Talk:Anne O'Tate

Trivia

The choice of 'Arrowsmith' as a name for the suite of resources may have been influenced by the 1931 Arrowsmith (film), based on a novel (1925) by Sinclair Lewis, which feature a range of medical ethical problems, such as the ethics of randomised controlled trials.

This kind of speculation is not appropriate for Wikipedia, without a source cited. Besides, there is also Arrowsmith, Illinois for that matter. W Nowicki (talk) 03:09, 4 July 2011 (UTC)

Thank you for your comments here and on the Requests for Feedback page. You are right, the Trivia section should be deleted, unless I can find an external source to validate my assumption. Sleuth21 (talk) 11:10, 4 July 2011 (UTC)

Anne O'Tate as part of the Arrowsmith suite of resources

The Anne O'Tate article is specifically and intentionally (sorry to use bold: I am not shouting...) about that most useful part of the range of Arrowsmith resources, so the Introduction should concentrate on what Anne O'Tate provides and why its relevant and notable. The first references should be about Anne O'Tate and explain its role. I will add more text and put Anne O'Tate in context and provide references as to its function in identifying suitable thesaurus terms when using PubMed and provide references from sources other than those who created the application. Some text on PubMed's role should perhaps also be added, so that readers don't have to guess (as you did) what this article is about. Thank you again, W Nowicki, for helping me to comply with standard rules about creating this, my first, WP article: you provided food for thought and action! Sleuth21 (talk) 11:10, 4 July 2011 (UTC)

Not sure what you are arguing about. My quick search gave me the impression that the Arrowsmith project as a whole was notable enough to survive the deletionists' efforts. That is why I suggested evolving it to the slightly more general topic, which seemed to not be covered at all in Wikipedia. You need to provide a notability source from somewhere outside of the subject of the article, and I could find those for Arrowsmith in general. I will add the GEN article for example. I was preparing to move the article to a title corresponding to this, although could not decide exactly what would fit our conventions. I would say something like Arrowsmith (website) Arrowsmith (software) or maybe Arrowsmith Project which is what I would propose. A "move" leaves behind a redirect so anyone searching for "Anne O'Tate" would go to the same article. Certainly if there is more material on the Anne O'Tate function than the others (e.g. it seems like it is sort of an "evolution"?) then the article could of course talk more about it. It just would seem odd to have an article about only this part of the project but not the project as a whole, especially if the project comes up with more tools in the future. It seems Don R. Swanson was involved at the start, so it probably makes sense to say this in the body since there is an article on him already (and that article should point here once we decide on its name). Similarly for the article on Literature-based discovery. I am not convinced separate articles on the project as a whole and this one tool would survive a notability challenge, if that is what you are proposing, but maybe. It is standard to embolden titles in the lead, so yes, we should put its current title there too. W Nowicki (talk) 16:10, 4 July 2011 (UTC)

OK I worked on it a bit more. Hope I did not introduce errors, it is not exactly my area of expertise. More prose might make it more readable. And by the way, the name= parameter on refs is only needed if yo refer to the same source again later in the article. Some of those probably would be useful, but you can also use more human-meaningful names instead of the PMID number which is a bit arbitrary. W Nowicki (talk) 17:22, 4 July 2011 (UTC)

Thank you, but I think you moved too fast and the article now tries too much, covering all the diverse components of the Arrowsmith Project in ‘one go’.

• I still propose to concentrate on the most notable resource, Anne O’Tate, which would survive a notability challenge, I am sure. For instance, Anne O’Tate is the only PubMed add-on mentioned in Lu’s survey of some 40 PubMed add-ons – Arrowsmith doesn’t get a mention.
• I have already added two references from sources others than the developers of Anne O’Tate, e.g. ref. Lu and Palidwor (ref. 7 and 8 in the current version of the article). More could be added, concentrating for instance on the ability of Anne O’Tate to identify authors mentioned in a set of PubMed records to be contacted as peer-reviewers or experts, identifying suitable thesaurus terms (MeSH headings) for comprehensive searches with high sensitivity, specificity, and precision or identifying specific journals for further searching of relevant studies for e.g. a systematic review of a subject in the context of, say, Evidence-based medicine. There is quite a range of other PubMed add-ons offering these facilities as well, but Anne O’Tate has the advantage that is uses the PubMed interface and its search syntax, and can handle larger sets of PubMed records to be analysed than some of the others, e.g. such as ClusterMed or GoPubMed.
• I am afraid you also introduced a number of errors and misleading remarks. For instance, Arrowsmith proper is the only tool for literature based-discovery, Anne O’Tate is not. Anne O’Tate (and the other Arrowsmith components) are specifically developed for PubMed data, not any other ‘medical publication database’.
• You mention the note from GEN at the end of your version: this is highly misleading, actually absurd. Neither Arrowsmith nor Anne O’Tate have a ‘stranglehold on […] scientific reference analysis[…]’ – the opposite is true: PubMed is the only professionally curated large database which can be accessed without password and makes its data available, again to free, to over 500 licensees. It has therefore become an playing field / testing ground of many PubMed add-ons with text-mining, graphic, word clouds, updating, search-saving etc. abilities. Some are excellent and exiting, some have been incorporated into PubMed, e.g. PubCrawler (1996) ability to e-mail updates when they become available. Some are very here-today, gone-today tools.
• My mentioning Arrowsmith in my original contribution was meant to indicate that its important component Anne O’Tate comes from a good stable, and is likely to be available well into the future.
• Again, I propose to concentrate on a focused WP article of Anne O'Tate, see whether it survives notability challenges. Some of your edits should of course be incorporated.
• I will delete the inappropriate, uninformed cite from GEN from the draft of this WP article now. Sleuth21 (talk) 11:19, 7 July 2011 (UTC)

Please do not presume that everyone has the same context as you. I admitted this was not my field, so I was only reading the sources I could find to learn what it actually does. Please do correct anything that is inaccurate as soon as you can, but keep relating to other articles that already exist, so us poor uninformed readers can guess what it is. Given that there is no article on Arowsmith (yet?) relating to that does not help most readers who are not familiar with the jargon and history. The GEN article was the only one I could easily access, and was given on the project's own web site. They even include the same quote, although they use a dead link to the actual article! If you are saying that the project web site is intentionally spreading misinformation, then that makes the site a bit dubious. The project page also says it was not updated since 2007, so if you know any of the folks there, maybe you could suggest them to fix it. [W Nowicki]

Thank you. Right from my [sleuth21] first invite for comments on this draft of a specific Anne O'Tate WP article and my notes on this talk page I was careful to indicate that I would give more details as required and as the article develops . I did not presume 'that everyone has the same context' as me. I am quite used to talk to a lay audience and tried to avoid jargon and certainly didn't want to leave 'poor uninformed readers' guessing ‘what it is'. I am sorry if you got that impression.

The quote from GEN on the Arrowsmith Project webpage was obviously made tongue-in-cheek at the time; it has no authority, and should not be quoted out of context.

I am afraid I am not knowledgeable enough to revert some of your amendments selectively and then reintroduce some of my Anne O’Tate-specific information, further details, and references I had lined up (I tried using the sandbox to no avail). I am reasonably certain an Anne O’Tate article would be of interest to medical literature analysts/reviewers, EBM practitioners, journal editors and other WP users.

I will give the whole matter more thought and come back as soon as possible. Sleuth21 (talk) 16:06, 8 July 2011 (UTC)

Sorry if you took the comments personally; they were meant to apply to the article only: that terms like MeSH and "PubMed" and "Arrowsmith" need to be explained a tiny bit (or linked to articles about them). Also apologize if I confuse issues like "medical publication database" and "database of references and abstracts on life sciences and biomedical topics" (or is the PubMed article wrong too?). As I said my doctorate is in a different field so am learning about the subject; will try to fix my damage. It still would be good to clarify where bibliographic records, abstracts, keywords, and full article text are used (and how PubMed is different than MEDLINE) for those of us who do not know. Evidently there is a text mining article so that should get a link too, and even biomedical text mining, which I would think might be relevant? Please do add more details on what Ann O'Tate does. The page says "drill down" but probably this is not talking about exploration for petroleum. :-)

I just realized some of the articles are under "creative commons" license, which I think means we could even, say, use some of the screen shots or other diagrams, if they might be useful. I would be happy to help with Wikipedia logistics. Normally we do not split articles until they become, say, a few dozen paragraphs. But if there really is enough material for separate Arrowsmith Project and Ann O'Tate articles we can do that too. Just means both need to be defended from deletionists. Thanks for your patience, collaboration takes time and is often frustrating. W Nowicki (talk) 21:36, 8 July 2011 (UTC)

OK, I tried to dig out the 2011 paper that you found and added that. Also linked in some other articles. They should link here too. It still needs work; wikipedia articles are never "done". W Nowicki (talk) 22:37, 8 July 2011 (UTC)

I have re-written most sections, focused the article on Anne O'Tate, added sections and references. Work still needs to be done (explain some terms, ?internal links) but the article reads much better now and describes notable and important aspects of Anne O'Tate. There should be no problem with 'deletionists'. One or two screen drops of the Anne O'Tate search interface with calculations done should perhaps be added later. I think the article now needs to 'breath' a bit. BTW, The choice of 'Arrowsmith' as a name for the suite of resources was influenced by the 1931 Arrowsmith (film), based on a novel (1925) by Sinclair Lewis, which feature Dr Martin Arrowsmith and a range of personal and medical ethical problems, such as the ethics of randomised controlled trials. Sleuth21 (talk) 18:14, 17 July 2011 (UTC)

Sleuth21 (talk) 18:14, 17 July 2011 (UTC)

Yes, thanks for the work, but not sure what you mean about "the article now needs to 'breath'". The ownership of articles policy states that no single editor can claim they "own" an article. If you are proposing protection, the burden of proof is on you to present the guidelines that have been violated. I do see some issues with recent edits.

You took out the links to computer software and database. From what I could tell reading the cited sources, it indeed involved developing some computer software. Certainly the leader of the team is in the department of psychiatry, not computer science. But removing this context totally would need to be justified. Why censor them? You changed it to say it is a "free, web-based application" and I am not sure that that means. I do not see any citation that says he gives away the source code. Certainly I get to the site via a web browser, but the research would seem just as valuable if the "web" were never invented and another query method were used. The "application" does not seem to be downloaded like smart-phone "apps" but runs on a server computer. There is an article web application but it is confusing since there are two almost opposite meanings.

I do not think text-mining and drill-down are "theoretical". At least they are not used in theoretical computer science, but in practical database management systems. They are a bit "slangy" anyway, since there is no literal "mine" where dynamite is used to blow things up etc. just a trendy word for certain kinds of analysis. There is an article on text mining (and the data drilling article generally avoids the extra hyphen). To me, text is just one kind of data, so it seems a bit buzzy to make the distinction from data mining, but I do see a more specific term might be appropriate. Perhaps biomedical text mining seems the most specific and therefore most appropriate to mention earlier on. But it is still not clear if these tools search entire bodies of articles, or just keywords added by authors (or reviewers), or abstracts?

Several paragraphs above you said:

"Arrowsmith proper is the only tool for literature based-discovery, Anne O’Tate is not."

but then you edited the claim that Anne O'Tate does this back in the article in the lead? So which is it?

The other red link to medical subject headings could be fixed by a move, or perhaps it is a proper noun, and should be in upper case after all? Looking at the sources on that page, it does seem to apply to one specific set, which is generally capitalized as a proper noun.

You removed the mention of when the projects were done. Wikipedia just had its tenth anniversary, and I hope it is around in another decade. Readers in 2020 might like to know when this took place. Why remove it?

A few other layout bugs seemed to have been introduced. Are the bullets meant to be sub-sections? A few puctuation and space issues also crept in. Not sure of the use of apostrophe for quotes vs. normal double quotes. The guidelines for headings capitalize only the first letter, so "PubMed Text-Mining Applications" might be "PubMed text-mining applications". But this section seems out of place. Do you mean "other applications"?

Twice it claims the PubMed interface is "familiar". Well it is not familiar to me, and doubt it would be to most Wikipedia readers. My guess is that I am more technical than most readers, (40 years experience in computer science and one of my friends Gio Wiederhold was a pioneer in medical databases, but I digress). Perhaps "familiar to biomedical researchers"?

It looked to me like the research was done in the USA, so by the National varieties of English guidelines, consistent US English would seem appropriate. Thus "analyze" and "25,000 instead of "25.000" if you mean twenty five thousand and not twenty five and zero thousandths. For that matter, mentioning the number of articles in PubMed in the lead seems an undue detail. It could easily get dated anyway. Ten years from now there might very well be more than that.

Per the guidelines, if you can cite a verifiable source about the name, that would indeed be a great addition. W Nowicki (talk) 18:21, 19 July 2011 (UTC)

Thanks. I will of make the changes you suggest to comply with WP style and format and adjust some of the terminology as soon as I find the time. My reference to the origin of Arrowsmith (film / novel, 1930s) has been confirmed by a personal communication, which would not constitute a WP verifiable source. Sleuth21 (talk) 10:27, 20 July 2011 (UTC)