3.3.3 Literature searching

Geneious Prime allows you to search for relevant literature in NCBI’s PubMed database. The results of this search are summarized in columns in the Document Table and include the PubMed ID (PMID), first and last authors, URL (if available) and the name of the Journal.

When a document is selected, the abstract of the article is displayed in the Document Viewer (Text View tab) along with a link to the full text of the document if available, and a link to Google Scholar, both below the author(s) name(s) (Figure 3.2 ).

As well as the abstract and links, Geneious also shows the summary of the journal article in BibTex format in a separate tab of the Document Viewer (BibTex tab). BibTex is the standard LATEX bibliography reference and publication management data format and the information in the BibTex screen can be imported directly into a LATEX document when creating a bibliography. Alternatively, a set of articles in Geneious can be directly exported to an EndNote 8.0 compatible format. This is usually done when creating a bibliography for Microsoft Word documents.

Note: If the full text of the article is available for download in PDF format, it can also be stored in Geneious by saving it to your hard drive and then importing it. This will allow full-text searches to be performed on the article. To view a .pdf document either double click on the document in the Documents Table or click on the View Document button. This opens the document in an external PDF viewer such as Adobe Acrobat Reader or Preview (Mac OS X). On Linux, you can set an environmental variable named “PDFViewer” to the name of your external PDF viewer. The default viewers on Linux are kpdf and evince.


Figure 3.2: Viewing bibliographic information in Geneious