How to render

Cross link with direct linking

Intriguing. Needs closer reading till I figure out a way where I can export the annotations on individual passages and notes to a text document. So, I'd keep integrating hypothesis and zotero together and write papers using Authorea or Jupyter notebooks using a bibtex formatted bibliography management system.

For this to happen, start with:

1. Open an article in the web browser (Google Chrome or Firefox) that can support pdf.js or epub.js or html if that is available
2. Open hypothesis app, and start annotating at passages (as in this annotation)
3. Add a consistent tag (see the other how_to tagged articles)
4. Then search all related hypothesis annotations and notes on pages using those tags and organise knowledge that way.

So, this page lays out the basic idea behind hypothes.is. The page note is an overarching summary, or can add another layer of information of related pages, annotate 'weblinkography', 'bibliography' if it is an article, a set of equations or perhaps even point to something like codes or jupyter notebooks that can flow from a 'page' or a 'document' level. Yet embedded within that document could be other commentaries that are marginal notes. What this system needs is a seamless way to extract these notes per user basis, so that I can collate a set of links strewn across the web with identical tags. For example, if have tagged this note along with other marginal notes I created with tags 'howto', and 'hypothesis_how_to'. These were created as I tried to get to understand this system. If I were able to now extract these various pieces of texts to a single document that would contain a link to this parent document, then I could use this to teach or let others know how to use this system as well, and for my future notes. In theory, the notes system could be used for a thought logging system as one were to read a 'paper' or a webpage, or add comments. Then these comments could be either emailed or 'shared' in some way that would make it useful to write a script (say a python script using Beautiful Soup or somehting) to scrape all comments to a theme based set of plain text, which in turn could be arranged to develop into an annotated bibliography with very little effort. The effort would be to read and annotate on the fly. it could also be used to curate knowledge across the web and bring everything into one place, in this case, hypothes.is user page.

This is more like a summary or a critique or a succinct account of a page that gets annotated. it could be a video site as well, say a youtube site. Or an audio site. It could provide additional information to a page or a related page.

This is step one. Set up a standard set of tags. These tags will then classify resources. Let's say I want to classify all studies on polygenic risk scores on the web. These documents come in the form of HTML, or PDF. If on the top of that, you'd also like to tag something like tutorial, or software to do the job, then write those tags as well when you come across a resource and tag it. So, a list of tags to learn about polygenic risk scores could be something like:

• polygenic risk score
• polygenic_risk_score
• tutorial
• utility
• why_how So, all resources that pertain to polygenic risk scores can now be divided into a set of main document types: some that discuss tutorials and how tos, others discuss the utilisation values and debates. Later, these could be reassembled.