QUOSA Information Manager usage guidance


Table of Contents

  1. Get full-articles from  PubMed, OVID, or other search site
  2. Retrieve first abstracts, then full-articles for a selected subset
  3. Save article references from a search or a folder into a citation manager
  4. Get from an EndNote or similar reference to full-article, even off-line
  5. Get individual article PDFs (or Word, HTML, PowerPoint)  into My Article Organizer
  6. Save full-articles to a QUOSA folder
  7. Update my searches
  8. Review full text of articles with Document Summary
  9. Re-highlight articles
  10. Search in Results (Boolean)
  11. Import folders of PDFs into My Article Organizer
  12. Get full-articles already in a citations manager (and link them)
  13. Save article references from a PubMed search into a citation manager
  14. Import articles via a search on My Computer
  15. Save full-articles to a Windows/Mac folder
  16. Extract concepts from articles
  17. Regular Expression & Wildcard Queries
  18. Automate Batch Queries
  19. Search My Articles with a list of terms
  20. Search My Articles with Gene terms
  21. Get full-articles from Google (The General Web)
  22. How to Backup QUOSA Information Manager
  23. Moving QUOSA between Computers
  24. What's wrong? No full-articles
  25. Use QUOSA with network drives
  26. Glossary

Get full-articles from a Journals gateway

Introduction

Journal gateways such as PubMed or OVID allow users to find articles based on search terms they specify. The gateways return a list of relevant articles in some order, often over several web pages. They may indicate how many articles in total have been found.

Once you have this list of articles, retrieving and managing the articles with QUOSA is very similar for all journal gateways. The most commonly used is PubMed, and in the main we describe the operations needed for the PubMed gateway below. Major differences for other gateways are indicated.

But first you do need to ensure that you have selected the correct gateway. Do this from the topmost QUOSA toolbar by clicking "Channels" and then the channel you need. If a channel has been customized for your institution, you need to select the customized option.

Finally, you should note that you can retrieve full-articles in one of 2 ways:

·         Directly from the search return page(s) of your gateway, or

·         By retrieving first a number of abstracts, reviewing these, and then getting the full-articles from the subset of abstracts of interest to you. See  "Retrieve first abstracts, then full-articles"

 

Operations

·         Make sure that the journal gateway search page that you want to use is in the QUOSA browser pane.

·         Enter your desired search term and initiate the search - e.g. click "Go" on the PubMed page.

·         Once your search results are back, decide whether you wish to select articles one by one or simply wish to get the first 20, 50, or whatever. This may depend on whether you want the articles as abstracts or as full-articles in the first instance.

·         If you want to select articles one by one, check the boxes on the search return page for the articles you want. Otherwise, enter the number of articles you want in the box to the right of "Retrieve" (Sigma) on the Browser pane toolbar.

·         Choose in which form you want first to get articles. You have a (drop down) choice of Abstracts, HTML, and PDF to the right of the box for the number of articles to be retrieved. If you choose  PDF, QUOSA will try to get a PDF version but retrieve HTML if it cannot (and vice versa).

·         Then press the Sigma icon next to/above the word "Retrieve" on the Browser toolbar. QUOSA will then open the Results pane (if closed) and start to fill it with key data on the files retrieved. It will also create a search list under "Searches" in My Article Organizer on the left. (It is useful to have the Organizer open.)

·         If you retrieved abstracts in the first instance and now want the full-articles for a selection of abstracts, first select the abstracts you want in the Results pane. Then (under the Advanced View) click on the hammer (Tools) icon and then the "Download Selected Full-Articles" option. This will attempt to replace your selected abstracts with the PDF versions of the full-articles, failing which with the HTML versions.

 

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Retrieve first abstracts, then full-articles for a selected subset

Introduction

See Get full-articles from a Journals gateway for a general description of how to get articles from a journals gateway.

Sometimes it is advantageous to download a number of abstracts first and then fetch the full-articles of those of interest to you. This may be because you need information on a large number of abstracts fast , or because you find it hard to hit exactly the right search terms before reviewing the abstracts, or that you wish to extract concepts from the abstracts before reviewing full-articles.

QUOSA allows you to download and review a large number of abstracts very fast, to review these, and select those of interest to you. And then to retrieve the full-articles you do want from PubMed with one click

 

Operations

·         First retrieve your abstracts from PubMed as indicated in Get full-articles from a Journals gateway. Obviously, the document type setting should be "Abstracts".

·         Conduct whatever review and further filtering you want with QUOSA tools. Make sure to keep you desired files all in one QUOSA folder, subfolder, or search list. Mark the files you want with the select flag. (Alternatively, create a folder all of whose files you want.)

·         Select all the files for which you want full-articles - either by selecting all flagged items or be selecting all items in a folder.

·         Under "Express View", go to the Commands menu (at the top of the QUOSA window) and select "Retrieve full-articles/abstracts" in the lower section of the drop-down menu.

·         Alternatively, under "Advanced view" click on the hammer (tools) icon and select "Download selected Full Articles". (The Commands menu selection is also possible.)

·         Either of these methods will update the version of the articles you have selected  to PDF full version, if that is available to you, failing which HTML full version, if that is available to you.

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Save article references from a search or a folder into a citation manager

Operations

·         These instructions are for adding citations to an existing library. If you want to put them in a new library, you need first to create this library under your citation manager.

·         After retrieving articles into the Results pane, you may immediately spot some references that you want to export. Select the ones of interest either by a selection of flagged articles or by selecting them all, then click on the To Citations button in the Results pane toolbar. You may also use Commands/Sync and Link selected articles to EndNote, Refman, etc.

·         If your citation management software is already installed on this computer, it should launch and you will be prompted for the 'library' or 'database' into which you wish to save the citations ... select one and click open.  You will immediately see the citations you selected in PubMed listed in your library/database.

·         For saving citations from a pre-existing search list or folder in My Article Organizer, double click the folder or list to bring its articles into the Results pane and then use a similar procedure.

 

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Get from an EndNote reference to full-article, even off-line

Introduction

Once you have saved articles into an EndNote or other citation manager with QUOSA, you can always thereafter get directly back to the full-article in PDF or HTML format from that citation library. There is a reference to QUOSA's My Article Organizer within the EndNote reference which (if necessary) launches QUOSA and puts the article into the Browser pane.

This works as long as EndNote can find the QUOSA folders. There are some issues to bear in mind with using network folders for QUOSA. See "How to use QUOSA with network drives" to guidance.

 

Operations

·         From within EndNote, select the reference of interest to you.

·         Scroll down the reference data until you find URL. The information here should show two file path names, one  including the word "Quosa" and end with the suffix ".qpw". The other URL is the link to the abstract source over the Internet. Both are functional, but be sure to click the one you want.

·         For this purpose, double click the URL including "Quosa". Wait (if necessary) for QUOSA to launch. Then the full article will appear in the QUOSA Browser pane.

Note that if you only retrieved the abstract when you saved to EndNote, it is the abstract that will be retrieved.

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Get individual article PDFs (and Word, HTML, PowerPoint) into My Article Organizer

Operations

·         Make sure QUOSA's Browser pane is open and "Restore" the QUOSA window so that you can drag and drop files into it from elsewhere on your computer.

·         Similarly open a non-maximized window showing the folder where the document you want to import is.

·         Select the document. This can be a PDF, Word, HTML, or PowerPoint document.

·         Drag and drop the document into the QUOSA Browser pane. It should then open in that pane.

·         Click the Save icon on the toolbar at the top of the Browser pane. (Alternatively select Commands/Save shown article to Article Organizer.) This will bring up a dialog box inviting you to enter information about the file the to save it either to the current folder or list or to another folder.

·         You need to enter some information here, for this is the information that QUOSA shows in the Results pane for each file.

·         We can retrieve the key data from PubMed if you enter the PubMed ID into the PubMed ID box and click "Get Article info". Note that there is no check that the article is indeed the one for which you have entered the ID, so check that what comes back makes sense.

·         Click OK to save the file to the selected folder.

 

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Save full-articles to a QUOSA folder

Operations

·         The folders discussed here are special QUOSA folders, which are not the same as regular Windows folders.  The motivation for saving references in this proprietary form is to preserve the formatting that supports features like the export of references to citation management software.  The disadvantage is that references saved into QUOSA folders can only be viewed with QUOSA.

·         To save references in the Results Pane into a QUOSA folder, first indicate (by flagging them) the articles you wish to save.  Click Select Flagged (Express View) or the Flag icon on the Results pane toolbar. (To select all articles, go to Commands/Select-Unselect / All Articles.)  Click on The Save to Disk button to bring up a folder selection dialog.  If a new folder is required, click on 'New Folder' button and enter a name for the folder.  Click 'OK' and 'OK' again to close the dialog box.

·         If you wish to save to an existing folder, select the folder then click 'OK' to close the dialog box.

·         Another quick way to save articles to an existing folder is to open My Article Organizer and click on the 'My Folders tab to reveal the complete list of existing folders.  Select some articles in the Results Pane  as above, then 'drag and drop' them into one of the folders in the My Folders list. (Multiple articles can also be selected by holding down the shift key while clicking for a contiguous range or holding down the Ctrl key while clicking if they are not contiguous.)

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Update Searches

Introduction

QUOSA  allows you to update searches you have made in the past so as to keep you up-to-date with the latest articles under various search headings. The update set-up for a search is called an Alert in QUOSA and searches to be updated are listed under My Alerts in the Organizer pane.

 

Updating can be done either:

·         by simply manually updating the search with one click whenever you wish , or

·         by setting a time and a frequency for automated searched. This method gives you the option to be sent emails alerting you of any change to your search list.

Note that QUOSA needs to be running in order for the automated search to run. One advantage of having QUOSA run as a background service (the QUOSA Accelerator option on installation) is that automated search will run whenever your computer is switched on.

 

You can choose the post-update presentation to be either of all articles from the search or just the new updates (plus earlier unread articles). If you choose "Show only updates", then it is important you first save the previous articles to a folder if you want to retain them. You can configure QUOSA automatically to save the new updates to that folder. This gives you the ability to view only the updates under your Alert list, while also keeping your folder of all articles on a subject up to date. These folders can include folders in QUOSA Virtual Library, so that team sharing folders can be kept up to date in this way.

 

Note that you can apply one or more Search in Results to an original search which is now in your Alert list. These search filters can be either on metadata (such as Author) or the full-text (hence the value in requesting the full text for the update). The searches in the updated article set are performed automatically by QUOSA after each update and the search results can then be automatically saved to another folder. This way, you can keep a folder up to date based on one or more search filters on the full text of articles retrieved from PubMed, Ovid, etc via broader searches. And the filtered updates are clearly visible to you.

 

Alerts for Ovid are set up a little differently from other channels.

 

Operations

·         In My Article Organizer either right-click on the search list which you want to be updated or click the Set Alert icon in the results pane when your search results are in that pane.  

·         (For Ovid only - skip otherwise) If you do this for an Ovid search, you will get a dialog box telling you to set up the alert in the Ovid search results page. If you have just done a search in Ovid, this page will be in your QUOSA browser pane. Otherwise you will need to repeat your search in Ovid, choosing the same databases as you used earlier. Click Save Search/Alert in the Ovid web page. The following message dialog appears: “Do you want to configure an Alert in QUOSA?” Click Yes. The Configuring Ovid Alert dialog appears. (If you get a message saying that saving an alert is not possible now and try later, try again after a short pause. The reason is limitations on concurrent use of Ovid sessions.)

·         Select "Update Now" for an immediate manual update.

·         To set an automated update Select Config Alert instead. This brings up an alert configuration dialog box. ( This is the box that the Set Alert button also brings up)

·         Select the time, frequency, and notification options for an automated update, then click "OK".

o        Remember that QUOSA needs to be running at the time scheduled for the update for this to work - see Introduction above

·         Setting an automated Search Alert on a search list will move that list to My Alerts in My Article Organizer. You can change the search update settings by right-clicking on the list under My Alerts and selecting Config Alert. You can also perform a manual update by clicking "Update Now" in the configuration dialog box.

·         To select the folder where you want to save updates (including  search in results filtered updates)  right-click the relevant list in My Alerts, select Update and then Save Update Results to... You can also set the folder for the unfiltered Alert via the Destination Folder tab in the Config Alert dialog box.

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Review full text of articles with Document Summary

Introduction

Document Summary is a powerful way of reviewing the content in full-articles that is relevant to your search. When you retrieve full -articles with a PubMed or other search, QUOSA automatically notes the passages containing  all or part of the search expression. It also does this if ever you use the highlight tool to highlight new search terms in  a body of articles.

 

Operations

·         Bring the list or folder of articles you want to review into the Results pane by double clicking on the list in My Article Organizer

·         If the list is a folder (i.e. not a search list)  - or if for any reason Document Summary appears not to work - then re-highlight the articles with the search expression you want to review against. Skip this part if you have just retrieved the articles from the Internet.

·         Select the Document Summary tab of the Organizer pane.

·         Either double click in the Results pane on the first article you wish to review or click the "Open Next" or down arrow at the far left of the Results pane toolbar. Clicking the down arrow will open the first article in the list or the next article down from that previously selected.

·         If there are any hits for the search expression in the article, excerpts from them will be shown in the top half of the Document Summary pane. Those passages with all elements of the search expression will be shown in one color (usually yellow) , those with only a partial hit in another (usually blue - you can change these colors as you wish). [ Certain PDFs resist this analysis. So, if you have a PDF where you expect there to be hits and none are shown, then you will need to read the text itself to find them.]

·         Click on an excerpt in Document Summary for which you would like to see the full passage. That passage will then be placed in the visible part of the Browser pane, highlighted in the same way as in Document Summary.

·         You may also see other terms in the lower, Concepts section of the Document Summary. Clicking on any of these will bring the first passage containing the term into the visible part of the Browser pane.

·         When you have finished with one article, click the "Open Next" or down arrow in the Results pane toolbar to view the next article and its Document Summary information. Alternatively, simply click directly on the next article you want to see or use the up arrow to move up the article list.

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Re-highlight documents

Operations

·         Bring the list or folder of articles you want to review into the Results pane by double clicking on the list in My Article Organizer.

·         Click the "Highlight" or yellow marker icon in the Results pane toolbar. This brings up a dialog box for you to enter the highlight expression in.

·         After entering the terms to highlight, press "OK" and wait for the circle at the top of the QUOSA window to go green again. This indicates that highlighting is complete.

·         The documents in the Results pane are now ready for review with Document Summary or extraction of related concepts with Concepts4Clustering.

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Search in Results (Boolean)

Terms

A query is broken up into terms and operators. There are two types of terms: Single Terms and Phrases.

A Single Term is a single word such as "protein" or "acid".

A Phrase is a group of words surrounded by double quotes such as "heat shock".

Multiple terms can be combined together with Boolean operators to form a more complex query (see below).

 

Term Modifiers

Boolean Search supports modifying query terms to provide a wide range of searching options.

Wildcard Searches

Boolean search supports single and multiple character wildcard searches.

To perform a single character wildcard search use the "?" symbol.

To perform a multiple character wildcard search use the "*" symbol.

The single character wildcard search looks for terms that match that with the single character replaced. For example, to search for "text" or "test" you can use the search:

te?t

Multiple character wildcard searches looks for 0 or more characters. For example, to search for test, tests or tester, you can use the search:

test*

You can also use the wildcard searches in the middle of a term.

te*t

Note: You cannot use a * or ? symbol as the first character of a search.

 

 

Fuzzy Searches

Boolean Search supports fuzzy searches based on the Levenshtein Distance, or Edit Distance algorithm. To do a fuzzy search use the tilde, "~", symbol at the end of a Single word Term. For example to search for a term similar in spelling to "roam" use the fuzzy search:

roam~

This search will find terms like foam and roams

Note:Terms found by the fuzzy search will automatically get a boost factor of 0.2

 

 

Proximity Searches

Boolean Search supports finding words are a within a specific distance away. To do a proximity search use the tilde, "~", symbol at the end of a Phrase. For example to search for a "heat" and "shock" within 10 words of each other in a document use the search:

"heat shock"~10

 

Boolean operators

Boolean operators allow terms to be combined through logic operators. Lucene supports AND, "+", OR, NOT and "-" as Boolean operators(Note: Boolean operators must be ALL CAPS).

OR

The OR operator is the default conjunction operator. This means that if there is no Boolean operator between two terms, the OR operator is used. The OR operator links two terms and finds a matching document if either of the terms exist in a document. This is equivalent to a union using sets. The symbol || can be used in place of the word OR.

To search for documents that contain either "heat shock" or just "heat" use the query:

"heat shock" heat

or

"heat shock" OR heat

 

 

AND 

The AND operator matches documents where both terms exist anywhere in the text of a single document. This is equivalent to an intersection using sets. The symbol && can be used in place of the word AND.

To search for documents that contain "heat shock" and "heat protein" use the query:

"heat shock" AND "heat protein"

 

 

+

The "+" or required operator requires that the term after the "+" symbol exist somewhere in a the field of a single document.

To search for documents that must contain "heat" and may contain "shock" use the query:

+heat shock

 

NOT

The NOT operator excludes documents that contain the term after NOT. This is equivalent to a difference using sets. The symbol ! can be used in place of the word NOT.

To search for documents that contain "heat shock" but not "heat protein" use the query:

"heat shock" NOT "heat protein"

Note: The NOT operator cannot be used with just one term. For example, the following search will return no results:

NOT "heat shock"

 

-

The "-" or prohibit operator excludes documents that contain the term after the "-" symbol.

To search for documents that contain "heat shock" but not "heat protein" use the query:

"heat shock" -"heat protein"

 

Grouping

Boolean Search supports using parentheses to group clauses to form sub queries. This can be very useful if you want to control the Boolean logic for a query.

To search for either "heat" or "shock" and "protein" use the query:

(heat OR shock) AND protein

This eliminates any confusion and makes sure that  either term heat or shock may exist.

 

 

Escaping Special Characters

Boolean Search supports escaping special characters that are part of the query syntax. The current list special characters are

+ - && || ! ( ) { } [ ] ^ " ~ * ? : \

To escape these character use the \ before the character. For example to search for (1+1):2 use the query:

\(1\+1\)\:2

 

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Import folders of PDFs into QUOSA

Operations

·         Select directory with your PDF files collection. Library can contain multiple folders with multiple levels of depth

·         Select or create new QUOSA folder where your PDF files will be exported. Structure of your PDF Library will be carried over into the destination QUOSA folder

·         Press Start Import button. Progress indicator shows How many total files will be exported and number of current file QUOSA processes.

·         QUOSA will perform the best effort to retrieve Title, authors, etc for each PDF files imported.

 

 

 

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Get full-articles already in a citations manager and link them

Introduction

Full text article references are added to existing Endnote or Reference Manager libraries in three steps:

·         Export of an existing library to a file from your citation manager

·         Import of this file into QUOSA

·         Export of the file created by QUOSA back to your citation manager (this step is preformed by QUOSA automatically)

 

Export  Library from your citation manager

 

 

EndNote

References in an EndNote library can be exported to a plain text file. The export command can be used to create files that may be imported into other applications. When you export references from EndNote, the references showing in the library window are formatted according to the current style.

To export a library from EndNote:

1.      Choose and Open the EndNote library from the File menu:

1.1.   Click on the File menu on the EndNote Toolbar.

1.2.   Choose Open.

1.3.   Click on the Library name you want to export.

2.      Choose Show All References command from References menu.

2.1.   Click on References on the Toolbar.

2.2.   Click on Show All References.

3.      Make sure Show All appeared in the Current Style window on the Toolbar. If not, repeat steps 2.1 and 2.2.

4.      Export Library: click on File on the Toolbar, then on Export.
 

 

 

Reference Manager

 

To export references to a text file from Reference Manager (Version 10)

1.      From the References menu, choose Export.

2.      In the File name drop-down, type the full path and file name of the file name into which you want references exported.

3.      In the Output format area, select the format type for the exported file.

4.      In the References options area, select the references you want exported.

5.      Click Export.

To export references from Reference Manager (Version 11)

1.  Open the database from which you will export, and select the references you want to export.
2.  Sort the references if necessary. You can click on a column heading to quickly sort by that field.
     References are exported in the order in which they are listed in the Reference list window. (Highlighted
     references are unselected during a sort, whereas marking is remembered until you close the database.)
3.  From Reference Manager's File menu, choose Export.
4.  Next to the File name text box, click the ellipses button to display a file dialog.
5.  In the file dialog:
     5.1.  Enter a name for the exported file and use the "Save in:" list to specify where it should be saved.
     5.2. Under the "Save File as Type" list at the bottom of the dialog, select the type of files to view in the
            open folder: text files or all files. Reference Manager will assign the appropriate extension to the
            file format you selected (such as adding .XML to an XML export file).
     5.3. Click OK to create the file and return to the Export References dialog.

Note: The Export feature creates a new file; it does not append to an existing file. If you enter the name
of a file that already exists, you will be advised to enter a different filename.

6. Select an output format: RIS, MEDLARS, Comma Delimited, Tab Delimited, or XML. (See Supported
    Export Formats for more information).
7. Under "References options," select the group of references you wish to export.
8. Click Export.

 

 

 

ProCite

 

 

To export records from ProCite

 

1.  Choose and Open the ProCite library from the File menu: 

1.1.    Click on the File menu on the ProCite Toolbar.

1.2.    Choose Open.

1.3.    Click on the Library name you want to export from.

2.  Mark selected records you want to export.
3.  Click on "Tools" and then on "Export Marked Records..." on the ProCite Toolbar.
4.  In the following "Export Marked Records" dialog choose preferences:

4.1    "Export Format" – “Custom”

4.2    "Fields Separated with" - "Tabs"

4.3    Records Terminated with" - "Carriage Returns"

4.4    "Optional Field Delimiters" – leave all three empty

4.5    "Included Fields" - check all three

4.6    Press OK button, when finished

5.      If message "All styles, including superscript and subscript, are removed from exported text"

     appears, press OK button.

6.  In the file dialog:
     6.1.  Enter a name for the exported file and use the "Save in:" list to specify where it should be saved.
     6.2. Click OK.

Note: The Export feature creates a new file; it does not append to an existing file. If you enter the name

of a file that already exists, you will be advised to enter a different filename.

 

 

 

 

 

Import Into QUOSA Information Manager

QUOSA allows you to import libraries exported from EndNote or Reference Manager.

QUOSA will retrieve articles these libraries contain references to in full text PDF format where possible.

To import the file exported from EndNote/Reference Manager into QUOSA Information Manager:

1.  Make sure you have selected the PubMed channel specific to your institution (e.g., NIH users should select PubMed – NIH)

2.  Click on Tools on the QUOSA Toolbar. Click on Import Citation Library/Database. QUOSA will display “Import From Citation Manager” wizard.

3.  Choose EndNote/Reference Manager file you want to import and click Next. QUOSA will display the “Citations Found” wizard.  It will display the number of citations found in the file.

      3.1. If you think this number is incorrect you should adjust your Citation Manager export setting and export the library again.  (Go back to EndNote or Reference Manager)

      3.2. If the number is correct, click on the Import button.

4.  Search and download process will start. The period of time required to complete this step depends on the size of your library and the speed of your Internet connection. 

Export Citations back to your  Citation Manager

After download is complete QUOSA Information Manager will automatically save all articles into the My Citations folder and will export references to your citation manager.

 

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Save article references from a PubMed search into a citation manager

Operations

·         This is easiest in Advanced View - but these instructions include those for Express View.

·         These instructions are for adding citations to an existing library. If you want to put them in a new library, you need first to create this library under your citation manager.

·         After performing a PubMed search, you may immediately spot some references that you want to export. Select the ones of interest by checking their check boxes on the PubMed results list, then click on the Export-Citation button in the Browser Panel toolbar (Advanced view). For Express View, use Commands/Sync and Link selected articles to EndNote, Refman, etc.

·          If your citation management software is already installed on this computer, it should launch and you will be prompted for the 'library' or 'database' into which you wish to save the citations ... select one and click open.  You will immediately see the citations you selected in PubMed listed in your library/database.

·         QUOSA will also retrieve the articles into a new search list with the name of your original search term in PubMed.

 

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Import articles via a search on My Computer

Operations

·         Configure the QUOSA Channel to either "My Documents" (to search under My Documents) or to Local Folders (to search pre-configured local folders.

·         To configure or re-configure your local folders, see "Creating a custom channel to search local documents" in the Tutorial.pdf

·         The QUOSA Browser pane will show a " Search for Documents" page, where you enter your search term and the maximum number of documents you want retrieved.

·         Then click the Sigma icon. This starts the search, creating a new search list in My Article Organizer and opening (if necessary) the Results pane.

·         When the search is finished, the files found are effectively already within QUOSA's Article Organizer, in the search list named after your search term.

·         You can save all the results or a flagged selection of them to folders in My Article Organizer via either the Save icon,  Commands/Save or Export selected articles, or by dragging and dropping the selection into the target folder.

 

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Save full-articles to a Windows/Mac folder

Operations

  • If you wish to send some or all of the  articles that you have saved into a QUOSA folder to colleagues who do not have an installed copy of QUOSA, then you should save them in their original form (HTML or PDF files).  Anyone with a browser like Internet Explorer will be able to view these files. 
  • Right click on an article you wan to save that is in the Results Pane to bring up a pop-up menu. Choose "Save as Windows (Mac) File"
  • If you wish to save all or a batch of the articles in the Results Pane, first select the articles you want to save by either flagging them and selecting the flagged files or by selecting all the files.
    • Then (under Advanced View) click on the Hammer  (Tools) icon and click 'Copy Selected  Documents to Windows Folder'
    • Alternatively, go to Commands/Save-Export selected articles/to Windows (Mac) Folder.
  • You can also save individual articles in search results to file.  Simply select the article, right click and choose "Save as Windows (Mac) File"
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Extract concepts from articles

Operations

  • This feature is best performed under "Advanced View".
  • Make sure that the rightmost Layout button in the main toolbar is depressed, so that the QUOSA window displays all three sub-panes. 
  • Click on the "Concepts4Clustering" tab in the Organizer Pane.  A confirming dialog will appear.  After you click OK you will observe a list of concepts appearing under the Organizer Tab. 
  • Make sure that the "In Cluster" field in the Results pane is visible. If it is not, use the scroll bar at the bottom of the Results pane to move across until it is visible. Then reduce the width of one of the fields to the left of it (typically the title filed) until the "In Cluster" field is visible without having to scroll to the right.
  • Select and right-click on one of the concepts in the concept list. Note the choices you get, including "Sort by Cluster Size".
  • The numbers to the left of each concept indicate the number of hits for the concept. Note also that the + sign indicates that the cluster is an aggregate of related sub-groups. Clicking on the + sign will reveal the sub-clusters and the number hits for each.
  • Select a concept - at any level in the hierarchy - and click on it.  The articles  in the Results Pane will be re-ordered such that articles most related to the Concept you selected will move to the top and be identified with a Concept icon in the In Cluster column. 
  • To extract and  process a list of articles in a cluster:
    •  Select the concept of interest under the "Concepts4Clustering" tab.
    • Click the "Search in Results" icon on the Results pane toolbar. Make sure the concept selected is entered as the search term and press "Search".
    • When the search is complete, close the  "Search in Results" dialog box. The articles you want will now be in the Results pane and a new, secondary search list will be created in My Article Organizer, appended to the original search list or folder.
    • Select the Highlight icon and make sure that the concept originally searched on is entered as the highlighting term.. (This may require entering the term manually.) Press "OK".
    • You can now review the new list of articles with Document Summary against the concept you selected from the  "Concepts4Clustering" analysis.
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Regular Expression and Wildcard Queries

 Introduction

Regular expressions are made up of normal characters and metacharacters. Normal characters include upper and lower case letters and digits. The metacharacters have special meanings and are described in detail below.

In the simplest case, a regular expression looks like a standard search string. In Quosa, regular expressions are case-insensitive. For example, the regular expression testing contains no metacharacters. It will match testing and 123testing and Testing but it will not match sting.

To really make good use of regular expressions it is critical to understand metacharacters. The table below lists metacharacters and a short explanation of their meaning.

Note: Regular Expression metacharacters in Quosa search on individual words, not phrases. Therefore some of the metacharacters have different meanings than in general Regular Expressions.

To match multiple-word phrases, separate each word with a single space. For example, the regular expression th.* .*s f.n.? will match this is fine and that was fun, but not the cat was found.

 

Metacharacters

 

Metacharacter

 

Description


 


.

 

Matches any single character. For example the regular expression r.t would match the strings rat, rut, rot, but not root or r t

^

 

Matches the beginning of a word. For example, the regular expression ^the would match the word therefore or on "the" in the string "in the event" but would not match "otherwise"

$

 

Matches the end of a word. For example, the regular expression weasel$ would match the word weasel but not the word weasels. 

*

 

Matches zero or more occurences of the character immediately preceding. For example, the regular expression .* means match any number of any characters. 

+

 

Matches one or more occurrences of the character or regular expression immediately preceding. For example, the regular expression 9+ matches 9, 99, 999.

?

 

Matches 0 or 1 occurrence of the character or regular expression immediately preceding.

\

 

This is the quoting character, use it to treat the following character as an ordinary character. For example, \$ is used to match the dollar sign character ($) rather than the end of a word. Similarly, the expression \. is used to match the period character rather than any single character. 

[ ] 
[c1-c2]
[^c1-c2]

 

Matches any one of the characters between the brackets. For example, the regular expression r[aou]t matches rat, rot, and rut, but not ret. Ranges of characters can specified by using a hyphen. For example, the regular expression [0-9] means match any digit. Multiple ranges can be specified as well. The regular expression [A-Za-z] means match any upper or lower case letter. To match any character except those in the range, the complement range, use the caret as the first character after the opening bracket. For example, the expression [^269A-Z] will match any characters except 2, 6, 9, and upper case letters. 

( )

 

Treat the expression between ( and ) as a group. Use with the quantity modifiers (*, +, ?, {}) and with |.

|

 

Or two conditions together. For example t(ry|op) matches try and top but does not match toy.

{i}
{i,j}

 

Match a specific number of instances or instances within a range of the preceding character. For example, the expression A[0-9]{3} will match "A" followed by exactly 3 digits. That is, it will match A123 but not A1234. The expression [0-9]{4,6} any sequence of 4, 5, or 6 digits.

 

Samples

The simplest metacharacter is the dot. It matches any one character (excluding the newline character). Consider a file named test.txt consisting of the following lines:

he is a rat
he is in a rut
the food is Rotten
I like root beer

The regular expression r.t matches an r followed by any character followed by a t. It will match rat and rut. It will also match the Rot in Rotten because regular expressions in
Quosa are case insensitive.

To match characters at the beginning of a word use the circumflex character (sometimes called a caret). For example, to find the words containing the string "he" at the beginning of each
word in the file test.txt you might first think to use the simple expression
he. However, this would match the in the third line. The regular expression ^he only matches the h at the
beginning of a word.

Sometimes it is easier to indicate something what should not be matched rather than all the cases that should be matched. When the circumflex is the first character between the square
brackets it means to match any character which is not in the range. For example, to match
he when it is not preceded by t or s, the following regular expression can be used: [^st]he.

Several character ranges can be specified between the square brackets. For example, the regular expression [A-Z] matches any letter in the alphabet, upper or lower case. The regular expression [a-z] is equivalent. The regular expression [A-Z][A-Z]* matches a letter followed by zero or more letters. We can use the + metacharacter to do the same thing. That is,
the regular expression
[A-Z]+ means the same thing as [A-Z][A-Z]*.

To specify the number of occurrences matched, use the braces. As an example, to match all instances of 100 and 1000 but not 10 or 10000 use the following: 10{2,3}. This regular expression matches a the digit 1 followed by either 2 or 3 0's. A useful variation is to omit the second number. For example, the regular expression 0{3,} will match 3 or more
successive
0's.

 

 

 

Wildcard

Wildcards are like a simplified version of regular expressions, with only two metacharacters. Like Regular Expressions, Wildcard searches in Quosa are case insensitive.

 *

An asterisk (*) may be used to specify zero or more alphanumeric characters. For example, searching for the term h*s would yield results which contain such words as “his”, “homes”
and “herbaceous”.  In Quosa, a
* at the beginning and end of each term is assumed, so that the term h*s would also match "these". A search term consisting of a lone asterisk and no
other alphanumeric characters will match every word in the file, which may take quite a long time.
 

 

 

The question mark (?) may be used to represent a single alphanumeric character in a search expression.  For example, searching for the term “ho?se” would yield results which contain
such words as “house” and “horse”.
 

 

 

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Automate Batch Queries

Introduction

With Import Query, multiple PubMed queries or author names can be saved to an Excel or CSV (Comma-Separated) file and imported to query PubMed. The file can also specify Regular Expression / Wildcard / Boolean searches to run on each set of results.

Import Query will use the values in the first column (column A in Excel) to query PubMed. The PubMed query  has to be surrounded by a pair of braces {}. It has to comply with PubMed Query language. The other columns specify Regular Expression / Wildcard / Boolean Searches. To search using a Regular Expression, prefix the search term with [R]. To search using Wildcards, prefix the search term with [W]. For Boolean search use [B]. If no prefix is specified, the default is Wildcard search.

For more information on Regular Expression / Wildcard / Boolean searches, including how to search on multiple-word phrases, see the Regular Expression / Wildcard Search Help Page and the Boolean Search Help Page.

 

Author Name List

To query PubMed on a list of authors, create an Excel or CSV file with names listed in the first column (column A in Excel), one name per row.

The Import Names Wizard allows you to choose whether to use all names in one search, or use each name in its own search.

Samples

 Excel File:

 

 

A

B

C

D

1

{Smith}

15342

[R]5.98.*3

 

 

2

{Koster}

emmision peaks

[W]3443*

[R]f.*i

3

{Hall}

ab*

[R]9.87a.3

[B]Peter AND Wolf


CSV (Comma-Separated) File:

{Smith},15342,[R]5.98.*3
{Koster},emmision peaks,[W]3443*,[R]f.*I
{Hall},ab*,[R]9.87a.3,
[B]Peter AND Wolf

Where:

[B] stands for Boolean Search

[R] stands for Regular Expression Search

[W] stands for Wild Card Search

 

 

PubMed Query List

To import multiple PubMed queries, specify each query in the first column of a row (column A in Excel0.

The PubMed query must be in braces {} and can have in it any characters defined in PubMed query  language, e.g. {"gene expression profiling"[MeSH] AND ("lung"[MeSH Terms] OR lung[Text Word]) AND ("carcinoma, non-small-cell lung"[MeSH Terms] OR nsclc[Text Word]) AND hasabstract[text] AND English[Lang] AND ("human"[MeSH Terms] OR "hominidae"[MeSH Terms]) AND ("2001"[PDAT] : "2004"[PDAT])}. The easiest way  to get a complex PubMed query is to formulate it with limits on the PubMed search page, perform the search, click on Details subheading to switch to Details view, and copy Query Translation text from the text box.

Samples

Excel File:

 

 

A

B

C

D

1

{pthrp}

expr

[R]S.H

[W]diff*

2

{heat stroke}

effect of

[W]bi*r results

[R]g.*th

3

{asthma}

pl*te

[B]"Annexin A8"

[R]a[0-9]+ b[0-9]+ c[0-9]+

CSV (Comma-Separated) File:

{pthrp}, expr, [R]S.h, [W]diff*

{heat stroke}, effect of, [W]bi*r results, [R]g.*th

{asthma}, pl*te, [B]"Annexin A8", [R]a[0-9]+ b[0-9]+ c[0-9]+

 

Where:

[B] stands for Boolean Search

[R] stands for Regular Expression Search

[W] stands for Wild Card Search

 

 

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Search My Articles with a list of terms

Introduction

This is sometimes informally referred to as a dictionary query. Suppose you have a saved search or folder within QUOSA Information Manager with full text articles on the subject of Asthma. You want to see what the incidence of hits (articles) is with any of a list of terms or search expressions.

 

QUOSA featureTerms4Clustering® allows you very rapidly to see the incidence of hits from that list (by search term) and to find the articles and the passages comprising those hits. Terms4Clustering® is not available in the Standard version of QUOSA. You may need to upgrade your license to use it.

 

You can use any list stored on your computer as a txt, csv, or xls file.

 

You can automatically compile a search term list from a query on NCBI’s Gene database. So – as a hypothetical example – you could get a gene term list from an “ageing” query on the Gene database and quickly see the hits for those gene terms in a large group of articles on asthma.

 

You can do a similar thing by getting your list of search terms by applying Concepts4Clustering to a group of articles from another search. (Do this by right-clicking on one of the concepts returned by Concepts4Clustering and selecting “Save concepts to file”).

 

Operations

·         Terms4Clustering® is best performed under the Advanced View interface.

·         Bring the list or folder of articles you want to review into the Results pane by double clicking on the list in My Article Organizer.

·         If you have not already, create and identify the list of terms you want to use for cluster analysis, as discussed in the Introduction above.

·         To apply this list to Terms4Clustering, go to “Tools” menu at the very top of the QUOSA window and select Tools/ Terms4Clustering/Configure Clustering. Then browse for the file which contains your list and click OK.  

·         Terms4Clustering will continue to use this list until you select any other. So if you have one list you use repeatedly,  there is no need to configure it each time. Notice you also get an option to edit the list if you want to make minor changes.

·         Make sure files from the folder you want to search are showing in the results pane, and then click the Terms4Clustering Tab on the left (stacked with the Documents Summary, Concepts4Clustering, and My Searches & Folders tabs). You will see the name of your search list and the number of hits for each search term.

·         Within the Terms4Clustering pane, click on one of the terms that has some hits. You will see that the order of files in the Results pane changes .The “hit” articles are put at the top of the list and a cluster icon appears against each of these under the "In Cluster" Field (column) in the Results pane. You can then see the articles in question by double clicking on them (and/or using the up and  down arrows) in the Results pane.

·         If you want to highlight the relevant text and find it via the Document Summary tab, then you need first to highlight the articles with the relevant search term. (Note that if you don’t do this, the document may be highlighted with a search term used earlier for that folder. To do this, select the Highlight icon above the Results pane and enter the search term you are interested in. Then click OK. The highlighter then highlights all relevant text for all articles in the folder.

·         You may find that the files get reordered in the Results pane, that you lose the cluster icons, or that the Terms4Clustering pane goes blank. You can get this back by clicking first on another tab (e.g. Document Summary) and then clicking back to Terms4Clustering and then the relevant search term. This won’t affect the highlighting. Now you can go through the documents having a cluster icon with the aid of the Document Summary tab, which shows the passages with hits for all words in the search expression and also those with only a partial hit.

 

One advantage of highlighting all the articles is that you can see the incidence of hits which are not selected as being in the cluster. This includes articles with only partial hits but also articles that have passages containing all search words but spaced further apart than the default proximity in Terms4Clustering

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Search My Articles with Gene terms

Introduction

This section describes how to create a dictionary (list) of Genes and Alias terms which can be used with Terms4Clustering®  to search articles in My Article Organizer to produce a cluster analysis of the document set against this list of terms.

See the Introduction to "Search My Articles with a list of terms"  for more information on the context.

 

Operations

·         Go to Tools/ Terms4Clustering/Create Gene Dictionary. You get a dialog box with an explanation of these next steps.

·         Click "Yes"  and Entrez Gene appears in the browser pane.

·         Enter a suitable search term into the search term field. The return page lists the first 20 returns.

·         In the QUOSA  Browser pane toolbar, set the “Retrieve” number to the maximum number of Genes you want terms for and click on the Sigma button (Don't worry about pop-ups describing this as retrieving articles). 

·         You then get a dialog box offering a choice between a dictionary with grouping and a flat list. The grouped dictionary will result in an hierarchical search and tiered search returns. A flat list will treat all search terms as equal and primary.

·         You also have the option to specify or browse for an output file name and location. The result of this process will automatically configure Terms4Clustering® to use the output file. So (later) just go to Tools/ Terms4Clustering/Configure Clustering to see the file name and location if you have not specified it.

·         Press "OK" to start the dictionary creation process. This can take some time. When it is complete, a dialog box will advise you of successful completion and of the number of terms retrieved.

·         Use this new search term list just like any other under "Search My Articles with a list of terms"

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Get full-articles from Google (The General Web)

Introduction

 

QUOSA can retrieve - on a best efforts basis - documents whose details are returned by a general search on the Web. This is done by utilizing a normal Google search, although the user will not see the Google search page.

 

The user gets a simple QUOSA search page and a box to indicate how many documents are to be retrieved. This search page is the "Home" page for the "General Web" channel.

 

Operations

  • Go to the topmost QUOSA toolbar and click "Channels" , then "General WEB" to select the Web channel.

  • QUOSA will go to a full Browser pane layout with a simple search page headed "Search for Documents".

  • Enter your search term in the longer, left-hand text box. There is a default value (probably 30) for the number of documents to be retrieved in the right-hand box.

  •  Enter the number of documents you want retrieved. (If you set 30, QUOSA will try to retrieve the first 30 documents referenced  by Google.)

  • Press the Sigma button to the left of the number box.

  • QUOSA will then open the Results pane and start to fill it with key data on the files retrieved. It will also create a search list under "Searches" in My Article Organizer on the left. (It is useful to have the Organizer open.)

  • The process is complete when the circle at the top of the QUOSA window has returned to green (having been blue while retrieving) and when the search list in My Article Organizer has a binocular symbol against it. There will not necessarily be as many documents returned as the number you entered into the search page.

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How to Back up QUOSA Files

Introduction

 

You may need to do this if you have to re-install your operating system or if you wish to move QUOSA Information Manager to another computer

 

This procedure allows you to save your QUOSA data archive and return it to the same or a new computer without loss of any data.

 

Operations

  • Go to QUOSA Settings | Algorithm Settings | Service tab and make a note of the data path. This is the location where QUOSA keeps all its data.
  • Click the Browse icon, go up 2 levels and zip the QUOSA folder.
  • For example: if the path to data is C:\Documents and Settings\JohnDoe\Local Settings\Application Data\Quosa\Data, you would go to C:\Documents and Settings\JohnDoe\Local Settings\Application Data and zip the QUOSA folder there.
  • Move this archive to another computer or to a network drive.
  • When you are are ready to install QUOSA again (either on the same computer or a new one), first extract the zipped data to the location corresponding exactly to the location of the QUOSA folder on the old computer. (Alternatively, select another location and once QUOSA is installed change the data path under Settings to the new data path; but this option will break EndNote links.)
  • Download QUOSA
  • When you start QUOSA it may tell you that it cannot validate registration information.
  • Quit and register again. All data should be intact.
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Moving Computers - Licensing Issues

Explanation

 

If you wish to move QUOSA Information Manager from one computer to another, first back up QUOSA data and transfer it to the new computer. Then install the free download version on the new computer. When you get your Authorization Code for the new computer by email, send an email to support@quosa.com asking to switch your license to that computer. Please include your ID #. You will be advised when the change has been made and that the QUOSA Information Manager on the new computer is fully enabled. You may switch between Windows and Mac computers within the same license class without any additional charge.

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What's wrong? No full-articles.

Introduction

 

There can be a number of reasons that you are not getting the full-articles you would expect to get. We list the more common ones below, with indications of how to address the problem.

 

Possibilities

·         Is your subscription out of date? If it is out of date, you will not be able to retrieve any articles, whether full-articles or abstracts with QUOSA. Purchase LiveUpdate! to restore this functionality.

·         Are you off-line or not authenticated? You need access to the Internet to get full articles, and you need to be properly authenticated with your journals' suppliers to get full-articles. You may therefore not be able to get full articles (even without QUOSA) if you are away from and not suitably connected with your institutional network.

·         Do you have a valid subscription to the journal which has published the article? This is necessary to get any articles that are not available free. You may wish to check with your librarian if in doubt.

·         QUOSA gets some full-articles but not for all the journals to which you subscribe. Two different situations may apply:

o        The full articles you are getting are freely available articles. No subscription access articles are being retrieved. This may be because you are using the wrong QUOSA channel for your institution. Check this first, if the problem persists, please contact support@quosa.com.

o        You get some subscription articles but there are some you should be getting which you do not. This is probably due to some reconfiguration made by the journal supplier or a change in your institution's supplier for the article. In this case, contact us at support@quosa.com. If you have an institutional license, please also advise your librarian.

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Use QUOSA with network drives

Introduction

QUOSA can be used with network drives but there are some restrictions on how it can be used, as well as some guidance on how to avoid problems.

 

Organizations intending to use QUOSA on networked drives should always ensure that their storage of full-articles and their users' access to them is compliant with the conditions of their journal subscription agreements.

 

It is a bad idea for many users to share the same QUOSA folder from multiple computers.  Simultaneous use of the folder messes up the QUOSA database.

 

There is no problem having QUOSA files kept on a private (single user) folder on a network drive.

 

By using a private network drive, a single user can (at different times) access the same files/QUOSA folders from different computers on the same network. Each computer used needs it own access code. This may or may not be available under the terms of your existing QUOSA license. If in doubt, ask info@quosa.com.

 

Multiple users using the same computer with folders on a network drive would be best advised to log onto the computer under separate user names (as well as using private folders for QUOSA on the network server). This ensures that QUOSA initializes to the settings (incl. folder location) of each user as appropriate - and that there is no cross contamination of file saving, etc.

 

Operations

·         First map a network drive to My Computer. Under Windows, right-click on My Computer, select Map Network Drive, and follow the instructions given.

·         If you wish to move existing QUOSA data to the new location, copy it there. The default location under Windows is:  Documents and Settings/username/Local Settings/Application Data.

·         Change the QUOSA file locations settings by going to Settings/Algorithm Settings, select the Service tab (it is probably already visible), and then change the data path to the desired data path. The change will not apply until QUOSA restarts.

·         Apply the change, which closes QUOSA.  Restart QUOSA to continue using it.

·         You can use available folder synchronization tools to synchronize the network folder with a local folder on a  laptop, so that you could have access when away from the network or VAN. But you should be aware that Windows' automated synchronization adds a considerable delay to the articles retrieval process, with QUOSA effectively immobilized during that time. It does have the advantage  that you don't need to change file locations and your EndNote (or similar) reference links work consistently.

·         If you want QUOSA searches or folders to be available on your laptop offline, while avoiding Windows Offline Files synchronization, the best way is to maintain an alternative QUOSA file location on your own hard drive for copies of such folders. While still online, select each folder you wish to copy to your hard drive and Export (File/Export) it to a temporary location on your hard drive. When you are offline, if necessary (see below), reset the QUOSA data path to the local drive (which will then mean restarting QUOSA). Then File/Import the searches and folders you previously exported. This has the advantage over full synchronization of not using up your own disk space with folders you will not need offline.

·         If you do change file locations when off-line and use the same user log-in as when on-line, you will need to reconfigure QUOSA settings to use the local folders when offline. This is not necessary if you use a different user log-on when you are offline.

·         You  also need to be aware that using 2 QUOSA folder locations with different path strings will mess up the EndNote references: EndNote reference URL's with the network drive path will not work when offline.

·         If, though, you use a separate (windows) log-in for use off-line, then you can avoid resetting QUOSA folder settings and can then  use the same folder location path string as you do when on-line. In this case, the EndNote URLs will be the same whether created on-line or off-line.

 

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Glossary

Introduction

 

We have listed here a number of terms we commonly use in describing QUOSA Information Manager and its functions. We try to make it clear here what is meant by them.

 

Words we use

Term  we use:

What is means

Browser pane

The pane or window within QUOSA through which you both search PubMed etc. but also view the text of articles. To maximize this pane. Click the Browser icon at the top right of the QUOSA window.

Results pane

The pane within QUOSA where search results or summary information on a folder of articles is displayed. If both the Results and the Browser pane are open, the Results pane sits above the Browser pane.

Organizer

This is a small pane to the left of the QUOSA window which is tabbed to show My Article Organizer, Document Summary, and some other features. If it is closed (by clicking the small 'X' at its top right corner), you can get it back by clicking the 'Show Organizer' button near the top left of the QUOSA window.

Sigma/ Retrieve

The Sigma icon is the button to use to retrieve in a batch either full-articles or abstracts from a search with one of the configured QUOSA channels. It is used in some other contexts, but always for batch retrievals from a channel or set of folders.

Channel

A channel is a configured context in which QUOSA is able to batch retrieve a set of articles through a prior or simultaneous search. Typically, it is PubMed, OVID, or similar search gateways, but also includes general web search (via Google) and folders on your own computer network.

Citation manager

Software that maintains libraries of article citations, such as EndNote, Reference Manager, and ProCite.

Full-articles

Full text versions of articles, typically in either PDF or HTML format. This term used to distinguish these from abstracts.

Articles

Either abstracts or full-articles

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Copyright © 2006-2009 QUOSA, Inc. All rights reserved.
Revised: 23/03/2006.