University of Glasgow

Roderic Page

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> The workflow & cost of my current Personal Knowledge OS setup, key
> tools includes
> [@RoamResearch](https://twitter.com/RoamResearch?ref_src=twsrc%5Etfw)
> [@readwiseio](https://twitter.com/readwiseio?ref_src=twsrc%5Etfw)
> [@instapaper](https://twitter.com/instapaper?ref_src=twsrc%5Etfw)
> [@AirrAudio](https://twitter.com/AirrAudio?ref_src=twsrc%5Etfw)
> [@reeder](https://twitter.com/reeder?ref_src=twsrc%5Etfw)
> [@evernote](https://twitter.com/evernote?ref_src=twsrc%5Etfw)
> [@obsdmd](https://twitter.com/obsdmd?ref_src=twsrc%5Etfw)
> [@SubstackInc](https://twitter.com/SubstackInc?ref_src=twsrc%5Etfw)
> [@Medium](https://twitter.com/Medium?ref_src=twsrc%5Etfw)  
>   
> Current Per Month Total Cost: \$48.83
> [pic.twitter.com/FtUy87zLFO](https://t.co/FtUy87zLFO)
>
> --- Zack Fan (@zackfan01) [August 25,
> 2020](https://twitter.com/zackfan01/status/1298197666782801921?ref_src=twsrc%5Etfw)

I stumbled across this tweet yesterday (no doubt when I should have been
doing other things), and disappeared down a rabbit hole. Emerging, I
think the trip was worth it.

<div>

  
 

### Markdown wikis

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Among the tools listed by [@zackfan01](https://twitter.com/zackfan01)
were [Obsidian](https://obsidian.md) and
[Roam](https://roamresearch.com), neither of which I heard of before.
Both Obsidian and Roam are pitched as \"note-taking\" apps, they are
essentially personal wikis where you write text in
[Markdown](https://en.wikipedia.org/wiki/Markdown) and use \[\[some text
goes here\]\] to create links to other pages (very like a Wiki). Both
highlight **backlinks**, that is, clearly displaying \"what links here\"
on each page, making it easy to navigate around the graph you are
creating by linking pages. Users of Obsidian share these graphs in
[Discord](https://discord.gg/9CGnTWD), rather like something from Martin
MacInnes\' novel \"Gathering Evidence\". Personal wikis have been around
for a long time, but these apps are elegantly designed and seem fun to
use. Looking at these apps I\'m reminded of my earlier post [Notes on
collections, knowledge graphs, and Semantic Web
browsers](https://iphylo.blogspot.com/2019/07/notes-on-collections-knowledge-graphs.html)
where I moaned about the lack of personal knowledge graphs that
supported inference from linked data. I\'m also reminded of the [Blue
Planet II, the BBC, and the Semantic Web: a tale of lessons forgotten
and opportunities
lost](https://iphylo.blogspot.com/2017/12/blue-planet-ii-bbc-and-semantic-web.html)
where I constructed an interactive tool to navigate BBC data on species
and their ecology (you can see this live at
<https://rdmpage.github.io/bbc-wildlife/www/>), and the fun to be had
from simply being able to navigate around a rich set of links. I imagine
these Markdown-based wikis could be a great way further explore these
ideas.

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</div>

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### Personal and global knowledge graphs

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Then I began thinking about what if the \[\[page links\]\] in these
personal knowledge graphs were not just some text but, say, a Wikidata
identifier (of the form \"Qxxxxx\")? Imagine that if you were writing
notes on say, a species, you could insert the Wikidata Qid and you would
get a pre-populated template that comes with some facts from Wikidata,
and you could then use that as a starting point (see for example Toby
Hudson Entity Explosion I [discussed
earlier](https://iphylo.blogspot.com/2020/08/entity-explosion-bringing-wikidata-to.html)).
Knowing that more and more scholarly papers are being added to Wikidata,
this means you could also add bibliographic citations as Qids, fetching
all the necessary bibliographic information on the fly from Wikidata. So
your personal knowledge graph intersects with the global graph.

</div>

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### Roam

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Now, I\'ve not used Roam, but anyone who has is likely to balk at my
characterisation of it as \"just\" a Markdown wiki, because there\'s
more going on here. The [Roam white
paper](https://roamresearch.com/#/app/help/page/Vu1MmjinS) talks about
making inferences from the text using reasoning or belief networks,
although these features [don\'t seem to have had much
uptake](https://roamresearch.com/#/app/help/page/sVXdjPQib). But what
really struck me as I explored Roam was the notion of not just linking
to pages using the \[\[ \]\] syntax, but also linking to parts of pages
(blocks) using (( )). In the demo of Roam there are various essays, such
as Paul Graham\'s [The
Refragmentation](https://roamresearch.com/#/app/help/page/gRj8-twSi),
and each paragraph is an addressable block that can be cited
independently of the entire essay. Likewise, you can see what pages cite
that block.

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original-height="868" original-width="617"
height="640"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiU43eaGIdRoEPklFaAtq6Qfi7ib0CEOXicwurTdspcoGsSCTBf5rVuAzyuVVBE_wKMsnRlUotIVJ-4_3ZKl2eIuRF05dQygfTbl05BIpWOfH89IHVITwhFdkcFdQfMgwr2qQW4/s868/Screenshot+2020-08-26+at+12.29.17.png){style="font-size: 18.719999313354492px; font-weight: bold; margin-left: 1em; margin-right: 1em; text-align: center;"}  
 Now in a sense these are just like fragment identifiers that we can use
to link to parts of a web page, but there\'s something more here because
these fragments are not just locations in a bigger document, they are
the components of the document.

### Xanadu

<div>

  

</div>

This strikes me as rather like Ted Nelson\'s vision of Xanadu, where you
could cite any text at any level of granularity, and that text would be
incorporated into the document you were creating via
[transclusion](https://iphylo.blogspot.com/2008/03/word-for-day-transclusion.html)
(i.e., you don\'t include a copy of the text, you include the actual
text). In the context of Roam, this means you have the entire text you
want to cite included in the system, so you can then show chunks of it
and build up a network of ideas around each chunk. This also means that
the text being worked on becomes part of the system, rather than
remaining isolated, say, as a PDF or other representation. This also got
me thinking about the [Plazi](http://plazi.org) project, where taxonomic
papers are being broken into component chunks (e.g., figures, taxonomic
descriptions, etc.) and these are then being stored in various places
and reassembled - rather like Frankenstein\'s monster - in new ways, for
example in GBIF (e.g., <https://www.gbif.org/species/166240579>) or
Species-ID (see
[doi:10.3897/zookeys.90.1369](https://dx.doi.org/10.3897/zookeys.90.1369) ).
One thing I\'ve always found a little jarring about this approach is
that you lose the context of the work that each component was taken
from. Yes, you can find a link to the original work and go there, but
what if you could seamlessly click on the paragraph or figure see them
as part of the original article? Imagine we had all the taxonomic
literature available in this way, so that we can cite any chunk, remix
it (which is a key part of floras and other taxonomic monographs), but
still retain the original context?

</div>

<div>

### Summary

<div>

  

</div>

To come back full circle, in some ways tools like Obsidian and Roam are
old hat, we\'ve had wikis for a while, the idea of loading texts into
wikis is old (e.g.,
[Wikisource](https://wikisource.org/wiki/Main_Page)), backlinks are
nothing new, etc. But there\'s something about seeing clean, elegant
interpretations of these ideas, free of syntax junk, and accompanied by
clear visions of how software can help us think. I\'m not sure I will
use either app, but they have given me a lot of food for thought.

</div>

</div>


I stumbled across this tweet yesterday (no doubt when I should have been doing other things), and disappeared down a rabbit hole. Emerging, I think the trip was worth it.    Markdown wikis     Among the tools listed by @zackfan01 were Obsidian and Roam, neither of which I heard of before.

Personal knowledge graphs: Obsidian, Roam, Wikidata, and Xanadu

The last few days I\'ve been re-reading articles about Ted Nelson\'s
work (including ill-fated [Project
Xanadu](https://en.wikipedia.org/wiki/Project_Xanadu)), reading articles
celebrating his work (brought together in the open access book
\"[Intertwingled](http://dx.doi.org/10.1007/978-3-319-16925-5)\"),
playing with [Hypothes.is](https://hypothes.is), and thinking about
annotation and linking. One of the things which distinguishes Nelson\'s
view of hypertext from the current web is that for Nelson links are
first class citizens, they are persistent, they are bidirectional, and
can be links not just documents but between parts of documents. In the
web we have links that are unidirectional, when I link to something, the
page I link to has no idea that I\'ve made that link. Knowing who links
to you turns out to be both hard to work out, and very valuable. In the
academic world, links between articles (citations) form the basis of
commercial databases such as the Web of Science. And of course, the
distribution of links between web pages forms the basis of Google\'s
search engine. Just as attempts to build free and open citation
databases have come to nothing, there is no free and open search engine
to compete with Google.

The chapters in \"Intertwingled\" make clear that hypertext had a long
and varied history before being subsumed by the web. One project which
caught my eye was
[Microcosm](https://en.wikipedia.org/wiki/Microcosm_(hypermedia_system)),
which lead me to the paper \"Dynamic link inclusion in online PDF
journals\"
([doi:10.1007/BFb0053299](http://dx.doi.org/10.1007/BFb0053299),
there\'s a free preprint [here](http://eprints.soton.ac.uk/250761/)).
This article tackles the problem of adding links to published papers.
These links could be to other papers (citations), to data sets, to
records in online databases (e.g., DNA sequences), names of organisms,
etc. The authors outline four different scenarios for adding these links
to an article.

In first scenario the reader obtains a paper from a publisher (either
open access from behind a paywall), then using a \"linkbase\" that they
have access too they add link to the paper.

![Links1](https://lh3.googleusercontent.com/-5FaxDZeQAtE/V2q2_yE3EpI/AAAAAAAAEN4/W3Em4l2J0oc/links1.png?imgmax=1600 "links1.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="460"}

This is very much what Hypothes.is offers, you use their tools to add
annotations to a paper, and those annotations remain under your control.

In the second scenario, the publisher owns the linkbase and provides the
reader with an annotated version of the paper.

![Links2](https://lh3.googleusercontent.com/-GN10sIHWtgo/V2q3Ah33DxI/AAAAAAAAEN8/HJsKmv_h7Sk/links2.png?imgmax=1600 "links2.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="460"}

This is essentially what tools like [ReadCube](https://www.readcube.com)
offer. The two remaining scenarios cover the case where the reader
doesn\'t get the paper from the publisher but instead gets the links. In
one of these scenarios (shown below) the reader sends the paper to the
publisher and gets the linked paper back in return, in the other (not
shown) the reader gets the links but uses their own tools to embed them
in the paper.

![Links3](https://lh3.googleusercontent.com/-4uf-KDIyXGk/V2q3BLlXwjI/AAAAAAAAEOA/i4bKSAOCnQQ/links3.png?imgmax=1600 "links3.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="460"}

If you\'re still with me at this point you may be wondering how all of
this relates to the title of this essay (\"What happens when open access
wins?\"). Well, imagine that academic publishing eventually becomes
overwhelmingly open access, so that publishers are making content
available for free. Is this a sustainable business model? Might a
publisher, seeing the writing on the wall, start to think about what
they can charge for, if not articles (I\'m deliberately ignoring the
\"author pays\" model of open access as I\'m not convinced this has a
long term future).

In the diagrams above the \"linkbase\" is on the publisher\'s side in
two of the three scenarios. If I was a publisher, I\'d be looking to
assembling proprietary databases and linking tools to create value that
I could then charge for. I\'m sure this is happening already. I suspect
that the growing trend to open access for publications is not going to
be enough to keep access to scientific knowledge itself open. In many
ways publications themselves aren\'t terribly useful, it\'s the
knowledge they contain that matters. Extracting, cross linking, and
interpreting that knowledge is going to require sophisticated tools. The
next challenge is going to be ensuring that the \"linkbases\" generated
by those tools remain free and open, or an \"open access\" victory may
turn out to be hollow.


The last few days I've been re-reading articles about Ted Nelson's work (including ill-fated Project Xanadu), reading articles celebrating his work (brought together in the open access book "Intertwingled"), playing with Hypothes.is, and thinking about annotation and linking.

What happens when open access wins?

A couple of articles in the tech press got me thinking this morning
about Bitcoin, Ted Nelson, Xanadu, and the [web that
wasn\'t](http://www.namahn.com/we-share/interviews/alex-wright-web-wasnt).
The articles are [After The Social Web, Here Comes The Trust
Web](http://techcrunch.com/2015/01/18/after-the-social-web-here-comes-the-trust-web/)
and [Transforming the web into a HTTPA
\'database\'](http://www.zdnet.com/article/transforming-the-web-into-a-httpa-database/).
There are some really interesting ideas being explored based on
centralised tracking of resources (including money, think Bitcoin, and
other assets, think content). I wonder whether these developments may
make lead to renewed interest in some of the ideas of [Ted
Nelson](http://en.wikipedia.org/wiki/Ted_Nelson).

I\'ve always had a soft-spot for Ted Nelson and his Xanadu project (see
my earlier posts on
[translcusion](http://iphylo.blogspot.com/2008/03/word-for-day-transclusion.html)
and [*Nature\'s* ENCODE
app](http://iphylo.blogspot.com/2012/09/decoding-nature-encode-ipad-app-omg-it.html)).
To get a sense of what he was after, we can compare the web we have with
what Nelson envisaged.

The web we have today:

1.  Links are one-way, in that it\'s easy to link to a site (just use
    the URL), but it\'s hard for the target site to find out who links
    to it. Put another way, like writing a scientific paper, it\'s easy
    to cite another paper, but non-trivial to find out who is citing
    your own work.
2.  Links to another document are simply launching pads to go to that
    other document, whether it\'s still there or not.
3.  Content is typically either \"free\" (paid for by advertising or in
    exchange for personal data), or behind a paywall and hence
    expensive.

Nelson wanted:

1.  Links that were bidirectional (so not only did you get cited, but
    you knew who was citing you)
2.  \"Transclusion\", where documents would not simply link (=cite) to
    other documents but would include snippets of those documents. If
    you cited another document, say to support a claim, you would
    actually include the relevant fragment of that document in your own
    document.
3.  A micropayment system so that if your work was \"transcluded\" you
    could get paid for that content.

The web we have is in many ways much easier to build, so Nelson\'s
vision lost out. One-way links are easy to create (just paste in a URL),
and the 404 error (that you get when a web page is missing) makes it
robust to failure. If a page vanishes, things don\'t collapse, you just
backtrack and go somewhere else.

Nelson had a more tightly linked web. He wanted to keep track of who
links to whom automatically. Doing this today is the preserve of big
operations such as Google (who count links to rank search results) or
the Web of Science (who count citations to rank articles and journals -
note that I\'m using the web and the citation network pretty much
interchangeably in this post). Because citation tracking isn\'t built
into the web, you need create this feature, and that costs money (and
hence nobody provides access to citation data for free).

In the current web, stuff (content) is either given away for \"free\"
(or simply copied and pasted as if it was free), or locked behind
paywalls. Free, of course, is never free. We are either handing over
data, being the targets of advertising (better targeted the more data we
hand over), or we pay for freedom directly (e.g., open access
publication fees in the case of scientific articles). Alternatively, we
have the paywalls well know to academics, where much of the world\'s
knowledge is held behind expensive paywalls (in part because publishers
need some way to make money, and there\'s little middle ground between
free and expensive).

Nelson\'s model envisaged micropayments, where content creators would
get small payments every time their content was used. Under the
transclusion model, only small bits of your content might be used (in
the context of a scientific paper, imagine just a single fact or
statement was used). You didn\'t get everything for free (that would
destroy the incentive to create), but nor was everything locked up
behind prohibitively expensive paywalls. Nelson\'s model never took off,
in part I suspect because there was simply no way to (a) track who was
using the content, and (b) collect micropayments.

What is interesting is that Bitcoin seems to deal with the micropayments
issue, and the HTTPA protocol (which uses much the same idea as Bitcoin
to keep an audit trail of who has accessed and used data) may provide a
mechanism to track usage. How is this going to change the current web?
Might there be ways to use these ideas to reimagine academic publishing,
which at the moment seems caught between steep open access fees or
expensive journal subscriptions?


A couple of articles in the tech press got me thinking this morning about Bitcoin, Ted Nelson, Xanadu, and the web that wasn't. The articles are After The Social Web, Here Comes The Trust Web and Transforming the web into a HTTPA 'database'. There are some really interesting ideas being explored based on centralised tracking of resources (including money, think Bitcoin, and other assets, think content). I wonder whether these developments may

Bitcoin, Xanadu, Ted Nelson, and the web that wasn't

Stumbled across [Project
Xanadu](http://en.wikipedia.org/wiki/Project_Xanadu), Ted Nelson\'s
vision of the way the web should be (e.g., [BACK TO THE FUTURE:
Hypertext the Way It Used To
Be](http://xanadu.com/XanaduSpace/btf.htm)). Nelson coined the term
\"[transclusion](http://en.wikipedia.org/wiki/Transclusion)\", including
one document in side another by reference. The screen shot of [Xanadu
Space](http://xanarama.net/) may help illustrate the idea:  
[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjGSyO-tIiEiaO-GAYhh5OvGKrF883tuh_WN93jQGfOLJiWVzHxfNEP6am8wtqJjnBW0sh8SynqTjPmSXl5yuyfYxarObLmL08JRdJbd6uuZyhil-LMt62dDYS19YtoHyRagtXv/s320/fwDemoOrigins-panorama2.png){#BLOGGER_PHOTO_ID_5174556763887519858
style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;"
border="0"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjGSyO-tIiEiaO-GAYhh5OvGKrF883tuh_WN93jQGfOLJiWVzHxfNEP6am8wtqJjnBW0sh8SynqTjPmSXl5yuyfYxarObLmL08JRdJbd6uuZyhil-LMt62dDYS19YtoHyRagtXv/s1600-h/fwDemoOrigins-panorama2.png){onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"}  
Nelson envisages a web where instead of just one-way links, documents
include parts of other documents, and one can view a document
side-by-side with the source documents. Modern web browsers transclude
images (the image file is not \"physically\" in the document, rather it
exists elsewhere), but mostly they link to other documents via
hyperlinks.  
Ted Nelson\'s writings are a fascinating read, partly because they
remind you just how much of the web we take for granted, and how thinks
could be different (better?). One thing he objects to is that much of
the the web simulates paper  

> Much of the field has imitated paper: in word processing (Microsoft
> Word and Adobe Acrobat) and the World Wide Web, whose rectangular page
> layouts become a focal issue. It should be noted that these systems
> imitate paper under glass, since you can\'t annotate it.

Nelson also advocates every element of a document having its own unique
address, not just at book or article level. This resonates with what is
happing with digital libraries. Gregory Crane in his article \"What Do
You Do with a Million Books?\"
([doi:10.1045/march2006-crane](http://dx.doi.org/10.1045/march2006-crane))
notes that:  

> Most digital libraries still mimic their print predecessors, treating
> individual objects -- commonly chunks of PDF, RTF/Word, or HTML with
> no standard internal structure -- as its constituent units. As digital
> libraries mature and become better able to extract information (e.g.,
> personal and place names), each word and automatically identifiable
> chunk of words becomes a discrete object. In a sample 300 volume, 55
> million word collection of nineteenth-century American English,
> automatic named entity identification has added 12,000,000 tags. While
> this collection focuses on name rich historical materials and includes
> several reference works, this system already discovers thousands of
> references to named entities in most book length documents. We thus
> move from single catalogue entries with a few hundred words to
> thousands of tagged objects -- an increase of at least one order of
> magnitude with named entities and of at least two orders of magnitude
> when we consider each individual word as an object.

I discovered Crane\'s paper via Chris Freeland\'s post [On Name Finding
in the
BHL](http://biodiversitylibrary.blogspot.com/2008/03/on-name-finding-in-bhl.html).
Chris summarises BHL\'s work on scanning biodiversity literature and
extracting taxonomic names. BHL\'s output is at the level of pages,
rather than articles. Existing GUIDs for literature (such as DOIs and
SICIs) typically identify articles rather than pages (or page elements),
so there\'s a need to extending these to pages.  
  
Chris also raises the issue of ranking and relevance \-- \"What do you
do with 19,000 pages containing Hymenoptera?\". One possibility is to
explore Robert Huber\'s
[TaxonRank](http://stratigraphynet.blogspot.com/2008/01/how-taxonrank-works.html)
idea (inspired by Google\'s PageRank). This would require text mining to
build synonomy lists from scanned papers, challenging but not
impossible. But I suspect that the network of citations is what will
help build a sensible way to rank the 19,000 pages.  
  
A while ago people were speculating what Google could do to help
biodiversity informatics. I found much of this discussion to be vague,
with no clear notion of what Google could actually do. What I think
Google is exceptionally good at are two things we need to tackle \--
text mining, and extracting information from links. I think this is
where BHL and, by extension, EOL, should be devoting much of their
resources.


Stumbled across Project Xanadu, Ted Nelson's vision of the way the web should be (e.g., BACK TO THE FUTURE: Hypertext the Way It Used To Be). Nelson coined the term "transclusion", including one document in side another by reference.

Messaggi di Rogue Scholar

Personal knowledge graphs: Obsidian, Roam, Wikidata, and Xanadu

What happens when open access wins?

Bitcoin, Xanadu, Ted Nelson, and the web that wasn't

Word for the day - "transclusion"