These tools are created and maintained by the Hypothesis community. Some are code experiments, some are full implementations being adopted by users every day.  If you have a project or know of one that should be listed here, please let us know!

Learning Management Systems (LMS)

LMS App

Link: https://web.hypothes.is/education/lms/

Description: An official Hypothesis application that enables integration with any LMS supporting IMS Learning Tools Interoperability (LTI), such as Blackboard Learn, Desire2Learn Brightspace, Instructure Canvas, Moodle, Sakai, and Schoology, to provide capabilities including single sign-on and automatic private group provisioning for each class.

Content Management Systems (CMS)

WordPress

Link: https://wordpress.org/plugins/hypothesis/

Screencast: http://jonudell.net/h/wordpress-via-pdf.mp4 (illustrates PDF activation)

Description: Built by Jake Hartnell and Benjamin Young. Adds the Hypothesis sidebar to your wordpress website. Converts links to PDFs in the Media folder to via.hypothes.is links.

WordPress Hypothesis aggregator

Link: https://github.com/kshaffer/hypothesis_aggregator

Description: A WordPress plugin that allows you to aggregate Hypothesis annotations on a single page or post on your WordPress blog.

OJS Hypothesis Plugin

Link: https://github.com/asmecher/hypothesis

Description: adds Hypothesis integration to the public article view of Open Journal Systems, permitting annotation and commenting.

Omeka Annotator

Link: https://github.com/ebellempire/Annotator

Description: A Hypothesis text annotation plugin for Omeka.

DocDrop.org

Link: http://docdrop.org/

Description: A place to upload PDFs and other documents for annotation using Hypothesis, as well as a Google Drive plugin for PDFs.

Drupal, from Little Blue Labs

Link: https://www.drupal.org/project/hypothesis

Description: This simple module embeds Hypothesis into your Drupal site.

Archiving and downloading annotations

Use any of the following community-provided tools to export (download) your annotations.

For note-taking apps

Send Hypothesis annotations directly into your notes.

Roam: (via RoamJS) Hypothesis Extension

Import your Hypothesis notes and highlights into Roam.

Readwise

Readwise has a built-in integration with Hypothesis. Visit your syncs to set it up.

Obsidian: Obsidian Hypothesis Plugin

Obsidian Hypothesis (Community Plugin) is an unofficial plugin to synchronize Hypothesis web article highlights/annotations into your Obsidian Vault.

Alternatives for technical users

• Gooseberry: A command line utility to generate a knowledge base from Hypothesis annotations
• Annotation tools: python tools to link Hypothesis and Pinboard annotations to Obsidian
• Chris Aldrich’s gist: retrieve your annotations into Obsidian (for templater plugin)

LogSeq: Logseq Hypothesis Plugin

Retrieve your online web annotations and insert them directly into Logseq. All you need to do is enter your API key, and then you can add all your annotations to your Logseq.

Org Mode: hypothesis.el

Import data from hypothes.is into Emac.

Online tools from the community

Standalone tools found on the web.

Facet

View annotations by user, group, URL, or tag. Export results to HTML, CSV, text, or Markdown. Screencast: https://jonudell.net/h/facet.mp4

Hypothesis collector

Create google sheets with annotations based on search queries.

Chrome extensions

Grab Hypothesis annotations directly from your browser.

Hypothesis to Markdown bullet points

Browser extension for fetching and formatting Hypothes.is annotations into markdown bullet points, ready for copying into Roam, Notion or similar apps.

For technical users

If you have some skills at the command line or in a text editor, these ones are for you!

Gooseberry CLI tool

A command line utility to generate a knowledge base from Hypothesis annotations. (Very slick, with Obsidian compatibility, too)

Hypotheiss + Steampipe

Steampipe is an open source CLI to instantly query cloud APIs using SQL. List annotations from Hypothesis.

hypothesis-to-bullet

Script to fetch Hypothes.is annotations or Twitter threads and output Markdown that is suitable for Roam for macOS computers.

recon16-annotations

Place annotations on a Cloudant database for analysis.

Added functionality

Slack notifications

Link: https://github.com/judell/h_notify

Description: Receive Slack notifications  made by specific users, or groups, or on specific urls or tags.

Hypothesis EPUB reader

Link: https://github.com/JakeHartnell/HypothesisReader

Description: A mashup of the open source Hypothesis and Epub.js projects.

Annotran: Annotate to translate

Link: https://github.com/birkbeckOLH/annotran

Description: Annotran is an extension to the hypothesis annotation framework that allows users to translate web pages themselves and to view other users’ translations. Read about it here and here.

Annotation Powered Survey

Link: https://github.com/judell/AnnotationPoweredSurvey

Description: A toolkit for building online surveys that ask questions to which answers are annotations.

ClinGen Workflow

Link: https://github.com/judell/ClinGen

Description: An approach to annotation-powered biocuration.

CopyAnnotations

Link: https://github.com/judell/CopyAnnotations

Description: Copy top-level annotations from one URL (and/or group) to another.

TagRename

Link: https://github.com/judell/TagRename

Description: Rename Hypothesis tags.

Programming tools

Hypothesis Ruby Gem

Link: https://github.com/javierarce/hypothesis

Description: Unofficial ruby gem for the Hypothesis API.

Hypothepy

Link: https://github.com/embo-press/hypothepy/tree/master/hypothepy

Description: A lightweight Python API for Hypothes.is

Pypothesis

Link: https://github.com/kshaffer/pypothesis

Description:  Python scripts for interacting with the Hypothesis API.

Hypothesis

Link: https://github.com/judell/Hypothesis

Description: Yet another Python wrapper for the Hypothesis API.

Hypothesisr

Link: https://github.com/mdlincoln/hypothesisr

Description: An R package that allows users to add, search for, and retrieve annotation data.

HypothesisPHP

https://github.com/asmecher/HypothesisPHP

Description: A simple PHP wrapper for the Hypothesis API.

Hypush

https://github.com/tgbugs/hypush

Monitor the Hypothesis websocket in order to push realtime notifications to other channels.

Integrations

SciBot

Link: https://github.com/SciCrunch/scibot

Description: This tool finds RRIDs in articles, looks them up in the SciCrunch resolver and creates Hypothesis annotations that anchor to the RRIDs and display lookup results. More info here.

AAAS/Discover

Link: https://github.com/judell/StandaloneAnchoring

Description: The American Association for the Advancement of Science (AAAS) uses Hypothesis for graduate students to annotate articles using specific highlight colors and categories. More info here.

Extracting structured findings from scientific papers

Link: https://gist.github.com/judell/ca913dd64a29f852afd3

Description: David Kennedy reviews the literature in his field and extracts findings, which are structured interpretations of statements in scientific papers. He’s using Hypothesis to create reports based on structured annotation. More here.

Hypothesis/Europe PubMed Central

Screencast: http://jonudell.net/h/scibot-epmc-v1.mp4

Description: Bring annotations from two systems together in the context of a document.

Infinite Ulysses

Link: https://github.com/amandavisconti/infinite-ulysses-public

Description: created by Amanda Visconti, Infinite Ulysses lets readers of James Joyce’s challenging novel Ulysses while annotating it with their questions and interpretations and perusing annotations from fellow readers.

Other ideas to try

Screen-reader-accessible annotation

Screencast: http://jonudell.net/h/accessible_annotation_02.mp4

Link: https://blog.jonudell.net/2016/09/28/towards-accessible-annotation-a-prototype-and-some-questions/

Description: Use a hotkey to select an element, hear it spoken, and open the annotation editor.

Copy annotation to clipboard

Screencast: http://jonudell.net/h/copy_paste_annotation_v1.mp4

Description: Copy the text of the annotation to the clipboard by clicking an icon.

Highlight groups with annotations

Screencast: http://jonudell.net/h/highlight-groups-with-annotations-v1.mp4

Description: Highlights the group name with a different color on the dropdown menu, when there are annotations on the group.

Group admin

Screencast: http://jonudell.net/h/group-admin-v1.mp4

Description: Enables a group of users who have given their H API keys to be subject to admin by an “admin user” who is the H user running the prototype extension. The admin user running can edit or delete annotations by subject users.

Controlled tagging

Description: Restrict tags to a controlled list.

Screencast:  http://jonudell.net/h/controlled_tagging_v1.mp4 (manage the list in a Google doc, activate it on a per-Hypothesis-group basis)

Screencast: http://jonudell.net/h/controlled-tagging-with-scigraph-ontology.mp4 (source the list from an external ontology service)

Screencast: http://jonudell.net/h/annotation-applet_03.mp4 (embed a single-page app in the annotation body to enable full control of tag interaction and context)

Search/faceted navigation

Description: An early prototype of faceted navigation

Screencast: http://jonudell.net/h/activity_pages_early_prototype.mp4