I have not been publishing research for a few years, but I am returning to it. So, I am updating my research and expanding my PKM process.
Here are the apps that I have been using (partially updated) and their roles. I usually use a Mac.
Source searching: Papers 3.4, Google, Google scholar, etc.
PDF Converter, OCR: Searching for something new
Citation Manager / PDF storage: Papers 3.4 (Legacy) exploring options.
Annotation: Highlights
Knowledge and Note management: Obsidian, may also use Devonlink 3
Content outlining and drafts: Obsidian, and possibly Typora
Final reviews and publication: Word or Scrivener depending on size
Preferences: I prefer to avoid Platform as a Service (PaaS) Internet apps and subscriptions. The reasons for these preferences are topics for another discussion. But, while I am not uncompromising, I’d like to keep these two types of apps to a minimum, which is one reason I like Obsidian.
Searching for source materials does not seem to be a problem. I often have more than I can use.
For pdf conversion and OCR, in the past I have used Adobe Acrobat, but they went to a PaaS subscription basis and de-supported and killed my stand-alone app. Everyone else seems to use the ABBYY FineReader engine, so they are all about the same. The problem I have faced in the past is pdfs are not good at maintaining structure, so during the highlighting annotation process, accurate highlighting and quotes can be problematic and distracting. I’d like and OCR system that allows me to easily correct it. Someone suggested converting to HTML? I am certainly open to options here.
Citation manager: Mekentosj Papers 3 before they were bought out by Digital Science & Research Solutions (Readcube) had its issues, but they were constantly improving and addressing customer complaints, and it does some things very well. However, as a legacy app, I hate to rely on it for much longer.
I have tried Bookends. it is OK. I have used Mendeley, EZBib, ReadCube, and Zotero, besides being PaaS apps, they were awkward to use, but I will review updated versions of those. Anything else?
Annotation I heartily recommend Highlights app for use with Obsidian, https://highlightsapp.net. It is just so easy to use. I “Open with…” Highlights from Papers. Highlights, underlines, photos, and tables go into a sidebar with metadata and a back link to the pdf in Highlights. A key feature for me is that I can add a notes to each item I annotate. These notes become the text for a content outline and are essential to learning. Highlights has a handy feature for linking citations from each article’s references section. I can add tags and links for Obsidian here, if I want. I paste links and citekeys from Papers 3. Then, it exports to markdown. Obsidian reads it beautifully. I add a any more links and my literature notes are done.
Adding links and backlinks has always been a PITA, so I am planning to have Obsidian to a lot a heavy lifting in the note management, content outlining and actual writing process.
I have to publish my final draft in Word for the Papers citation manager to work. I would enjoy some alternatives here too.