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Hey Geometry guy, I worked a little on Soddy's hexlet today; I hope that you like it! :) I was wondering, though, whether you could make some nice pictures for it, and also whether you could track down a reference for the cyclide thing. It seems pretty obvious, but I couldn't find a good reference online nor in my slim collection of books. Thanks muchly! :) Off to work again, heigh ho, Willow 22:54, 1 March 2007 (UTC)[reply]

Hi there Geometry girl. I had a a look at Soddy's hexlet already yesterday and it is a perfect signature for you, in the way that it uses a coordinate transformation to reduce a fascinating theorem to something entirely easy to see. I guess a geometers' version of this statement would be something like: "For any three mutually tangent spheres there is a unique Dupin cyclide tangent to to each of them along a circle". I'll ask around for a good reference and or pictures, but I'm not sure it will be easy to produce nice pictures because the geometry is a bit complicated. Well I can probably draw 6 pennies around a central one, but I think you are looking for a bit more...! Geometry guy 00:14, 2 March 2007 (UTC)[reply]

I saw your edits to (really, your complete rewrite of) Soddy's hexlet. It's much improved, of course. The fact is, I originally wrote that in about fifteen minutes and knew it was horrible, so I never wanted to go back and look at it. Thank you! --N Shar (talk • contribs) 01:54, 2 March 2007 (UTC)[reply]

I've now added some references and additional comments, and copied in the image from Dupin cyclide. Feel free to add life to my prose in your inimitable way. Geometry guy 12:24, 2 March 2007 (UTC)[reply]

Thanks, Geometry guy! I'll check it out instanter, although I've got to dash off again... Willow 12:39, 2 March 2007 (UTC)[reply]

I am amazed by your forbearance on the Immune system talk page. The urge to rend and tear those rude and insulting newbies into little meaty chunks must have been overwhelming. TimVickers 17:19, 1 March 2007 (UTC)[reply]

You're so good to me; thank you yet again. :) It wasn't difficult at all to keep my lioness leanings at bay, since I also see the world through their eyes. My mind does have a tendency to bring things to life, usually a happy, playful life; I often don't even notice myself doing it. It's a gift I covet in the real world: the power to restore things to a happy life, at least the innocent and the good. Sorry if that sounds really strange, but thank you again, not least for fixing the writing, Willow 17:46, 1 March 2007 (UTC)[reply]

P.S. Why is immune system unprotected? I hate to think of your time being spent chasing after vandals, however good you are at it. :(

It's on the main page today, so policy says we can't protect it. Oh well. P.S. if you have time in the coming week, could you have a good critical read of the antioxidant article and comment in its FAC? Thanks TimVickers 20:17, 1 March 2007 (UTC)[reply]

I'll be happy to; I read it this morning, and I've been brooding on it before writing, as I usually do. Things often percolate up from the depths, even if nothing occurs to me initially; somewhere, some gear is turning, if ever so slowly. ;) I'll have to do it quickly, though, because I'm leaving soon to visit my sister, who's even more Luddite than I am. ;) Don't be surprised if you don't hear from me for a while; I'll be having fun, though — we're thicker than thieves. ;)

I also have a favor to ask of you, or perhaps something for you and Opabinia to brood over. On a really random whim, I created a little nightingale yesterday, a remarkable bird with such good vision that she can read all the NCBI taxonomy files and vocal enough to generate decent Wikipedia stubs for all 350,093 taxa that the NCBI knows about. My new pet passerine is really nice and smart enough to know all the taxonomic ranks, so she can even craft taxoboxes herself and give references and categories at the bottom. The thing is, I'm not sure how to upload her files, or even if I should; I seem to remember a WP rule that one shouldn't upload luscine-generated files, no matter how lucid. ;) What do you think I and my little bird should do? She's eager to help out at Wikipedia, and sing her heart out, but doesn't want to offend with her music. Anthropomorphically in love with the world, Willow 22:13, 1 March 2007 (UTC)[reply]

I meant to respond to this yesterday, but got distracted reading the reams of text generated by the whole Essjay mess. How does your script work - is it a javascript screenscraper type of thing that runs within the browser, or would it require a machine to run on? The question here is the same as the question I had on the Pfam thing - which I never did get back to thinking about much - how do you avoid redundancy with existing articles? Maybe you should try a test run on a small group that's unlikely to have many articles already. I like the idea of just creating the upper-level articles and getting progressively more specific. The main difference that I can think of between something like this and Rambot is that these articles, once created, probably won't get edited much at all, while starter articles on locations have an obvious population of contributors to draw on and expand from.

On your image-creation question, the first thing that comes to mind is POV-Ray, which is nice in being flexible but mathematically precise, and having lots of geometric primitives to work with. It's kind of deceptive, though, if you're not patient with it; you do a couple of simple examples and think 'hey, this is pretty easy!' and then the next thing you know, you put your camera inside a sphere. But I'm really not the person to be asking about images; I've created exactly one good non-protein image in my life and I reused it everywhere for months. Opabinia regalis 00:55, 3 March 2007 (UTC)[reply]

Daisy is a relatively simple nightingale (sorry, little bird) wrought of C that just makes the WP stubs with the taxoboxes, refs, and categories, plus some plausible text, but doesn't upload them. She's knows all the taxonomic ranks by name, number and Latin name, and know which rank is the parental to another. For the rest, Daisy relies on her crib sheets, the NCBI files, which she mines for the scientific and common names of the taxon and its parents, as well as the references. Since she also has the NCBI taxID, she can make an external link to the NCBI taxon page, which itself has other nifty external links. (The idea for Daisy came to me from my day making Dactylella, Daonella, Dasycladales and Dendroceratida.) To avoid duplication, I suppose I could make a list of the taxa now in WP; there are only about 80,000, and (I hope) neatly sorted into categories. Daisy could then check whether the page was in the list and not make it if it was. I'm clueless about the uploading, though; any ideas? There'd be roughly 350,000-80,000 = 270,000 files, making a compressed tar file of maybe 150M.

I haven't read up on Essjay, but from what little I know, it does sound like a mess. Pity that they didn't interview Tim! Or you: "Hi, I'm a 5-eyed worm who fell asleep in a cozy mud-bank in the Cambrian and didn't wake up until just now. I'm disappointed that I missed out on so many birthday parties, but it was a really good nap. I would love to hear from any other Problematica; I enjoy seafood dinners and long walks along the sea-shore." ;) It's disappointing that Essjay lied, but it's also disappointing that he and Wikipedia have an Adversary of such devoted malice; the underwear initiation rite for admins is starting to seem plausible... ;) He does remind me of Milton's Satan; being uncreative himself, he descends from nobility to pitiful delight in ruining others' creativity. :( Willow 12:44, 3 March 2007 (UTC)[reply]

Haha, I would actually quite enjoy an interview as a Cambrian Rip van Winkle ;) I'm not sure Daniel Brandt is as bad as his caricature as the enemy of all that is wikigood - if you spend all your time digging around in the mud, you might eventually pan some gold, I suppose - but he certainly is an intrusive puffbag who enables and encourages a lot of lesser puffbags. I suppose the whole thing shouldn't be overly surprising, since lies are probably second only to porn in terms of total volume of internet content. (Category #3 is 'things you wish were lies, but are depressingly true'.)

From what I remember, uploading your files sounds like a good pywikipedia job. I downloaded the pywikipedia framework once a long time ago to test some tagging thing that I then got sick of - maybe it was around the time of the mcb assessment getting started? - anyway, I'm quite sure it has a facility for creating a new page, so a python script to fish out the appropriate file from your dataset and upload it is probably pretty straightforward. (Insert muttering about my dislike of python here ;) As a first approximation, it may well be that any taxa stubs that aren't correctly categorized might just as well be obsoleted by your stubs anyway. Opabinia regalis 07:16, 4 March 2007 (UTC)[reply]

Good to see your typeface again. TimVickers 19:18, 11 March 2007 (UTC)[reply]

They look very good. Would it be possible to import the references on the Tree of life page of a phylum and add it as a standard list to all the stubs in that Phylum? I don't think you can copyright references, as they are not your work. TimVickers 00:52, 13 March 2007 (UTC)[reply]

Daisy could easily do that, but she has a question: how far down the taxonomic tree should the phylum references be used — just in the class articles, or all the way down? Her idea had been to use the references provided by the NCBI, but only for the taxonomic rank of the article, e.g., phylum-specific references in phylum articles, and class-specific references in class articles. However, it would be just as easy to include the NCBI references of the immediate parent taxonomic rank, or of all higher taxonomic ranks. Which do you think would be most sensible? Please reply quickly, since I'm apt to do it tomorrow; thanks much! :) Willow 04:42, 13 March 2007 (UTC)[reply]

P.S. Oh, and where should the references go — perhaps under "Further reading"?

Further reading is best, since they do not support specific points in the article. If a specific list of references is possible then the more specific the better. Looking forward to the results! TimVickers 16:41, 13 March 2007 (UTC)[reply]

Thanks! :) One last favor: would you please look at, say, Talk:Methanomicrobia and tell me your opinion about which WikiProject banners should be included? I'm now inclined to include only the Microbiology banner (not {{Wikiproject MCB}} and {{Tree of Life}}), but I'd also like to alert people that a photo or a taxobox is needed. Perhaps I should add the "needs-photo" and "needs-taxobox" flags to the {{WikiProject Micro}}? It wouldn't take much work. Please reply as soon as you can — thanks muchly! :) Willow 16:52, 13 March 2007 (UTC)[reply]

I agree with Tim on which references to bring in and where to put them. The most specific reference list possible is best; probably don't bother with anything more than one level up, since it probably won't contain much of interest.

I'm a little skeptical about tagging them as needing a diagram/picture/taxobox/etc, as the relevant projects might not really want thousands of articles dumped into their queues, and at the volume of articles this could grow to, it could overwhelm the global image request system too. Or does the project tag not use the same categories as {{reqimage}} et al? Opabinia regalis 01:00, 14 March 2007 (UTC)[reply]

See my repurposed User:Opabinia robotus/upload_taxa.py for a very simple pywikipedia script that can upload these things (uploaded by itself, naturally) - or at least, can upload an arbitrary text file. It's trivial to tweak so that it loops over a directory of files or whatever; it just needs to know how your files are organized. If you want to try it, the instructions for downloading the pywikipedia framework are at m:Pywikipedia (I suggest the Jan 30 version on Sourceforge; tonights CVS build didn't work for me.) It takes one filename as an argument, and (currently) puts it at User:Opabinia robotus/filename. (Hm, and I just remembered to add an edit summary.) Opabinia regalis 03:04, 14 March 2007 (UTC)[reply]

Wow, thanks, O! I even sort of follow your program, which does you great credit since I've never learned Python. But it's not trivial for me; could I maybe generalize your program to multiple files on the command line with a for loop like this?

for taxofile in sys.argv[1:]:

Should the program sleep between uploads to spare the poor server? Also, do I need to do that login.py thing?

I'm also tempted to put the file directly into its spot in Wikipedia, but I don't want to touch an existing page. Could I add something like

if len(articlepage) == 0:
  articlepage.put(articlecontent,editsummary)

Does len pertain to articlepages, or should I use some other method, maybe like articlepage.exists or something?

Let's see: there's lots else to ask and to answer!

• First and foremost, thanks for your support on the stub controversy, which caught me by surprise.

• The "needs-photo" tag categorizes the page in Category:Microbiology articles needing photos, although maybe that's implicit with "Stub".

• I totally agree with your and Tim's suggestions on the references, which I hope to tackle today. There are a few annoying bugs (e.g., "...is a order") that I still need to fix in the simple program.

Important problem: I need advice on how to categorize the taxonomic stubs. My original idea was to make a category for every major taxon (that's what Daisy does right now), but there are sometimes too few members. I've taken to grouping everything under the phylum (e.g., Category:Euryarchaeota) but that doesn't group articles by their taxonomic rank. Perhaps I should make new sub-cats such as Category:Archaea phyla, Category:Archaea classes, etc.? Please give me your advice — thanks! :) Willow 12:12, 14 March 2007 (UTC)[reply]

I'm afraid I know little about taxonomy, so have no useful advice except encouragement. TimVickers 16:55, 14 March 2007 (UTC)[reply]

Oh, how I know what you mean! I honestly don't know why I'm always getting distracted by bright shiny things that I know dangerously little about and that my poor powers will never attain — a little Icara with Daedalin dreams. ;) But that makes the encouragement all the more welcome.

But really, Tim, you're ideally suited to judge which categorization makes the most sense for smart non-experts, no? I'm going to try out the new idea, and please let me know if you like it. Willow 17:42, 14 March 2007 (UTC)[reply]

See updated version of the python script, which iterates over an input list, won't clobber existing pages, and throttles its edit rate. (To answer the above question, you'd want to do for taxofile in sys.argv, since sys.argv[1] is just the first element in the input list.) That's probably the minimum functional version to let loose anywhere ;) To start creating hundreds of thousands of pages, we'll presumably need a bot flag.

On the taxonomy categories: have you mentioned this at the tree of life project? They 'maintain' those categories as far as I know, so they're probably the ones in the best position to decide what's most useful, and consistent with existing standards. I like David's idea at first glance, anyway. Opabinia regalis 01:41, 15 March 2007 (UTC)[reply]

Hi -i - I see you have recently created two new stub types. As it states at Wikipedia:Stub, at the top of most stub categories, and in many other places on Wikipedia, it is recommended that new stub types are proposed prior to creation at Wikipedia:WikiProject Stub sorting/Proposals, in order to check whether the new stub type is already covered by existing stub types, whether it is named according to stub naming guidelines, whether it reaches the standard threshold for creation of a new stub type, and whether it crosses existing stub type hierarchies. Your new stub types are currently listed at WP:WSS/D - please feel free to make any comments there as to any rationale for them. And please, in future, consider proposing new stub types first! Grutness...wha? 01:36, 14 March 2007 (UTC)[reply]

One solution might be to use lists rather than categories if there are too few members. In that way you have a full page but can preserve the taxanomic ranks too. One problem is that you would not be able to automate such a process since it would probably require the human touch. David D. (Talk) 12:34, 14 March 2007 (UTC)[reply]

Thanks, David! But I'm not sure that I understand your idea? Every stub should have at least one category, isn't that right? Including the stubs in list pages would also be nice, although how do you think the lists should be organized? Eager for your insights, Willow 12:40, 14 March 2007 (UTC)[reply]

Do all pages need a category? From a taxonomic point of view it makes little sense to have unpopulated categories. What i would do is consolidate all your loners and pairs into a list that defines some sensible group (sensible from a taxonomic and numbers perspective). Then categorise that list in the appropriate category. There is nothing more frustrating than clicking down through categories to find only one or two aritcles. Much better get get stopped short to see an article in the form of a well organised list that allows some context to be gleaned from all the relationships. May be i could set up an example if you give me a group to work with? David D. (Talk) 18:03, 14 March 2007 (UTC)[reply]

Sure, I'll try to bore down all the way to species for one segment of the taxonomic tree to give you something to work with. Can you wait a few hours? Thanks, User talk:David! :) Willow 18:09, 14 March 2007 (UTC) P.S. I guess I'd like every page to have at least one category; that way, the pages could always be found by prowling the categories rather than the articles themselves. Does that make any sense? I somehow intuit that will be useful someday.[reply]

Here is a solution I just found, before you start the tedious bore. It's not exactly what i am saying but i think the problem is similar and it might be a better compromise. Category:True_vipers pretty much stops trying to subdivide the vipers further with this big category. Note that also listed in thecategory is the List_of_viperine_species_and_subspecies. So may be the solution is to have fairly big category AND lists. David D. (Talk) 18:14, 14 March 2007 (UTC)[reply]

That does seem like a good idea! I think my little bird could make such a list pretty easily. What do you think would be the minimum and maximum limits on the number of (sub)species that we could get away with putting in a single list? I somehow doubt that people would want to dig through a list of thousands of species, even if it were alphabetized, although I might well be wrong about that. Maybe there are general policies or guidelines here at Wikipedia? I seem to be woefully ignorant of those. :( Willow 18:22, 14 March 2007 (UTC)[reply]

Hard to say on length and the natural break point may be different depending on the organism. i can say that this list is far too long. List_of_dog_breeds. i could live with a couple of pages, about 100-200? The nice thing about a list is you can add a comment here and there to make it more useful than the bog standard alphabetical lists set up by the categories. David D. (Talk) 18:33, 14 March 2007 (UTC)[reply]

Brilliant, David! :) Of course we don't need an alphabetical list, since the categories provide them already. So perhaps the list should be organized by taxonomy? Perhaps use the intermediate taxonomic ranks as subheadings? :) Then a reader could surf the list from the table of contents. Are there other sortings we should consider? This is fun! Willow 18:44, 14 March 2007 (UTC)[reply]

P.S. What does "bog" mean?

Bog standard TimVickers 19:51, 14 March 2007 (UTC)[reply]

"Perhaps use the intermediate taxonomic ranks as subheadings? " Exactly :) David D. (Talk) 20:44, 14 March 2007 (UTC)[reply]

Got it, chief — I'm on it. ;) Willow 20:59, 14 March 2007 (UTC)[reply]

OK, Daisy did it; please check out List of Archaea genera. :) Is that what you had in mind, kind of? Perhaps it's too long? We could reduce it to "List of Archaea families", if that'd be better. Willow 17:49, 15 March 2007 (UTC)[reply]

Hi all,

It looks like Daisy won't be able to sing those exhaustive reference lists before she has to go to sleep tonight. (I'm helping her work out the various bugs in her throat.) But it would be really helpful if you all could proofread, say, one randomly chosen page each from Category:Archaea phyla, Category:Archaea classes, Category:Archaea orders, Category:Archaea families, Category:Archaea genera, and Category:Archaea species. (As an aside, here's a fun, risqué mnemonic for the taxonomic ranks: King Phylip came over for good sex.) We should try to catch everything awry before Opabinia encourages Daisy into polyphony; it would be awful to repeat the same mistake in 270,000 pages! Thanks muchly for your help and time, Willow 20:59, 14 March 2007 (UTC)[reply]

P.S. Another difficult question: is there a semi-automated way to find free-use images for a given species? I was thinking of using Google Image and filtering with "site:.gov", but I honestly don't know that government images are free. Does anyone have any good ideas?

PPS. Daisy figured out how to add the synonyms to the taxobox. :)

Maybe filter for wikipedia? i did one random search and it looks like the German wiki might be well ahead. Have you looked to see how they categorize things? David D. (Talk) 21:44, 14 March 2007 (UTC)[reply]

That's excellent, and also raises another good point — should we add interwiki links to other wiki's? Perhaps the French, German, Japanese and Russian ones, which seem to have the greatest number of taxa. But there's also no harm in adding others, e.g., the Swedish, except for a higher chance of a broken link. It's easy to implement however we want it. Willow 21:55, 14 March 2007 (UTC)[reply]

Actually i might have got lucky when i picked Nanoarchaeum_equitans, if you look at Euryarchaeota you'll find there are a lot of red links. Looks like you might be the leader in wiki world. David D. (Talk) 22:06, 14 March 2007 (UTC)[reply]

On a second look, it would likely be hard to do the interwiki links, since the other wiki's don't generally use the Latin taxonomic name, but rather some adaptation, e.g., de:Halobakterien. The foreign alphabets (say, for the Russian and Japanese wikis) would've been hard, too. But if we can get this going, perhaps we can send them the code so that they could do it themselves?

A semi-automated way of finding species pictures would be wonderful, but that too may be just a pipe dream. Let's keep looking, though! :) Willow 22:24, 14 March 2007 (UTC)[reply]

.gov websites can definitely host copyrighted/unfree images. I think you'd have to search a site that explicitly licenses all of its content under a free license, like PLoS. I have to say I don't think this will work, though, or at least would need a lot of human oversight; there's a danger of finding non-representative or otherwise poor images. Opabinia regalis 02:30, 15 March 2007 (UTC)[reply]

Hi Willow, Opabinia regalis pointed me your way from this discussion as someone who may be willing and able to help beautify a template. Actually, I'm trying to nest two templates together but have so far failed. The example I'm playing with is on ITK (gene). Any thoughts you have would be much appreciated...

Actually, in reading a bit of the discussion above on NCBI's taxonomy data, I think there is quite a similarity of your effort and the one I proposed here, essentially doing the same for all genes in the mammalian genome. The previous discussion was pretty lengthy (mostly my fault for lumping too many issues together), but if you're interested in working together or sharing notes, I'd definitely be open to it! Cheers, AndrewGNF 01:07, 15 March 2007 (UTC)[reply]

Hi Andrew!

You're right, they do seem analogous, now that you mention it! That hadn't occurred to me before. I'll be glad to help with the template and with setting up the mammalian gene pages; but you need to know from the start that I have huge holes in my background — in computers, biology and, well, everything — so you'll have to be patient with me and also not assume that I know stuff. My knowledge is pretty much stitched together from conversations and what I can dig up on the web. You'll have to forgive me straight away, since I didn't follow all of the previous discussion; can I review just a bit and perhaps you re-explain at a slightly lower level?

From what I remember, you wanted to create a Wikipedia page for all mammalian genes, right? My first question: is there a general code for each such gene, with which one could query different databases? Is the same code used for non-mammalian genes — like, if an analogous gene were found in rats and spiders, would it have the same code in each? Or, maybe there's a table of gene synonyms somewhere? Knowing about such codes would be really helpful in setting up the "External links" section of the Wikipedia page.

Still other questions: should we have separate pages for a gene and its product (say, like, the gene dnaK and the protein DnaK)? What is the scope of the information on each gene page, and where can the information be found? It's all about book-keeping, but some books are kept better than others. ;)

Hopefully you won't get flustered by praise, but I think you and Novartis are great for tackling this. Your heart's in the right place, and I'm pleased as anything that even a half-educated shepherdess can help. Looking forward to a friendly collaboration, Willow 11:31, 15 March 2007 (UTC)[reply]

Hi Willow, Great, glad you’re enthusiastic about this. Don’t worry about holes in knowledge. Bioinformatics is filled with people who are jacks of many trades, masters of none. In fact, up until a few years ago, you couldn’t even find a “card carrying” bioinformatician because there were no such academic programs. Anyway, you’ll fit right in… On to your questions…

First, an overview… There is consensus that there are roughly 25,000 – 30,000 genes in the human genome, and a comparable number for all “close” relatives (primates, mouse, dog, rat, etc.). However, a big problem is not everyone agrees on the exact list of genes, and moreover, people can’t agree on what to call genes that everyone agrees exist. The ITK (gene) is a reasonable example. You’ll see here links to many different databases, all of which have a different ID for the same gene. Keeping track of all the cross-references between databases is quite a chore, so many examples of “gene portals” have been created to essentially keep up-to-date as each database evolves and new ones are added. We at GNF have one too (called SymAtlas) and we are somewhat unique in that we use our gene portal to also present data which we’ve generated and released to the public domain.

SymAtlas (and other gene portals) are great at displaying structured data – information stored in tables and databases. But, of course, they are not good for storing (much less collecting and displaying) “free text” information, and this is of course a strength of a wiki. My proposal is pretty straightforward. We can take our structured content in SymAtlas (which we’ve collected and maintain from a large number of public databases) and use these data to seed protein infoboxes for all genes ‘’en masse’’. We’ll also hyperlink from SymAtlas to Wikipedia to give our (somewhat sizeable) user community a place to add that “free text” knowledge. The stubs hopefully will lower the barrier for SymAtlas users to contribute (since they’ll be editing a page rather than creating one). In turn, the Wikipedia community can contribute the extensive editing, beautifying, vandalism-fighting, and everything-else expertise (and also the domain knowledge contributed by the MCB project) and really help things take off.

By analogy, biology journals often publish “review articles” which summarize the current knowledge in the literature for a particular gene or gene family. I would love it if the Wikipedia community maintained (and SymAtlas linked to) a continually-updated review article for every gene in the mammalian genome.

And in response to a couple of your questions (which are good questions, by the way, that point to important issues in the field)… There is an effort here to standardize gene names (ITK, for example), so it is this name that I suggest we use as the title for the Wikipedia pages. And regarding genes versus their protein products, personally I believe all that information should go on one page. We commonly refer to “gene function” when we really mean the function of the protein product, and although SNPs are a property of the gene, they are highly relevant to the protein product.

Whew! I hope you made it through all of that without falling asleep. If you want to break out the discussion into smaller bits, I’m happy to do that too. Let me know if you have any other questions or topics of discussion. When we have a common framework of understanding, we can move on to the specifics of what should be done and how we might work together… Cheers! AndrewGNF 22:04, 15 March 2007 (UTC)[reply]

Hi, I did make it all the way through, but I don't have time to reply right now, unfortunately. Could you send me a few gene portals besides SymAtlas so that I can get an overview? Thanks muchly, Andrew! Talk soon, Willow 23:03, 15 March 2007 (UTC)[reply]

Sure, here you go:

• http://www.genecards.org/index.shtml
• http://source.stanford.edu/cgi-bin/source/sourceSearch
• http://www.genelynx.org/
• and in some sense, NCBI Entrez and Ensembl are both gene annotation providers and gene portals

... but of course, our SymAtlas is the best... trust me... ;) (In all the examples above, you can view a gene report by typing a gene symbol into the text box -- ITK, BTK, AKT, etc.) AndrewGNF 00:05, 16 March 2007 (UTC)[reply]

Hi Willow, I recall your interest in looking at unassessed articles. I am trying to set up an IRC meeting to plan a strategy for this. The starting point is this discussion. Your input (and help) is most welcome - can you make it? Thanks, Walkerma 04:53, 15 March 2007 (UTC)[reply]

Hi Walkerma, I'm hugely flattered to be invited to a strategy meeting, but I don't think I can make it, for a few reasons. First and foremost, I'm getting stretched too thin. :( I really shouldn't be contributing to Wikipedia at all, since I received a stern warning from my boss about being "lazy" and not getting enough done there. I've been working pretty hard to keep her happy, since it would be a real blow if I lost that job. :( Also, I'm no good at strategizing; I generally just dive in and make things that others want or need — whether they know it or not. ;) Least importantly, I've never actually used IRC and I'm a little daunted about learning how it works. I was brought up rather sheltered from technology, so I'm learning about computers rather fitfully.

I'm glad to help as I can, though. After the strategy meeting, just let me know what needs to be done, and I'll try to weave magic. ;) Affectionately, Willow 11:52, 15 March 2007 (UTC)[reply]

OK, thanks for the offer of help. Don't feel daunted, I regularly feel that way when I talk with the techie people here! IRC is actually very low tech (rather like IM, which I've used only once!), which is why I can handle it. But I'll let you know what we come up with. Meanwhile, get into your boss's good books. Cheers, Walkerma 02:15, 16 March 2007 (UTC)[reply]

..should use templates where possible? For external links a template similar to this {{Daisy | genus=Nanoarchaeum | species=equitans | microbe=yes }} could be used to give the following type of output.

• NCBI taxonomy page for Nanoarchaeum equitans

• Tree of Life page for Nanoarchaeum equitans

• Species2000 page for Nanoarchaeum equitans

• MicrobeWiki page for Nanoarchaeum equitans

The advantage of such a strategy is that if the formating for the links changes later you only have to adjust the template rather than geting a bot to change all the pages. Another thing to consider is that the target links can be modified in the future to account for new resources, or removed as they become obsolete.

How about this, for your workhorse species?  :) {{Daisy | genus=Luscinia | species=megarhynchos | microbe= }}

• NCBI taxonomy page for Luscinia megarhynchos

• Tree of Life page for Luscinia megarhynchos

• Species2000 page for Luscinia megarhynchos

or Daisy can be more general and only go with genus, like this: {{Daisy | genus=Luscinia | species= | microbe= }} or the minimalist look: {{Daisy | genus=Luscinia }}

• NCBI taxonomy page for Luscinia

• Tree of Life page for Luscinia

• Species2000 page for Luscinia

Strangely Daisy is not represented on tree of life website!!!!!, but understandably not present on microbes are us. Clearly this template needs tweeking but you get the idea. You can find the template in your user space at User:WillowW/Daisy. David D. (Talk) 22:08, 15 March 2007 (UTC)[reply]

By the way, you could have an 'if statement' coded into the template such that if the species is not a microbe the microbes are us website will not be shown. David D. (Talk) 22:34, 15 March 2007 (UTC)[reply]

Another super-brilliant idea — I'm on it, chief! ;) Here's another list to peruse; there are minor changes. Are there too many entries, or is it OK? I like the way the Table of Contents came out. I guess the references will have to wait another day, though; I'm dashing off to work soon. BTW, my boss was really nice about the L-thing, you shouldn't have a wrong impression of her; it's just that she might have to let me go, because business isn't so good, despite our best efforts. :( Willow 22:39, 15 March 2007 (UTC)[reply]

Just added an if statement for the microbe function too. Now only get the microbe site if add some text after the microbe option in the template. See the changes to the examples above. David D. (Talk) 22:57, 15 March 2007 (UTC)[reply]

Really have to run, but here's another list to proofread. I'm trying to keep the list around 50-150 entries long. Please send along any suggestions — thanks! :) I'll tinker with the template when I get the chance. Willow 22:59, 15 March 2007 (UTC)[reply]

I'm so excited that you're on board for the wikiproject. Looks like you keep busy with a bunch of other stuff, but any contributions are welcome! I was really amazed when I started looking at how bad all the fashion coverage on wikipedia is. Normally I wonder how anyone even knows the half stuff that gets posted on wikipedia, but it's actually kind of fun to find a topic that's still in its infancy, so amateurs can contribute meaningfully too!

Thanks for your offer to help with MathBot--I don't even know what that is but it sounds good and I'll take any help I can get... :)

And as far as calliopes go, I just had a picture book with one in it when I was little that I really liked. Most of the time, I get people asking me about the muse Calliope, but I guess you sensed I'm not high-brow enough for that! Calliopejen 02:46, 16 March 2007 (UTC)[reply]

Hi Jen,

It is fun starting from scratch! I'm really glad that you started the WikiProject, since it's way more fun to edit when you feel part of a community and not all alone, don't you agree? I'll try to do my part; the MathBot is what produces those brightly colored tables of article assessments, counting the numbers of good and important articles. The WikiProject banners that you put on the Talk pages allow you to assess each article for "quality" and "importance". I'll try to set it up on Monday; it's mainly a question of creating some categories. Willow 22:11, 16 March 2007 (UTC)[reply]

Not sure about your promised new User Page: it seems to move away from the wonder and fascination of the main image, which (in addition your incredible talent to work on a huge variety of wikipedia articles across the namespace) seems to me to capture many of your individual qualities, but hey, what do I know :) ! Geometry guy 19:39, 16 March 2007 (UTC)[reply]

Not to worry, I'm just tinkering. The lists of articles are getting rather long and unwieldy, and I don't like to seem like I'm putting on airs, so I was trying out ways of hiding the information. I wanted to just put the lists into default-hidden NavFrames, but I couldn't seem to make it work correctly. :(

Tinker away: it looks good, and this is your space!

I'm so relieved and glad that you liked that other thing, too, although it's not yet meant for public viewing. It still needs work to get the tone right: impishly mischievous but also elusively affectionate. I'm hoping that over 50% of its readers will find it wickedly funny, not merely wicked. ;) Thanks for your suggestions! :) Willow 21:56, 16 March 2007 (UT\EvC)

I found it fabulously funny, even as the willing target of your rapier wit! I wish I had time to write the reposte you ask for! Geometry guy 00:22, 17 March 2007 (UTC)[reply]

Happy news, Daisy cleared her throat and can now sing all the NCBI taxonomic references note-perfect (I think). She'll try to weave it together with David's template idea, and try it out on Monday. Please send along any other suggestions you might have for the taxonomic pages and lists. Doesn't it feel like the time before a concert, when the orchestra is tuning up? :) Willow 22:42, 16 March 2007 (UTC)[reply]

P.S. If anyone else has suggestions for how I should improve my user-page, I'd very much appreciate it. Thanks!

Just for you info those icons on your "prettier" page don't suit you at all. The're too generic. David D. (Talk) 23:17, 16 March 2007 (UTC)[reply]

thanks so much for getting the article-counter thing set up! do you know why the WP:FASH page looks all screwy though? it seems that whenever the right pane gets beyond a certain width it makes the left pane super-small. i know basically nothing about table set-up and just copied the layout from another wikiproject, so i am helpless to fix it! :) any further ideas/help much appreciated! Calliopejen 17:41, 18 March 2007 (UTC)[reply]

Stumbled on it by accident and was blown (gently) away. What a page, what a person, what a devotion! My hat is off to you. Arcfrk 13:13, 19 March 2007 (UTC)[reply]

I'm fond of hats, too, especially ones with broad brims and maybe a nice ribbon. :) Thanks ever so much for your kind note; people are so wonderfully nice here, I often feel like the guest at a surprise birthday party. :D I also feel like I've stumbled into a little garden, an echo of Eden, where all of us can work together for something truly good. Looking forward to reading your contributions, Willow 14:39, 19 March 2007 (UTC)[reply]

Hi all,

What's the Wikipedia citation template for a book chapter? There's a zillion taxonomic references to chapters in Bergey's Manual. :)

The taxonomic references and synonyms appear to be working, as long as the reference is to a journal and the NCBI entry itself is OK. I'm still working on fixing glitches in the NCBI file itself; stay tuned! :) Willow 23:14, 19 March 2007 (UTC)[reply]

Hi Willow. If you mean citing a book chapter instead of a specific page or section (is that it?), I'd just use {{cite book}}, which provides a | chapter = parameter. I presume you're familiar with it, but you can find more usage instructions by following the link to the template page. Fvasconcellos 23:57, 19 March 2007 (UTC)[reply]

Hi, the taxonomic references seem to be working, but they should be proofread before they're uploaded en masse. To warm up, Daisy made a list of the 4428 NCBI taxonomic references that she thought were journal articles. They're grouped into 19 sub-pages (listed below) of roughly 200 references each, sorted by the NCBI reference ID number. Would you all be so kind as to pick one sub-page for proofreading, and note which references aren't journal articles and other mistakes? Please list your name and your chosen section here, so that we don't overlap. Thanks muchly! Willow 21:47, 20 March 2007 (UTC)[reply]

P.S. I know that some articles don't have a dot in front of them; that's a bug for single-author articles that I've fixed already.

P.P.S. There appears to be a glitch in Wikipedia, so only the first few hundred references are visible, although they're all formatted correctly. Here are the individual sets:

• User:WillowW/List of NCBI taxonomic journal references (part 01) (references 1-1000)
• User:WillowW/List of NCBI taxonomic journal references (part 02) (references 1001-2000)
• User:WillowW/List of NCBI taxonomic journal references (part 03) (references 2001-3000)
• User:WillowW/List of NCBI taxonomic journal references (part 04) (references 3001-4000)
• User:WillowW/List of NCBI taxonomic journal references (part 05) (references 4001-5000)
• User:WillowW/List of NCBI taxonomic journal references (part 06) (references 5001-6000)
• User:WillowW/List of NCBI taxonomic journal references (part 07) (references 6001-7000)
• User:WillowW/List of NCBI taxonomic journal references (part 08) (references 7001-8000)
• User:WillowW/List of NCBI taxonomic journal references (part 09) (references 8001-9000)
• User:WillowW/List of NCBI taxonomic journal references (part 10A) (references 9001-9500)
• User:WillowW/List of NCBI taxonomic journal references (part 10B) (references 9501-10000)
• User:WillowW/List of NCBI taxonomic journal references (part 11) (references 10001-11000)
• User:WillowW/List of NCBI taxonomic journal references (part 12) (references 11001-12000)
• User:WillowW/List of NCBI taxonomic journal references (part 13) etc.
• User:WillowW/List of NCBI taxonomic journal references (part 14)
• User:WillowW/List of NCBI taxonomic journal references (part 15)
• User:WillowW/List of NCBI taxonomic journal references (part 16)
• User:WillowW/List of NCBI taxonomic journal references (part 17)
• User:WillowW/List of NCBI taxonomic journal references (part 18)
• User:WillowW/List of NCBI taxonomic journal references (part 19)

You'll want to flag misformatting inappropriate journal names or article titles, as well as publication dates, volumes or page numbers. All of these articles should have a valid {{PMID}} for convenient cross-checking. Noting duplications is good, too, although that's intrinsic to the NCBI, not to Daisy; I'll try to write a script that at least identifies them all. Thanks so much for your help! :)

OK, I've uploaded two other reference files that need to be proofread

• User:WillowW/List of NCBI taxonomic nonjournal references (1st half)
• User:WillowW/List of NCBI taxonomic nonjournal references (2nd half)

If you all have time to look them over, that'd be great! We may wish to eliminate some.

List of proofreaders of journal references:

• Willow, refs 1-1000, one glitch: Skinner (1992)
• David D. (Talk), ref 1001-2000 done all look good. Thanks, wow, you're fast! :)

List of proofreaders of nonjournal references:

• Willow, refs 1-1000
• I'm doing 2001-3000 TimVickers 22:56, 20 March 2007 (UTC)[reply]

These references are duplicated, is this a problem?

1. Wiedenmayer, F. (1977) Shallow-water sponges of the western Bahamas. Birkhauser Verlag, Basel and Stuttgart. (reference ID 2376 in the NCBI citation database) and
2. to be published in Flore de la Nouvelle-Calédonie (P. Lowry, pers. comm., May, 2000). (reference ID 2431 in the NCBI citation database)
3. Martin, A.P. and Bermingham E. (1998). Systematics and evolution of lower Central American cichlids inferred from analysis of cytochrome b gene sequences. Molecular Phylogenetics and Evolution 9 (2):192-203. (reference ID 2533 in the NCBI citation database)
4. Roe, K.J., Conkel, D. and Lydeard, C. (1997) Molecular systematics of Middle American cichlid fishes and the evolution of trophic-types in 'Cichlasoma (Amphilophus)' and C. (Thorichthys).' Molecular Phylogenetics and Evolution 7 (3):366-376. (reference ID 2531 in the NCBI citation database)
5. Murphy, W.J., Nguyen, T.P., Taylor, E.B., and Collier, G.E. (1999). Mitochondrial DNA phylogeny of West African aplocheiloid killifishes (Cyprinodontiformes, Aplocheilidae). Molecular Phylogenetics and Evolution 11 (3):343-350 (reference ID 2528 in the NCBI citation database)
6. Sano, R., M. Takamiya, S. Kurita, M. Ito and M. Hasebe. 2000. Diplazium>subsinuatum and Di. tomitaroanum should be moved to Deparia according to>molecular, morphological, and cytological characters. Journal of Plant>Research 113:157-163, 2000 (reference ID 2617 in the NCBI citation database)
7. Nakazawa, A., Krienitz, L. and Nozaki, H. 2001. Taxonomy of the unicellular green algal genus Vitreochlamys (Volvocales), based on comparative morphology of cultured material. Eur. J. Phycol. 36:113-128. (reference ID 2705 in the NCBI citation database)

Otherwise 11 corrections made. TimVickers 23:43, 20 March 2007 (UTC)[reply]

Thanks, Tim, I made the corrections in the original NCBI file! :)

Note that

• Wilson, D. E. and Reeder, D. M. (eds.) Mammal Species of the World A Taxonomic and Geographic Reference. 2nd edition. Smithsonian Institution Press, Washington and London 1993. Nowak, R. M.: Walker's Mammals of the World. 5th ed. The Johns Hopkins University Press, Baltimore and London, 1991.

contains two separate sources (Wilson and Reeder, 1993, and Nowak, 1991) that have somehow been combined. --Aranae 23:55, 20 March 2007 (UTC)[reply]

Thanks, Aranae, that's also a true error in the NCBI file, but I could fix it by creating a new reference. Thanks for pointing that out! :) Willow 20:21, 21 March 2007 (UTC)[reply]

I can barely even load these huge pages at the moment, but did you intend to use a) a semicolon between the first and second authors but a comma thereafter, or b) no period between the last author and the date? Not that those are important in any case. Also, the thread below is technically correct; these should be in projectspace. Opabinia regalis 04:10, 22 March 2007 (UTC)[reply]

Hey O, the semicolon does look strange, no? But it's part of the {{cite journal}} template; it separates the first author from the coauthors. Whether the period appears at the end of the author list has (so far) depended on what's in the NCBI file, but I can fix that. Thanks for your help and also the advice; in retrospect, it was really dumb to put these lists into article space. :( Hopefully, I won't always be such a clueless Chloe. ;) Willow 09:31, 22 March 2007 (UTC)[reply]

Hi, WillowW. I have noticed that you have created a lot of lengthy articles like List of NCBI taxonomic journal references (part 15). I can imagine such an info developed by a collaborative project can be quite useful, but I do not believe it belongs to the article's space. Per WP:NOT Wikipedia is not an indiscriminate collection of information.

Would you consider transwiki the texts to Wikisource? Or maybe as a subpage to a Wikipedia project? Alex Bakharev 20:55, 21 March 2007 (UTC)[reply]

Hi Alex,

First off, welcome to my Talk page! I've admired your work, especially the AlexNewArtBot, so I feel as though I'm being visited by a celebrity. :) Won't you come in and have some tea?

Thanks for being so nice about pointing out my poor judgment in putting those lists into article space; it was thoughtless. They've now been deleted and I'll reconstitute improved versions elsewhere, probably as subpages of my user page. They're not really useful in themselves; rather, they're a useful exercise to check whether our taxonomic references are being formatted correctly.

Thanks for stopping by! Hopefully, your next visit will have a happier occasion. Willow 09:44, 22 March 2007 (UTC)[reply]

Thanks for the nice words. I agree with your decision Alex Bakharev 11:04, 22 March 2007 (UTC)[reply]