👓 Who says neuroscientists don’t need more brains? Annotation with SciBot | Hypothesis

Read Who says neuroscientists don’t need more brains? Annotation with SciBot by Maryann Martone (web.hypothes.is/blog/)
You might think that neuroscientists already have enough brains, but apparently not. Over 100 neuroscientists attending the recent annual meeting of the Society for Neuroscience (SFN), took part in an annotation challenge: modifying scientific papers to add simple references that automatically generate and attach Hypothesis annotations, filled with key related information. To sweeten the pot, our friends at Gigascience gave researchers who annotated their own papers their very own brain hats.
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Reply to Florian Weil on annotations and webmention

Replied to Florian Weil on Twitter (Twitter)
“@memotv Isn't the annotations standard by w3c for this kind of needs? https://www.w3.org/TR/annotation-model/ this article summarised the key points very good https://scholarlykitchen.sspnet.org/2018/08/28/all-about-open-annotation/ for some more functional link back, I can highly recommend to check the indieweb webmentions”

Reminds me that I need to circle back to this discussion:

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👓 Marginal Syllabus at 2018 Connected Learning Summit | Remi Kalir

Read Marginal Syllabus at 2018 Connected Learning Summit by Remi KalirRemi Kalir (marginalsyllab.us)
The Marginal Syllabus project is excited to participate in next week’s 2018 Connected Learning Summit at the MIT Media Lab in Cambridge. First, the following Marginal Syllabus researchers, partners, and collaborators will be attending: Christina Cantrill, National Writing Project Joe Dillon, Aur...
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Replied to a post by Greg McVerryGreg McVerry (INTERTEXTrEVOLUTION)
For today’s #edu522 #dailyponderance you need to highlight some cool #edtech tools. Give us 3-5 apps or websites we should try in class.

Some of my favorite and often used edtech tools:

Hypothesis – a service that allows me to quickly highlight and annotate content on almost any web page or .pdf file

IFTTT.com – a service which I use in combination with other services, most often to get data from those sites back to my own. For example:

Huffduffer.com – a service I with audio related content I find online. I use its bookmarklet to save audio from web pages. Huffduffer then creates a custom RSS feed that I can subscribe to in any podcatcher for catching up on podcasts while I’m on the go.

Post Kinds Plugin for WordPress – since many in the class are also using it, I’ll mention that I love using its bookmarklet functionality to quickly bookmark, favorite, or reply to other posts on the web.

URL Forwarder – This is an Android-based app that I’ve configured to dovetail with the Post Kinds Plugin and my website for posting to my site more quickly via mobile.

Jon Udell’s media clipper – I use this audio/video tool for finding and tagging the start and stop points of media so that I can highlight specific portions for others

Reply to Kevin Marks et al on Webmention and Annotations

Replied to a tweet by Kevin Marks (Twitter)

@dangillmore, @froomkin and other journos have played around with @hypothes_is (which has private group functionality):

@dwhly et al have started discussing adding webmentions as well:

There’s also a lot of potential useful overlap of the broader area of IndieWeb technologies with journalism I think.

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🔖 Timelinely

Bookmarked Timelinely (Timelinely)

Create interactive video stories on Timelinely. Timelinely empowers people to go beyond just video.

Highlight interesting parts of a video on a timeline with interactive comments, pictures, links, maps, other videos, and more.

This tool reminds me of a somewhat more commercialized version of Jon Udell’s Clipping tools for HTML5 audio, HTML5 video, and YouTube. I wonder if this is the sort of UI that Hypothes.is might borrow? I can definitely see it being useful functionality in the classroom.  

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An Outline for Using Hypothesis for Owning your Annotations and Highlights

I was taken with Ian O’Byrne’s righteous excitement in his video the other day over the realization that he could potentially own his online annotations using Hypothesis, that I thought I’d take a moment to outline a few methods I’ve used.

There are certainly variations of ways for attempting to own one’s own annotations using Hypothesis and syndicating them to one’s website (via a PESOS workflow), but I thought I’d outline the quickest version I’m aware of that requires little to no programming or code, but also allows some relatively pretty results. While some of the portions below are WordPress specific, there’s certainly no reason they couldn’t be implemented for other systems.

Saving individual annotations one at a time

Here’s an easy method for taking each individual annotation you create on Hypothesis and quickly porting it to your site:

Create an IFTTT.com recipe to port your Hypothesis RSS feed into WordPress posts. Generally chose an “If RSS, then WordPress” setup and use the following data to build the recipe:

  • Input feed: https://hypothes.is/stream.atom?user=username (change username to your user name)
  • Optional title: 📑 {{EntryTitle}}
  • Body: {{EntryContent}} from {{EntryUrl}} <br />{{EntryPublished}}
  • Categories: Highlight (use whatever categories you prefer, but be aware they’ll apply to all your future posts from this feed)
  • Tags: hypothes.is
  • Post status (optional): I set mine to “Draft” so I have the option to keep it privately or to publish it publicly at a later date.

Modify any of the above fields as necessary for your needs. IFTTT.com usually polls your feed every 10-15 minutes. You can usually pretty quickly take this data and turn it into your post kind of preference–suggestions include read, bookmark, like, favorite, or even reply. Add additional categories, tags, or other metadata as necessary for easier searching at a later time.

Here’s an example of one on my website that uses this method. I’ve obviously created a custom highlight post kind of my own for more specific presentation as well as microformats markup.

A highlight from Hypothesis posted on my own website using some customized code to create a “Highlight post” using the Post Kinds Plugin.

Aggregating lots of annotations on a single page

If you do a lot of annotations on Hypothesis and prefer to create a bookmark or read post that aggregates all of your annotations on a given post, the quickest way I’ve seen on WordPress to export your data is to use the Hypothesis Aggregator plugin [GitHub].

  • Create a tag “key” for a particular article by creating an acronym from the article title followed by the date and then the author’s initials. This will allow you to quickly conglomerate all the annotations for a particular article or web page. As an example for this article I’d use: OUHOAH062218CA. In addition to any other necessary tags, I’ll tag each of my annotations on the particular article with this somewhat random, yet specific key for which there are unlikely to be any other similar tags in my account.
  • Create a bookmark, read, reply or other post kind to which you’ll attach your annotations. I often use a bookmarklet for speed here.
  • Use the Hypothesis Aggregator’s short code for your tag and username to pull your annotations for the particular tag. It will look like this:
    [hypothesis user = 'username' tags = 'tagname']

    If you’re clever, you could include this shortcode in the body of your IFTTT recipe (if you’re using drafts) and simply change the tag name to the appropriate one to save half a step or need to remember the shortcode format each time.

If you’re worried that Hypothes.is may eventually shut down, the plugin quits working (leaving you with ugly short codes in your post) or all of the above, you can add the following steps as a quick work-around.

  • Input the shortcode as above, click on the “Preview” button in WordPress’s Publish meta box which will open a new window and let you view your post.
  • Copy the preview of the annotations you’d like to keep in your post and paste them over your shortcode in the Visual editor tab on your draft post. (This will maintain the simple HTML formatting tags, which you can also edit or supplement if you like.)
  • I also strip out the additional unnecessary data from Hypothesis Aggregator about the article it’s from as well as the line about who created the annotation which isn’t necessary as my post will implicitly have that data. Depending on how you make your post (i.e. not using the Post Kinds Plugin), you may want to keep it.

As Greg McVerry kindly points out, Jon Udell has created a simple web-tool for inputting a few bits of data about a set of annotations to export them variously in HTML, CSV, or JSON format. If you’re not a developer and don’t want to fuss with Hypothesis’ API, this is also a reasonably solid method of quickly exporting subsections of your annotations and cutting and pasting them onto your website. It does export a lot more data that one might want for their site and could require some additional clean up, particularly in HTML format.

Perhaps with some elbow grease and coding skill, sometime in the future, we’ll have a simple way to implement a POSSE workflow that will allow you to post your annotations to your own website and syndicate them to services like Hypothesis. In the erstwhile, hopefully this will help close a little of the data gap for those using their websites as their commonplace books or digital notebooks.

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📺 Closing the loop on feedback using Hypothesis annotations | YouTube

Watched Closing the loop on feedback using Hypothesis annotations by W. Ian O'Bryrne from YouTube
Really excited about the possibility of moving closer to my dream of a transparent, revision trail of audits, edits, and feedback in my online writing.
The posts I discuss:
https://wiobyrne.com/interviewing-my-domains/
https://boffosocko.com/2018/06/21/interviewing-my-digital-domains-w-ian-obyrne/
https://boffosocko.com/2018/06/21/some-thoughts-on-highlights-and-marginalia-with-examples/
https://web.hypothes.is/

Some thoughts on highlights and marginalia with examples

Earlier today I created a read post with some highlights and marginalia related to a post by Ian O’Bryne. In addition to posting it and the data for my own purposes, I’m also did it as a manual test of sorts, particularly since it seemed apropos in reply to Ian’s particular post. I thought I’d take a stab at continuing to refine my work at owning and controlling my own highlights, notes, and annotations on the web. I suspect that being able to better support this will also help to bring more self-publishing and its benefits to the halls of academe.

At present I’m relying on a PESOS solution to post on another site and syndicate a copy back to my own site. I’ve used Hypothesis, in large part for their fantastic UI and as well for the data transfer portion (via RSS and even API options), to own the highlights and marginalia I’ve made on the original on Ian’s site. Since he’s syndicated a copy of his original to Medium.com, I suppose I could syndicate copies of my data there as well, but I’m saving myself the additional manual pain for the moment.

Rather than send a dozen+ webmentions to Ian, I’ve bundling everything up in one post. He’ll receive it and it would default to display as a read post though I suspect he may switch it to a reply post for display on his own site. For his own use case, as inferred from his discussion about self-publishing and peer-review within the academy, it might be more useful for him to have received the dozen webmentions. I’m half tempted to have done all the annotations as stand alone posts (much the way they were done within Hypothesis as I read) and use some sort of custom microformats mark up for the highlights and annotations (something along the lines of u-highlight-of and u-annotation-of). At present however, I’ve got some UI concerns about doing so.

One problem is that, on my site, I’d be adding 14 different individual posts, which are all related to one particular piece of external content. Some would be standard replies while others would be highlights and the remainder annotations. Unless there’s some particular reason to do so, compiling them into one post on my site seems to be the most logical thing to do from my perspective and that of my potential readers. I’ll note that I would distinguish annotations as being similar to comments/replies, but semantically they’re meant more for my sake than for the receiving site’s sake. It might be beneficial for the receiving site to accept and display them (preferably in-line) though I could see sites defaulting to considering them vanilla mentions as a fallback.  Perhaps there’s a better way of marking everything up so that my site can bundle the related details into a single post, but still allow the receiving site to log the 14 different reactions and display them appropriately? One needs to not only think about how one’s own site looks, but potentially how others might like to receive the data to display it appropriately on their sites if they’d like as well. As an example, I hope Ian edits out my annotations of his typos if he chooses to display my read post as a comment.

One might take some clues from Hypothesis which has multiple views for their highlights and marginalia. They have a standalone view for each individual highlight/annotation with its own tag structure. They’ve also got views that target highlights/annotation in situ. While looking at an original document, one can easily scroll up and down through the entire page’s highlights and annotations. One piece of functionality I do wish they would make easier is to filter out a view of just my annotations on the particular page (and give it a URL), or provide an easier way to conglomerate just my annotations. To accomplish a bit of this I’ll typically create a custom tag for a particular page so that I can use Hypothesis’ search functionality to display them all on one page with a single URL. Sadly this isn’t perfect because it could be gamed from the outside–something which might be done in a classroom setting using open annotations rather than having a particular group for annotating. I’ll also note in passing that Hypothesis provides RSS and Atom feeds in a variety of ways so that one could quickly utilize services like IFTTT.com or Zapier to save all of their personal highlights and annotations to their website. I suspect I’ll get around to documenting this in the near future for those interested in the specifics.

Another reservation is that there currently isn’t yet a simple or standard way of marking up highlights or marginalia, much less displaying them specifically within the WordPress ecosystem. As I don’t believe Ian’s site is currently as fragmentions friendly as mine, I’m using links on the date/time stamp for each highlight/annotation which uses Hypothesis’ internal functionality to open a copy of the annotated page and automatically scroll down to the fragment as mentioned before. I could potentially see people choosing to either facepile highlights and/or marginalia, wanting to display them in-line within their text, or possibly display them as standalone comments in their comments section. I could also see people wanting to be able to choose between these options based on the particular portions or potentially senders. Some of my own notes are really set up as replies, but the CSS I’m using physically adds the word “Annotation”–I’ll have to remedy this in a future version.

The other benefit of these date/time stamped Hypothesis links is that I can mark them up with the microformat u-syndication class for the future as well. Perhaps someone might implement backfeed of comments until and unless Hypothesis implements webmentions? For fun, some of my annotations on Hypothesis also have links back to my copy as well. In any case, there are links on both copies pointing at each other, so one can switch from one to the other.

I could imagine a world in which it would be nice if I could use a service like Hypothesis as a micropub client and compose my highlights/marginalia there and micropub it to my own site, which then in turn sends webmentions to the marked up site. This could be a potential godsend to researchers/academics using Hypothesis to aggregate their research into their own personal online (potentially open) notebooks. In addition to adding bookmark functionality, I could see some of these be killer features in the Omnibear browser extension, Quill, or similar micropub clients.

I could also see a use-case for adding highlight and annotation kinds to the Post Kinds plugin for accomplishing some of this. In particular it would be nice to have a quick and easy user interface for creating these types of content (especially via bookmarklet), though again this path also relies on doing individual posts instead of a single post or potentially a collection of posts. A side benefit would be in having individual tags for each highlight or marginal note, which is something Hypothesis provides. Of course let’s not forget the quote post kind already exists, though I’ll have to think through the implications of that versus a slightly different semantic version of the two, at least in the ways I would potentially use them. I’ll note that some blogs (Colin Walker and Eddie Hinkle come to mind) have a front page that display today’s posts (or the n-most recent); perhaps I could leverage this to create a collection post of highlights and marginalia (keyed off of the original URL) to make collection posts that fit into my various streams of content. I’m also aware of a series plugin that David Shanske is using which aggregates content like this, though I’m not quite sure this is the right solution for the problem.

Eventually with some additional manual experimentation and though in doing this, I’ll get around to adding some pieces and additional functionality to the site. I’m still also interested in adding in some of the receipt/display functionalities I’ve seen from Kartik Prabhu which are also related to some of this discussion.

Is anyone else contemplating this sort of use case? I’m curious what your thoughts are. What other UI examples exist in the space? How would you like these kinds of reactions to look on your site?

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👓 Interviewing my digital domains | W. Ian O’Byrne

Read Interviewing my digital domains by W. Ian O'ByrneW. Ian O'Byrne (W. Ian O'Bryne)

Alan Levine recently posted a series of questions to help others think through some of thoughts and motivations as we develop and maintain a domain of our own.

I’ve written a lot about this in the past, and I’ll try to include some links to content/posts as I respond to the prompts. This is a bit long as I get into the weeds, so consider yourself warned.

And now…let’s get to it…

Highlights, Quotes, & Marginalia

Having a domain is important to me as I research, develop, and teach.

example of a domain as thinking out loud or thought spaces
blogging as thinking


This should be a space where you can create the identity that you want to have. You can write yourself into existence.

I like this sentiment. Had René Descartes been born a bit later might he have said “Blogeō, ergo sum”?


Most of this work is focused on collaboration, transparency, and working/thinking in the open.


The plan is to use the site to share surveys, interviews, and researcher notes.

Note to self: I need to keep documenting examples of these open labs, open notebooks, etc. in the open science area.


teachers hid their Facebook accounts for fear of being fired.

The sound of this to me know reminds me of the type of suppression of thought that might have occurred in the middle ages. Of course open thought and discussion is important for teachers the same way it is for every other person. However there are a few potential counterexamples where open discussion of truly abhorrent ideas can run afoul of community mores. Case in point:


PLN

personal learning network perhaps marking it up with <abbr> tags would be useful here?


luck

lucky


.A

space


I feel like this culture in academia may be changing.


academia is built on the premise (IMHO) of getting a good idea, parlaying that into a job and tenure, and waiting for death. I’ve had a lot of colleagues and acquaintances ask why I would bother blogging. Ask why I share all of this content online. Ask why I’m not afraid that someone is going to steal my ideas.

Though all too true, this is just a painful statement for me. The entirety of our modern world is contingent upon the creation of ideas, their improvement and evolution, and their spreading. In an academic world where attribution of ideas is paramount, why wouldn’t one publish quickly and immediately on one’s own site (or anywhere else they might for that matter keeping in mind that it’s almost trivially easy to self-publish it on one’s own website nearly instantaneously)?
Early areas of science were held back by the need to communicate by handwriting letters as the primary means of communication. Books eventually came, but the research involved and even the printing process could take decades. Now the primary means of science communication is via large (often corporate owned) journals, but even this process may take a year or more of research and then a year or more to publish and get the idea out. Why not write the ideas up and put them out on your own website and collect more immediate collaborators? Funding is already in such a sorry state that generally, even an idea alone, will not get the ball rolling.
I’m reminded of the gospel song “This little light of mine” whose popular lyrics include:
“Hide it under a bushel? No! / I’m gonna let it shine” and
“Don’t let Satan blow it out, / I’m gonna let it shine”
I’m starting to worry that academia in conjunction with large corporate publishing interests are acting the role of Satan in the song which could easily be applied to ideas as well as to my little light.


Senior colleagues indicate that I should not have to balance out publishing in “traditional, peer-reviewed publications” as well as open, online spaces.

Do your colleagues who read your work, annotate it, and comment on it not count as peer-review? Am I wasting my time by annotating all of this? 🙂 (I don’t think so…)


or at least they pretend

I don’t think we’re pretending. I know I’m not!


PDF form

Let me know when you’re done and we’ll see about helping you distribute it in .epub and .mobi formats as e-books as well.


This is due to a natural human reaction to “Google” someone before we meet them for the first time. Before we show up to teach a class, take a class, interview for a job, go on a date…we’ve been reviewed online. Other people use the trail of breadcrumbs that we’ve left behind to make judgements about us. The question/challenge is that this trail of breadcrumbs is usually incomplete, and locked up in various silos. You may have bits of your identity in Facebook or Twitter, while you have other parts locked up in Instagram, Snapchat, or LinkedIn. What do these incomplete pieces say about you? Furthermore, are they getting the entire picture of you when they uncover certain details? Can they look back to see what else you’re interested in? Can they see how you think all of these interests fit together…or they seeing the tail end of a feverish bout of sharing cat pics?

I can’t help but think that doing this is a form of cultural anthropology being practiced contemporaneously. Which is more likely: someone a 100 years from now delving into my life via my personal website that aggregated everything or scholars attempting to piece it all back together from hundreds of other sites? Even with advanced AI techniques, I think the former is far more likely.
Of course I also think about what @Undine is posting about cats on Twitter or perhaps following #marginaliamonday and cats, and they’re at least taking things to a whole new level of scholarship.


Guide to highlight colors

Yellow–general highlights and highlights which don’t fit under another category below
Orange–Vocabulary word; interesting and/or rare word
Green–Reference to read
Blue–Interesting Quote
Gray–Typography Problem
Red–Example to work through

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👓 Annotations are an easy way to Show Your Work | Jon Udell

Read Annotations are an easy way to Show Your Work by Jon Udell (Strategies for Internet citizens)
In A Hypothesis-powered Toolkit for Fact Checkers I described a toolkit that supported the original incarnation of the Digital Polarization Project. More recently I’ve unbundled the key ingredients of that toolkit and made them separately available for reuse. The ingredient I’ll discuss here, HypothesisFootnotes, is illustrated in this short clip from a 10-minute screencast about the original toolkit. Here’s the upshot: Given a web page that contains Hypothesis direct links, you can include a script that pulls the cited material into the page, and connects direct links in the page to citations gathered elsewhere in the page.

Jon is always building something interesting. Here he covers some useful tools for journalism as well as education.

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There’s been some recent revival of chat about fragmentions and the fragmentioner within the IndieWeb community which enable the ability to more easily highlight and annotate individual portions of a web page and target them directly via URL.

This caused me to take a look at where the conversations on webmentions went within the Hypothesis project. Unless they’re hiding offline or somewhere else, it would appear that they’ve stalled, though I have a feeling that it could be an interesting notification method for Hypothesis to indicate to a site that it’s been highlighted or annotated. Also given that the Webmention spec is a W3C recommendation as of January 2017 compared to its status in 2014 when the topic was last brought up on the GitHub repo.

As a result of the above, if they’re free, I’d love to extend an invitation to Dan Whaley (t), Jon Udell (t), Jeremy Dean (t), Nate Angell (t), or anyone else working on the Hypothes.is project to join us in Portland this June 26-27 for the annual IndieWebSummit / IndieWebCamp.  I highly suspect there will be some heavy interest in the topics of open ways of annotating, highlighting, and notifying websites as well as UI/UX discussion around this area which we can all continue to expand and improve upon. And naturally there are sure to be a broad area of other topics at the summit that will be of interest in addition to these.

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👓 Building a Text Editor for a Digital-First Newsroom | Times Open (Medium)

Read Building a Text Editor for a Digital-First Newsroom by Sophia Ciocca (Times Open | Medium)
An inside look at the inner workings of a technology you may take for granted

A topic which is tremendously overlooked in the CMS world, but which can provide a lot of power.

h/t Jorge Spinoza

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👓 Librarian tweetstorm by @green_grainger

Read Librarian tweetstorm by Georgia | Saoirse (Twitter)
So there was a MYSTERY at the library today.

A wee old women came in and said "I've a question. Why does page 7 in all the books I take out have the 7 underlined in pen? It seems odd."
"What?" I say, thinking she might be a bit off her rocker. She showed me, and they did.

I asked if she was doing it, she said she wasnt and showed me the new book she was getting out that she hadnt even had yet. It also had the 7 underlined! "I don't know, maybe someone really likes page 7?" I said, assuming of course that there is a serial killer in the library.

I checked some other books. Most didn't have it, but a lot in this genre did - they're "wee old women" books (romances set in wartime Britain etc). Lots of underlined 7s. The woman who pointed it out shrugged and went on her way, "just thought you should know".

My manager came back from doing arts and crafts with some of the kids and I decide to tell her about the serial killer in the library.
And that’s how I found out that a lot of our elderly clientele have secret codes to mark which books they’ve read before.

Our computers do it automatically but many have been doing it since before that was possible, so Esther might underline page 7, while Anne might draw a little star on the last page, and Fred might put an “f” on the title page. Then when they pick it up, they can check!

It’s quite clever really but now I’m dying to just underline page 7 of every new wee old women book we get in.

So, good news: there’s not a serial killer in the library whose MO include the number 7 and wartime romances. Bad news: people are defacing books rather than just asking us to scan them (smiling face with smiling eyes)

I'm now concerned that the amount of people enjoying this thread means there's going to be a new spate of readers using secret codes - apologies to librarians everywhere!
(although, in truth, I find it hard to be annoyed about it - better than torn pages and felt pen graffiti!)

(Also, I am new to the library job, hence why I hadn't seen it before! The library and our customers are great though (smiling face with smiling eyes))

Just had another victim of the page 7 vandal returned!!!
(Now checking every book that looks like it might be their taste...)

This is such an interesting little story including some cultural anthropology.

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