Abstracts Window


The Abstracts window shows the contents of an abstracts file, one abstract at a time. Two different kinds of abstract files can be read: plaintext and embedded markup. See the file formats page for details about these files. The Abstracts window contains two text display fields, arranged as a split view. The border between the two fields can be raised or lowered by dragging the mouse, in order to resize the fields. The second text display field displays the PL, PN, and PF fields of the abstract, which indicate the protein and gene symbols and names which might be related to the abstract. The first text display field shows all other fields in the abstract. If a PGML (Protein/Gene Markup Language) embedded markup file has been read, all marked strings in the abstract are displayed in color, with red, blue, and green text alternating for each separate category in the markup.

Reading abstracts files

To read an abstracts file, click the 'Read Abstracts...' button. Navigate through the Mac file system using the Open dialog, and choose a file to read. The file will be read and parsed, and all abstracts stored in memory. WARNING: Each time you read an abstracts file, the current set of notes displayed in the Notes window are erased.

Navigating through abstracts

Click the 'Prev Abstract' or 'Next Abstract' buttons to move through all the abstracts in the file, one at a time. Enter a number into the lower right text field of the window and click 'Go To #:' to go directly to a specific abstract in the file.

Searching for PMIDs

Enter a PMID number of an abstract into the second from the top text field of the window, and click 'Find PMID:' to search for an abstract with that PMID number. If an abstract mathing the PMID is found in the file, it will be displayed.

Finding selected proteins

You can automatically search the proteins database (see the Proteins window page for details) for a string contained in the PL, PN, or PF fields of an abstract. Select one or more characters of a line in the second text display field of the split view and click 'Find Selected Protein'. The entire line of text will then be selected and copied into the 'Search For:' field of the Proteins window, and a search for that string will be performed on the currently loaded proteins database, if any.

Selecting the font

Both of the text display fields of the split view are editable so that you can change their fonts. Changes to either of these fields are not written to the abstracts file. To change the font of a display field, click the mouse in the field and choose 'Select All' from the Edit menu. You can then access the Font menu and change the font with 'Show Fonts' or any of the other menu items. Only if you selected the entire display field will changes to the font persist to other abstracts.

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İSky Coyote 2002