QUOSA Information Manager usage guidance

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.

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.

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.

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.

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.

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.)

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.

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.

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.

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).