wiki but it is not so well known in the community consciousness. I think that if its story were told in a way that a general audience could understand, then Gene Wiki could become a celebrated success even among layman contributors. Gene Wiki as a project is in a class of its own because of the large amount of content which has been shared and how closely it is tied with sharing the results of monumental research projects in genetics.

Wikimania this year is in Montreal August 11-13, with some preconference events including a medicine meetup on August 10. Next year it will be in the summer also in South Africa.

Could you float the idea in the Gene Wiki group that I think that if you made a proposal, you would be invited to present in the general schedule? As an example, submissions will be taken at wm2017:Submissions from 2 February - 30 March for this year. There is a similar process every year. Thanks for your attention and consideration. If you ever make a proposal then I would rally support. Blue Rasberry (talk) 18:57, 24 January 2017 (UTC)

Hi @Bluerasberry: Hmmm, this is a very tempting idea. Obviously I would love to make some more in-person contacts with the community. The limiting ingredients (as always) are time and money. We usually prioritize the academic biomedical conferences to try to spread the word in those communities. But then again, more outreach within our own WD/WP community would clearly be valuable too... Hmmm, let me give it some thought. Thank you for reaching out! Cheers, Andrew Su (talk) 21:58, 24 January 2017 (UTC)
There was Open biomedical knowledge: Wikipedia, Wikidata, and beyond which your team did in 2015. Scholarships are offered for Wikimania and a representative from your team would be a good candidate, and really in another league as compared to typical applicants, but your own time matters also. Another consideration is the ripeness of things. Your project is ripe, but I am not sure that the wiki community is ready to begin understanding what you do. I care, and I hardly understand. It is nice to have some preparation so that attendees are not completely overwhelmed, and I am not sure it is possible to talk about a project like this and be understood.
For now I will leave the idea out. There are conferences every year - this is not a fleeting opportunity. Other options for outreach could be a video presentation. Webcam works, or I think you are at a university - they must have a team which could help and at least the right viewers would find that. I am not sure what is right, but thanks for coming to WikiProject Medicine to respond. Blue Rasberry (talk) 00:03, 26 January 2017 (UTC)

Proposal of using full size image for RNA expression pattern[edit]

Hello Andrew! In infoboxes of gene/protein articles, there are small thumbnail images of RNA expression pattern which you created. Thank you for your great images! Then I proposed switching these small thumbnail to full size image, because Wikipedia/Mediawiki image system was changed. I suppose you already noticed. Since image data are recalled from Wikidata, I post the proposal at Wikidata page (wikidata:Property talk:P692#How about using full size image instead of small thumbnail?). I would like to get your thoughts on that. Thank you. --Was a bee (talk) 06:35, 18 March 2017 (UTC)

Gene Infobox[edit]

Your bot is creating stubs that display an error stating that there is a problem with the infobox. I have pulled the error text from the most recent stub that the bot created. Please take a look at what the bot is doing. This happened with other recent stubs. I have marked the most recent stub as unreviewed, so that another reviewer may look at it and also get in touch with you. Robert McClenon (talk) 01:27, 23 March 2017 (UTC)

@Robert McClenon: thanks for the note. We are looking in to this now and will post an update shortly... Best, Andrew Su (talk) 18:03, 23 March 2017 (UTC)

Facto Post – Issue 1 – 14 June 2017[edit]

Facto Post – Issue 1 – 14 June 2017
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Editorial

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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MediaWiki message delivery (talk) 09:33, 14 June 2017 (UTC)

Invitation to editathon at ISMB/ECCB 2017[edit]

Facto Post – Issue 2 – 13 July 2017[edit]

Facto Post – Issue 2 – 13 July 2017
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Editorial: Core models and topics[edit]

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

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

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

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

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Facto Post – Issue 3 – 11 August 2017[edit]

Facto Post – Issue 3 – 11 August 2017
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Wikimania report[edit]

Interviewed by Facto Post at the hackathon, Lydia Pintscher of Wikidata said that the most significant recent development is that Wikidata now accounts for one third of Wikimedia edits. And the essential growth of human editing.

Internet-In-A-Box

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.

Link[edit]

  • Plaudit for the Medical Wikipedia app, content that is loaded into Internet-In-A-Box with other material, such as per-country documentation.
Editor Charles Matthews. Please leave feedback for him.

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MediaWiki message delivery (talk) 10:55, 12 August 2017 (UTC)

Facto Post – Issue 4 – 18 September 2017[edit]

Facto Post – Issue 4 – 18 September 2017
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Editorial: Conservation data[edit]

The IUCN Red List update of 14 September led with a threat to North American ash trees. The International Union for Conservation of Nature produces authoritative species listings that are peer-reviewed. Examples used as metonyms for loss of species and biodiversity, and discussion of extinction rates, are the usual topics covered in the media to inform us about this area. But actual data matters.

Dorstenia elata, a critically endangered South American herb, contained in Moraceae, the family of figs and mulberries

Clearly, conservation work depends on decisions about what should be done, and where. While animals, particularly mammals, are photogenic, species numbers run into millions. Plant species lie at the base of typical land-based food chains, and vegetation is key to the habitats of most animals.

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

Links[edit]

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MediaWiki message delivery (talk) 14:46, 18 September 2017 (UTC)

Nomination for deletion of Template:HPO[edit]

Ambox warning blue.svgTemplate:HPO has been nominated for deletion. You are invited to comment on the discussion at the template's entry on the Templates for discussion page. Ten Pound Hammer(What did I screw up now?) 18:08, 28 September 2017 (UTC)

ISCB Wikipedia Competition: call for participation[edit]

Facto Post – Issue 5 – 17 October 2017[edit]

Facto Post – Issue 5 – 17 October 2017
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Editorial: Annotations[edit]

Annotation is nothing new. The glossators of medieval Europe annotated between the lines, or in the margins of legal manuscripts of texts going back to Roman times, and created a new discipline. In the form of web annotation, the idea is back, with texts being marked up inline, or with a stand-off system. Where could it lead?

1495 print version of the Digesta of Justinian, with the annotations of the glossator Accursius from the 13th century

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[edit]

Editor Charles Matthews. Please leave feedback for him.

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MediaWiki message delivery (talk) 08:45, 17 October 2017 (UTC)

Facto Post – Issue 6 – 15 November 2017[edit]

Facto Post – Issue 6 – 15 November 2017
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WikidataCon Berlin 28–9 October 2017[edit]

WikidataCon 2017 group photo

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.

WD-FIST explained

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[edit]

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MediaWiki message delivery (talk) 10:02, 15 November 2017 (UTC)

ArbCom 2017 election voter message[edit]

Scale of justice 2.svg Hello, Andrew Su. Voting in the 2017 Arbitration Committee elections is now open until 23.59 on Sunday, 10 December. All users who registered an account before Saturday, 28 October 2017, made at least 150 mainspace edits before Wednesday, 1 November 2017 and are not currently blocked are eligible to vote. Users with alternate accounts may only vote once.

The Arbitration Committee is the panel of editors responsible for conducting the Wikipedia arbitration process. It has the authority to impose binding solutions to disputes between editors, primarily for serious conduct disputes the community has been unable to resolve. This includes the authority to impose site bans, topic bans, editing restrictions, and other measures needed to maintain our editing environment. The arbitration policy describes the Committee's roles and responsibilities in greater detail.

If you wish to participate in the 2017 election, please review the candidates and submit your choices on the voting page. MediaWiki message delivery (talk) 18:42, 3 December 2017 (UTC)

Facto Post – Issue 7 – 15 December 2017[edit]

Facto Post – Issue 7 – 15 December 2017
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A new bibliographical landscape[edit]

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

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

WikiCite wordmark.svg

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!

November 2017 map of geolocated Wikidata items, made by Addshore

Links[edit]


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MediaWiki message delivery (talk) 14:54, 15 December 2017 (UTC)