This is my reference collecting workflow (given for journal articles - other searches are similar); it may be long and repetitive.
Search for scientific journal articles using SciFinder, Web of Science, Google Scholar, etc.
Download, rename (full title of the journal article), and save as PDF to EagleFiler.
In my ReferenceArchive library, I created a minimum folder structure to facilitate accessing files from outside of EagleFiler (Articles, BookChapters, Books, ConferenceProceedings, JournalArticles, Magazines, Patents, Presentations, References, TechnicalReports, Theses, and UserManuals). I save files (PDF, Word, Text, Excel) directly to the relevant folder and then use the “Scan for new files” command to add them to the library. I might also have to apply the “file name to title” script.
- Assign tags to documents in EagleFiler
I assign a tag to each document that is the same as the storage folder (articles, book_chapters, books, conference_proceedings, journal_articles, magazines, patents, presentations, references, technical_reports, theses, and user_manuals). This is to facilitate smart folder searches. For books and patents, I also assign relevant tags for content (engineering, civil, chemical, electrical, mechanical, instrumentation, software, mathematics, etc.).
- Download and import citation + abstract in BibTex or plain text format to BibDesk
I use SciFinder, Web of Science, etc. to download citation + abstract in BibTex format (or plain text format). When connected to my University network, I use a Web of Science search directly in BibDesk.
I import the reference to BibDesk. I then use a top (BibDesk) bottom (EagleFiler) split/divided screen orientation. With the new import selected in BibDesk, I drag the document from EagleFiler up to the BibDesk sidebar. This creates an alias in BibDesk.
- Assign “BibDesk” tag to document in EagleFiler
I go back and add an additional tag to the document so that I keep track of the EagleFiler documents that have a bibliographic entry in BibDesk.
- If the keywords did not import to BibDesk, I will copy and paste them from the document in EagleFiler or create them based on the document title.
To summarize, I use two applications to manage my references. EagleFiler to “hold” the documents and BibDesk to organize citations.
I maintain only one EagleFiler library and one BibDesk bibliography for all of my references (1000+ documents and counting). For individual projects, I will create temporary BibDesk bibliographies to hold relevant citations (easy since they are really only text documents).
I assign keywords only in BibDesk and use limited broad tags in EagleFiler. This is to keep from duplicating function and also to limit tag “clutter” in EagleFiler.
When I start a new project, I will search BibDesk by keyword and then open documents by double-clicking the included link. At this point, the only reason that I would open EagleFiler is if I think that I forgot to import a document to BibDesk.
To get the citations into a manuscript, I use Microsoft Word 2011 and BibDesk to Word. That website has not been updated in awhile, but the latest version does work with Word 2011.
I tried to force myself to use Sente because they came out with a great looking iPad app, but I just did not like the Mac application . . .
Instead, I use PDF Expert (or ReaddleDocs) with a Synk Pro script to synchronize my Books and JournalArticle folders in EagleFiler (occasionally I run the “Update Checksome” command) to my iPad. I like PDF Expert because my highlights and notes are viewable and can be edited back in Acrobat or Preview.
It would be nice to get searchable abstracts from BibDesk to the iPad, but I haven’t tackled that one yet . . . maybe I will join the BibDesk development community and write an iPad app . . . in my spare time . . . yeah . . . spare time . . . as a doctoral candidate . . .