Summarise Highlight as Markdown - Internal links

After highlighting a PDF document, and subsequently extracting these highlights with Tools>Summarize Highlights>as Markdown, links are created/attached to specific words in the document, that seem to point to groups or files within my database that matches the specific words.

It is important for me to keep the link to the PDF location provided in this document (Page 61 in the image), but would like to know how I can disable the creation of the other links (indicated by the red marks) as these serve no purpose in my workflow and just creates unnecessary rework for me when transferring the data in other tools.

Showing the source of the MD file might help.

Do you mean to show the PDF with the highlights from which the MD was created with Summarize Highlights? (Apologies if I am not understanding correctly)
If so, the relevant page looks like below:
CleanShot 2022-12-09 at 15.25.20

In the above, “Business” links to a group within my Database with the same title, while “money” links to a random web article I clipped to PDF titled “money.pdf”

No. I meant what I wrote: “the source of the MD file”. Your screenshot is the MD rendered as HTML. I’m talking about the editable markup.

Background: It should be easy to remove the links from the source with a short JavaScript script. But I need to see this source before I can write the code. Obviously.

Sorry, I think I understand.
Please see below:

## [Page 61](x-devonthink-item://FB05896C-61C3-42FB-848D-F41CCF8DF9AF?page=60)
* {==Projects are really about changing the organization by achieving a measurable outcome.==}

* {==From a business perspective, projects are initiated to move the organization from its current state to the desired future state==}

* {==Projects drive change by undertaking the work to achieve the specific goals of the project. If you achieve the goals of the project, specifically the scope of the project, then the goal becomes a reality for the organization and the business will achieve the desired future state.==}

* {==Creating Business Value==}

* {==When a project takes place in a business organization, one of the primary goals is to achieve a return on the investment of money, time, and energy for the project.==}


Those are WikiLinks. See

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It seems so obvious now that you have pointed it out, but I was not familiar with the feature and hence did not even know what term to use to search for an answer. Thanks for the assistance. I have disabled it, replicated the action, and all is well now with the links removed.

Well spotted. I wouldn’t have noticed, and one can’t do anything about them in the source file, either.

Following up on @pete31’s comment, from Preferences > WikiLinks from the built-in Help and manual

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Gotcha. Thanks again

Is there a way for one to mark individual highlights as headers (i.e. h1, h2, h3) or perhaps to nest highlights during the highlighting process so that these show up correctly arranged when summarising highlights?

I recently got access to the Readwise Reader app. While this app certainly looks very promising, I have not yet come across a way in which it can provide me with the highlighted text location within the PDF in the same way that the Summarise Highlights function does. (when clicking on the highlight in the Reader app, I am able to navigate to the text location, but this location is not available when the highlights are exported to, for instance, Tana or Roam Research).

My current workflow consists of importing the highlights (copy from .md summary) and pasting to the relevant note-taking app, from where I need to apply the relevant headers and nesting to organise the notes before conducting further synthesis. It would be significantly easier to apply these headers/nesting while reading/during the highlighting process, as one would then not need to open the source to confirm the organisation of the text as afterwards, as I am currently doing.

I’m not sure I understand your question but I noticed no-one else has answered, so I will take a shot.

In DT, the summarise highlights function works in order of appearance but also chronologically, and I think others have spoken before about how you can make it do weird things if you highlight something, then scroll back up and highlight above the first highlight (I’ve not done that for a while so cannot confirm - I was aware it was a quirk so try to avoid doing it). So if your highlights are showing up out of order in your markdown doc it’s either because you didn’t highlight from top to bottom in the doc, or because you’ve added notes that are “above” the highlight they refer to (I always situate my comments slightly below the highlight to ensure that they are compiled below the relevant comment in Markdown). You wouldn’t need “nesting” if you solve either of these issues? The highlights and notes would then be in the correct order in the Markdown doc.

I don’t understand your question about Reader. If you’re doing your highlighting in Reader, it of course cannot render item links for you, as the document is not stored in DT, Roam, etc. It’s on Reader’s servers. At present, it is not possible to export annotated PDFs from Reader. This is coming in a future update. Once that is possible, your workflow would be:

  • read and annotated pdf in Reader
  • export final pdf to DT
  • Summarise highlights inside DT (i.e. not from Reader).

That would then give you the item links you’re used to. Only the reading experience would actually change, as that would be in Reader - all post-reading processing would happen in DT. You’d also then have Reader and DT storing the same highlights. But, the export pdf function doesn’t exist yet.

Personally. I am waiting for this function before I test annotating PDFs in Reader. I see no value in marking up PDFs in Reader when I cannot export the final version to my database.