What I’m trying to do
I am a PhD student looking to create a literature matrix for my literature review . Here is a detailed account of what I am trying to achieve:
- I have annotated pdfs in Zotero. Each annotated text has a highlight of the same colour [yellow] and also has a tag I think is relevant . For example :
Caspases, also known as Cysteine ASPartyl proteASES, are a vital family of protease enzymes integral to various cellular processes, with a prominent function in apoptosis [13,14]
I have highlighted this text with yellow and kept the tag as #caspases and # apoptosis.
-
I want to import all the pdfs and their annotation with tags and comments as new note in Obsidian.
Example: Highlighted text with highlight colour, page number , tags and comments and images if annotated. -
I want to link the secondary source of that annotated text in my note , preferably directly from Zotero and reference section of that paper , or Obsidian .
Example : [13,14] = [Green 2022; McArthur 2018] -
I am trying to synthesise information based on topics . So I want all annotated texts for each tag separately.
Example : for # caspases- I want a new note, and all annotated text that has #caspases tag should be in this note. Similarly for other tags such as # OxS, # apoptosis etc.
This note should also contain the highlighted colour and page number , with secondary citations, so that I know where the primary paper sourced that text from.
Similarly, If I have tagged images as well, I want the images also in this same note .
This will allow me to see what different papers and sources mention regarding that particular topic.
- If possible, I would like to just highlight different themes with different colour without putting tags in Zotero , and I would like tags to be automatically assigned to the annotated text based on highlight colour.
And then go back to step 4.
Example : if I have identified certain text that talk about caspases on 5 different papers, I will highlight those texts in orange colour.
When I import that paper in Obsidian , I want to automatically tag all text with orange colour as #caspases. Then go to step 4.
Things I have tried
1)I have created a base template with title, authors, keywords and citation .
2) I can also import annotated text with highlight colour and page number.
3) I can also import images if taken.
This is my template code-
---
title: "{{title}}"
year: '{{date | format("YYYY")}}'
authors: "{{authors}}"
citation: "{{bibliography}}"
---
---
📖 pdf {{pdfZoteroLink}}
🏷️ tags {{hashTags}}
🗝️ citekey {{citekey}}
---
{% for annotation in annotations -%}
{%- if annotation.annotatedText -%}
{% if annotation.color %}
<mark class="hltr-{{annotation.colorCategory | lower}}">
"{{annotation.annotatedText | safe}}"</mark>
{% else %}
{{annotation.type | capitalize}}
{% endif %}
{%- endif %}
📖 **Page:** [Page {{annotation.pageLabel}}](zotero://open-pdf/library/items/{{annotation.attachment.itemKey}}?page={{annotation.pageLabel}}&annotation={{annotation.id}})
{%- if annotation.imageRelativePath %}
![[{{annotation.imageRelativePath}}]]
{%- endif %}
{% if annotation.comment %}
### 🗨 Comment:
{{annotation.comment | safe}}
{% endif %}
{% if annotation.allTags %}
🏷 **Tags:** {{annotation.allTags}}
{% endif %}
{% endfor %}
And output-
I am stuck after this . Any help would be greatly appreciated.
Thank you .