Mtbhelp:Metatextbook Help Page

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Metatextbook of Medicine - the encyclopedia of free medical review articles

The Medline-PubMed System is immediately explained at point 1.7 in the box below. The whole document starts with my 86.000 review collection Metatextbook-of-medicine. Both systems are coupled by some common structures.

Contents

Metatextbook and Medline&more - passive and active ways to scientific knowlegde

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From the Alphabetic List to a single Topic

This is a collection of 73.000 free downloadable medical review articles, which are categorized to 12.000 topics. The complete alphabetical list of topics is here. If you select one, e.g. Babesiosis, by clicking on the bold blue term left, an external web page on www.kidney.de opens, Metatextbook of Medicine - Instructional picture 01

which shows 1 a table with references - these are the reviews which are tagged babesiosis, and above this table, 2 some links going to similar subjects (any topics which include at least one review which is tagged babesiosis) and which will open similar styled pages.

To access the papers of this collection immediately, you will Arrow 3 click on the small number to open the PubMed website of this article. Most PDFs will be available form that page which is familiar to you.

The Common Linkout Box

The more visible Arrow 4 citation-embedded link will open a thing which I have called the common linkout box. Metatextbook of Medicine - Instructional Picture 02

For about 90% of citations in the metatextbook, it was sufficient to linkout via PubMed as described above. This complex-looking common linkout box allows essentially the same, 1 as the PubMed Linkouts are given for try-and-error. Most versatile is the representation of my own database of online medical journals, which is reflected in 2 as one or more bars of different color. Yellow, Green and Pink will open the journals archives, so you can look there manually to get the PDF. Some Journal archives are framed with metadata above so you need not to remember yr vol pages, and for those Journals which disenable framing, this simple solution is given. Metatextbook of Medicine - Instructional Picture 14Pg/Is/Vol/Yr in reverse direction in case of multiple opened tabs !!!

A red bar means NoGo - you can buy them at least. Blue is of use only to people who live in germany who have assigned a contract with this institution which grants free access to the backfiles of the most renowned medical publishers. 3 You can search immediately G Scholar, Base Bielefeld, Edoc Berlin and Worldcat for repository based access to a given paper, or you can submit an automatic reprint request email if the blue box allows it. 4 For urgencies, Deepdyve and for those whose libraries are reflected-by, PubGet is feedable. 5 German users can order documents from this country's largest medical collector library 38m in Cologne, as well as locals can obtain the magazine codes all by metaactivating the www.medpilot.de system. 6 This box shows under which Concepts I have tagged this one review article in the Metatextbook.

Searching the Metatextbook

The Metatextbook of Medicine has an intrinsic search function. The non-wiki-style resource homepage is located here. Metatextbook of Medicine - Instructional Picture 03

1 Here you can run a simple as well as a boolean search to retrieve topics which are related to your query. 2 The link to the subsections, best is the Nephrology one, is given, as well as the 3 alphabetical list of topics.

Subject area collections - Metatextbook of Nephrology

Starting with the Metatextbook of Nephrology, the original concept of this project becomes visible - and enjoyable. It has the appearance of the table-of-contents section of a 3-Volume Textbook set, and this is what I expected to implement as I did the first draft of this project.

The Metatextbook of Nephrology allows you to search for your concept in a logical way to get a bunch-of-reviews displayed in a standard bibliography-like style:

Pre-formatted PubMed Search Terms

It is prepared to give you an additional linkout option - pre-formatted PubMed search terms !

Remember, the bold blue link led you into the Bibliograpies, and the right read dead-links starting with mtb... are pre-designed to open a wiki-topic with the same name as the bibliography. This wiki-topic will include the pre-formatted search terms as exemplified by this worked-out example. Metatextbook of Medicine - Instructional Picture 04

You can copypaste the PubMed search term from the screen, or you can click on it to open my Medline & More system. The Pages are designed to contain a lot of different search term expressions, hence, to be more specific or to get more records on the cost of nonspecificity. Even subcollections as 'my personal favourites are ' and a simple list of pmids is possible.

Medline & More System

Metatextbook of Medicine - Instructional Picture 05 Open this example in a NEW TAB


In 1, you can modify the search term. The other similar textfields will contain content to AND or content to NOT in relation to the first field. All 3 fields can contain complex boolean, but I prefer only to use phrases and OR operators - as shown in the example.

To load the page with the search term you typed in, press 2 the orange enter bar.

Now, 3 press in the green area the NCBI PubMed link - it opens the original pubmed search run on your search terms. Without doing anything other, now press This Medline Version as specified by the red arrow in the screenshot. I will explain the resulting table-of-citations below.

You can shift your search terms to any of the about 50 ressources in the tabele 4 simply by clicking on the links. Without problems, the blue links will run boolean searches.

The other colors (not shown in the scout view) specify at which reductions of search term complexicity the less comfortable external search engines operate; your search terms will be simplified automatically, but it could result into really trashful expressions. With some experience, you will primarily adapt your search terms for the requirements of search angines which only do any of these words A(OR), all of these words A(AND), unpredictable g-style searches A(GOO) or phrase A(phrase) or even - A(single) a single word. Obviously, it should not be the tast of third-party-vendors like me to do that babylonic work. Publishers are encouraged to set up boolean compatibility modes to their search engines- in 2013 !!

List of Citations

Your results will be displayed on and by the external ressources which were feeded with your search term, so it is beyond my task to give tutorials on any host. Some remarks (Highwire accepts maximum search term lenghth of 80 words) are given where appropriate.

The searches which were run on This Medline Version are run by API on NCBI and post-analyzed by my system of a few php's and a mysql database to show you a printable list of citations with accessibility information. Only Firefox is able to give a valid printout; fonts are sized to give optimal readability on a 2:1 page printout. (Opera, Safari cannot print it valid, its a pity !) You will learn later that it is advantageous to use Firefox, indeed. The screenshots provided are self-explanatory, any field or structure is commented on the shots. The common linkout box has been discussed above. The header section looks like this: Metatextbook of Medicine - Instructional Picture 06

PubNeph is not supported anymore, it has some bugs but it was the precursor of the idea to search the journals on their hosts. Metatextbook of Medicine - Instructional Picture 07

The free items is anything you can get from PubMed if you ask for free.. Metatextbook of Medicine - Instructional Picture 08

The rest is not without hope - according to my databases, the marked records could be free with a fair roc of my system. Metatextbook of Medicine - Instructional Picture 09

Only applicable to indigenous or visiting people in germany - the Deutsche Nationallizenz für Privatpersonen gives access to quite a lot of backfiles. Remember, if you would like to run a sitesearch on a publisher covered. e.g Wiley, you will take Wiley_de which then runs via Nationallizenz. Metatextbook of Medicine - Instructional Picture 10

The High-Capacity user - and the Standard user who could afford the investment of 35 Euro for a hand-held barcod39 Barcode-Scanner - should install both of the fonts included in the zip of this free supplier. Thanks alot !

Working off-line with the Citation list

No valid search today is less than 500 records output, 5.000 is not very much, and it takes hours to scan it. Not without reason, I implemented the barcodes - but how can you open the common linkout box for pdf retrieval ? The solution lies here. The top line should include your email address only in case you would like to send email-requests when other options failed; into the bigger PMID box, you could scan in the barcodes (beep-beep-beep), or, you can type-in manually the PMID numbers separated by Commata or with a click to the Enter-key on your keyboard (the latter because of the barcode-reader gives an enter for each scanned number). The big green button will do the rest. About 10-20 records a time is optimum to be able to read the tab's titles. Thats all folks... A common linkout box opens for every record you selected.

Tips and Tricks

Matching third parties results to PubMed/Common Linkout Box

Only for the Firefox-Browser, you will get an extension (mine of course...) wich does the following: Mouse-marked-Text --- RightClick-(Addons)-PubMed(simple) --- opens a Citations page of matching articles. Imagine you run a fulltext search on Wiley or EMBASE, you could ask - could I obtain the paper in another way ? You simply mark its title and do the things shown above to run a pubmed search on its title to check all other resources if it went well. PubMed has some errors in searching for Titles since it transforms 'on a' into 'on-a[AUTH]' and gets nothing. Some term reductions will help if negative. I have another one which targets G-Scholar in case PubMed had nothing.

Matching PRINTED references to PubMed content

File:Profiline01.png
Metatextbook of Medicine - Instructional Picture 11

Imagine you have a retro-style citation like Zhang X et al., 1992 J Comp Neurol 323:432 and no idea what it could be about, and not pleased to type hieroglyphs into PubMed - this is your solution to anything between a printed citation and your steno-type notes of citations displayed on congress slides for tens of seconds:

Here is your link to it

Enter the One-Letter-Code of the Journal (first 3 if more), space, Volume, space, FirstPage, and press the 1--Vol--Page button.

Metatextbook of Medicine - Instructional Picture 12

Click the appropriate Journal Link (J Comp Neurol)

Metatextbook of Medicine - Instructional Picture 13

The Pubmed search is done and this is the result of it:

Metatextbook of Medicine - Instructional Picture 14

You can open the common linkout box from here.

A button 1--year--author with first author-without-initials is available. A button 1--year--page is avialable.


Writing your Wish List when you go USBing your medical library

This is a disturbingly complicated function. Read this when you have become familiar with the Medline & more System. You could be frustrated by misunderstanding this paragraph and disregard using my pretty system.
There is a fraction of about 30% of papers which are not available for the home-based reader, so you need a solution to do the work of scrolling the journals archives and downloading the pdfs to USB stick. I am 85 km away from my marvellous 38m library at cologne, so a visit is at 35 Euro for ride&hide. But it's only half an hour highway so I decided to settle here in Olpe. I wanted to have a linklist on my usb which I open in the Library, click one time to open 14 pdfs in parallel and to save them all. Proven, it makes 120 papers per hour library time (and another at home for preparation). The following steps have to be done:

1. The page which links to the pdf has to be opened (by link from pubmed, by link from medpilot.de via common linkout box if the first failed)
2. Sometimes, the paper is open by editors choice or by payed OA - you happy one !
3. Else, the link of the opening file has to be bookmarked.
4. The hacker-type user would create in Opera Browser a bookmark directory mysearchFeb2013 and simply bookmark the link whereas the title of the bookmark was replaced by the PubMed number.
5. The rest would better use what I have created.
6. You need the PubMed number in case your pdf-link would fail in your library so to retrieve whole metadata to obtain alternate access.

How to get it running: This has to be opened in Firefox, the window has to be set to the right 1/3 of your screen. The above-decribed ways to your pdf should proceed in another instance of Firefox or in any other webbrowser, best Opera, and you should have arrived in the common linkout box of your paper. Take this as an educationally worthful hard task. Open it in another browser, best is Opera. Metatextbook of Medicine - Instructional Picture 11

There is no pubmed link out, and my blue Nationallizenz would not work outside germany. So click on Open Medpilot Cologne and scroll down the resulting webpage.

File:Medpilotgetjournalhomepage01.png
Medpilot.de (Deutsche Zentralbibliothek für Medizin, Cologne/Köln) finds the homepage of any online-journal. Special advice: Search directly for PMID numbers in PubMed-slang. Or best, approact it from the Metatextbook of Medicine.

At the lowest right bottom corner, there is a Zur Zeitschrit link which means show the journals archive, where you can proceed. You will arrive ultimately here. The link is in the browsers navigation bar, and the PMID number is in the common linkout box 2 - below the pubmed links and right-to the deepdyve link. Copypaste is best if run in Opera browser. So, you have a way to PMID number and Link to the PDF opening page. Where to paste the stuff ? The Link goes into the 1 Profiline, the PMID into 2 the only-other-input-field, left to the 3 Memorize button. Once both are typed in, you will press the memorize button.

Metatextbook of Medicine - Instructional Picture 12 The re-loading page now contains two links, one 1 will open the paper in the library, the other 2 will open the CLB=common linkout box, if you should experience trouble in the library (This is the reason of the pmid requirement). The blue bar 3 will open (if javascript is allowed) 14 items in parallel. The amount is optimized because you can identify errors on this scale in while downloading stuff, and you do not want to exert too many operation like these, which is required:

As you see, the page contains one double link (or maximum 14 of them), then you get the command to save it. You have now to save this page from the browsers control menue (from where you would print a webpage); give some variation of the proposed filename including date, theme and a counter (part01, part02...). Dont forget to save the last one, too !

Put them all on your usb stick. In the library, you will open one of them, click the open-14-items bar and, in best-case, you will have 14 PDFs open after 2 minutes in parallel. There is one typical error I have encountered while benchmarking the system: The PDF-viewers control bar does not in every case correspond to the PDF displayed, but to another one; it is disturbing, and beyond the scope of mine to fix such a systematic bug of modern browsers/plugins. My 38m has the combination Firefox/FoxitPDF.

As disclaimed above, I know that this is the hardest part auf my systems documentation, because the steps and ideas cannot be anticipated by a 2013 standard web user, so i have to explain my thoughts rather to give advice to do something which cannot be understood on itself.

I would really appeal to you not to get frustrated by this particular (working) solution, and to run a little test before going into 100+ papers dimensions.

Contributing Contents to the Metatextbook

Proposing Papers to be included

Adding or modifying a PubMed Search Term

People have varying styles to perform a task. While the wikipedia spirit is to get one solution which fits the habits of all its authors, this would drive a search term expression into chaos. So, I propose not to modify an existing search term, rather to add your preferred version as a parallel entry - even my first page includes two terms on the same subject with quite different sensitivity/specificity relations. There is no reason not to have 100 search-terms from 50 different users.

The Template to use is

*{{y|Neonatal Fc Receptor /sp/|fcrn OR neonatal fc receptor OR neonatal fcr OR fcgrt OR hfcrn|}}
which means
*{{y|Term description /personal comment/|search term field A|search term field B}}
so take this
*{{y| //||}}

Search term B is ANDed to A and left intentionally blank in the example above.

The Title of the page which contains the search term should be the Metatextbook name preceded by mtb:

Mtb:Receptors (FcRn)

If there is no acceptable Metatextbook name (I have 12k, the genome has 20k genes, so I have too little), create your own and deposit it on the page mtb:NewLemma simply as a wikilink to the new items page.

Accessing Components and Functions of the Metatextbook from 3rd parties solutions

  • Linking and Deeplinking are allowed
  • Fullpage-Framing is allowed without restriction. It is my job to make your users knowing that it is my work.
  • Deep-Framing is generally not allowed.
  • Funneling GET/POST parameters in URL is *greatly appreciated* - I really like it seeing my work being accepted and used by others to generate better applications.
  • As a rule of thumb: If someone recognizes that there is some well performed work done by me and he or she is in need of such a function, usage should be permitted. If my server didnt sustain ddos-traffic, some *agreement* should be reserved not to drive me into ruin.

I will come along soon with documentation of the GET parameters.

Running a search on your search term

follows soon.

Linking a bibliography into your application

follows soon.

Publications on my Resources

Literaturrecherche: Metatextbook of Medicine, Groth-O, Dtsch Arztebl 2012; 109(7): A-330 / B-285 / C-281 First draft of the Metatextbook.
Literaturrecherche: Medline für die deutsche Nationallizenz, Groth-O, Dtsch Arztebl 2012; 109(46): A-2313 / B-1881 Medline & more as a means to check PDF availability to Germany-based users by Nationallizenz für Privatpersonen
Medline web application with valuable add-on functionality. Groth-O, Poster (P042) 4. Jahrestagung der Deutschen Gesellschaft für Nephrologie, in: ISSN 1869-9405 04/2012 Medline & more - common linkout box to search repositories.
Metatextbook of Medicine - Nephrological Bibliographies. Groth-O, Poster (P343) 4. Jahrestagung der Deutschen Gesellschaft für Nephrologie, in: ISSN 1869-9405 04/2012 Metatextbook of Nephrology in a non-Wikipedia representation.

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