How-to use Hypothesis for researchers — Paulo PintoSkip to content<br>Paulo Pinto<br>I&rsquo;m using Hypothesis for my research because it lets me annotate primary texts and secondary literature directly in their original context, creating a searchable, shareable layer of precise notes and threaded discussion that maps onto the structure of arguments; this transforms isolated highlights into organized evidence I can filter by tag, trace through replies, and link straight into drafts and bibliographies. I find it amazing for how seamlessly it supports collaborative close reading—groups can build a living interpretive archive, preserve minority readings alongside mainstream ones, and maintain transparent provenance for every claim—so it speeds literature review, deepens interpretive rigor, and makes peer feedback immediate and traceable.<br>Setup<br>Install the Hypothesis browser extension or bookmarklet (Chrome/Firefox/Safari) or use the web client.<br>Create an account (or sign in via institution) and join/create a private group for your project.<br>Organize projects & sources<br>Create one group per project or research question.<br>Use consistent naming conventions for groups and tags (e.g., project_abbrev, lit_review, dataset).<br>Add metadata in each annotation: short title, authors, year, source URL, and concise note.<br>Reading & annotating workflow<br>Open a paper/webpage/PDF and enable Hypothesis.<br>Highlight key passages and add focused annotations:Summary: 1–2 sentence gist of the passage.<br>Note: relevance to your research question.<br>Method/Data: record methods, sample size, key measurements.<br>Quote: exact text you may cite (use tags like quote).<br>Critique/Question: limitations or follow-up ideas.

Use tags for quick filtering: e.g., methods, result_conflict, support_hypothesis, to_check.<br>Collecting & organizing evidence<br>Use the sidebar’s search and filters (by group, user, tag, page) to assemble evidence.<br>Create saved searches or export annotation lists (CSV/JSON) for offline analysis.<br>Pin or star pivotal annotations.<br>Collaboration & peer review<br>Invite collaborators to the project group and set visibility (private/group/public).<br>Use replies for threaded discussion and to resolve interpretation disagreements.<br>Assign tasks by tagging collaborators or adding TODO notes in annotations.<br>Integrating with research tools<br>Export annotations to reference managers or note apps (manual copy, CSV/JSON, or integrations).<br>Link Hypothesis annotations in manuscripts or lab notebooks by URL.<br>Use Hypothesis with institutional platforms (JSTOR, library proxies, LMS) where available.<br>Managing literature reviews & writing<br>Build an annotated bibliography by tagging annotations as bib_entry and summarizing key citation info in the annotation body.<br>During drafting, search tags like support_hypothesis and contradiction to pull evidence for each claim.<br>Include direct annotation links in review drafts for reviewers to see context.<br>Reproducibility & transparency<br>Keep groups public or provide read-only links for reproducibility when appropriate.<br>Preserve raw notes: avoid overwriting—add new annotations instead of editing old ones when tracking interpretive changes.<br>Export annotation data as a project snapshot alongside code and data deposits.<br>Tips & best practices<br>Keep annotations concise and consistently structured.<br>Adopt a short tag taxonomy (5–10 tags) and document it in a group overview note.<br>Regularly review and reconcile duplicate or conflicting annotations.<br>Use private notes for tentative ideas; move important ones to the group when ready to share.<br>==> go to https://hypothes.is