LiteratureResearcher - where graphs, PDFs, and BibTex happily live together

On 1 Nov 2017, at 22:39, Dimitris Chloupis <[hidden email]> wrote:

Super cool more detailed recommendations when I try it on practice

A cheap pdf viewer in Pharo would be to turn pdf pages to JPG images which you can load via image morph so you won’t have to have two separate windows. There are ton of converters out there that can do this.

On Wed, 1 Nov 2017 at 23:17, Manuel Leuenberger <[hidden email]> wrote:

Hi everyone,

I was experimenting in the last few weeks with my take on literature research. For me, the corpus of scientific papers form an interconnected graph, not those plain lists and tables we keep in our bibliographies. So, here is the first prototype that has Google Scholar integration for search, can fetch PDFs from IEEE and ACM, extracts metadata from PDFs - all this results in hyperlinked PDFs!

See a demo here: https://youtu.be/EcK3Pt_WnEw

Also slides from the SCG seminar here: http://scg.unibe.ch/download/softwarecomposition/2017-10-31-Leuenberger-ILE.pdf

I plan on packaging it, so that those who are interested can check it out themselves (help wanted!). Currently, it only works on macOS.

What do you think of my approach? Which use cases should be added?

Cheers,

Manuel

On 2 Nov 2017, at 00:06, Bernardo Ezequiel Contreras <[hidden email]> wrote:

really nice! ted nelson talks about something like that in his xanadu project.

On Wed, Nov 1, 2017 at 6:16 PM, Manuel Leuenberger <[hidden email]> wrote:

Hi everyone,

I was experimenting in the last few weeks with my take on literature research. For me, the corpus of scientific papers form an interconnected graph, not those plain lists and tables we keep in our bibliographies. So, here is the first prototype that has Google Scholar integration for search, can fetch PDFs from IEEE and ACM, extracts metadata from PDFs - all this results in hyperlinked PDFs!

See a demo here: https://youtu.be/EcK3Pt_WnEw

Also slides from the SCG seminar here: http://scg.unibe.ch/download/softwarecomposition/2017-10-31-Leuenberger-ILE.pdf

I plan on packaging it, so that those who are interested can check it out themselves (help wanted!). Currently, it only works on macOS.

What do you think of my approach? Which use cases should be added?

Cheers,

Manuel

--

Bernardo E.C.

Sent from a cheap desktop computer in South America.

On 2 Nov 2017, at 18:03, Offray Vladimir Luna Cárdenas <[hidden email]> wrote:

Hi Manuel,

This is really interesting! I like the idea of a graph and the way ILE manages metadata importation. Grafoscopio [1][2][3], is the software I'm creating for reproducible research and literate computing (mixing prose, code, queries, data and visualizations). It has alpha support for Zotero and I think that ILE and Grafoscopio could work together to provide researcher support for creating and working with research literature.

[1] http://mutabit.com/grafoscopio/index.en.html
[2] http://mutabit.com/repos.fossil/alvicoda/doc/tip/index.html
[3] http://joss.theoj.org/papers/c92ed13fa746bc681081f9b31678841b

Now my research workflow includes Pharo, TeXStudio, Grafoscopio, Zotero, Docear[4] and Hypothesis[5] to map and annotate research literature, but there is a lot of context switching, as you point in your presentation, and lack of moldability that we could get rid of, if those tools were integrated into Pharo. To manage this, I usually have two screens (see screenshot below) where I made annotated reading (in hypothesis) and map readings (in Docear). That is because Docear is not integrated (yet) with Hypothesis, which has a superb annotation system.

[4] http://www.docear.org/
[5] https://web.hypothes.is/

I would like to have a similar tree like Docear reading interface , connected with the annotated reading of hypothesis (tags and comments), inside Pharo/Grafoscopio. In my ideal workflow I would add a bibliography item to Zotero (using add item by ID or dropping the URL/PDF), open it (getting the table of contents map inside Pharo, ala Docear and thanks to Hypothesis) and I would start to annotate and tag my readings. After that, some DSL would allow me to recover, visualize and export such annotations to be put inside of or connected with a Grafoscopio notebook and there I would finish the research writing.

What do you think of this workflow? Could ILE support or be part of it in some way?

Once you have packaged ILE, I could help as a tester in Gnu/Linux.

Cheers,

Offray

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On 01/11/17 16:16, Manuel Leuenberger wrote:

Hi everyone,

I was experimenting in the last few weeks with my take on literature research. For me, the corpus of scientific papers form an interconnected graph, not those plain lists and tables we keep in our bibliographies. So, here is the first prototype that has Google Scholar integration for search, can fetch PDFs from IEEE and ACM, extracts metadata from PDFs - all this results in hyperlinked PDFs!

See a demo here: https://youtu.be/EcK3Pt_WnEw

Also slides from the SCG seminar here: http://scg.unibe.ch/download/softwarecomposition/2017-10-31-Leuenberger-ILE.pdf

I plan on packaging it, so that those who are interested can check it out themselves (help wanted!). Currently, it only works on macOS.

What do you think of my approach? Which use cases should be added?

Cheers,

Manuel

On 2 Nov 2017, at 18:08, Stephane Ducasse <[hidden email]> wrote:

Hi manuel

this is super cool :)
Could you describe how you did the pdf integration?
And yes please package it :)
I want to try it.

Stef

On Wed, Nov 1, 2017 at 10:16 PM, Manuel Leuenberger
<[hidden email]> wrote:

Hi everyone,

I was experimenting in the last few weeks with my take on literature
research. For me, the corpus of scientific papers form an interconnected
graph, not those plain lists and tables we keep in our bibliographies. So,
here is the first prototype that has Google Scholar integration for search,
can fetch PDFs from IEEE and ACM, extracts metadata from PDFs - all this
results in hyperlinked PDFs!

See a demo here: https://youtu.be/EcK3Pt_WnEw
Also slides from the SCG seminar here:
http://scg.unibe.ch/download/softwarecomposition/2017-10-31-Leuenberger-ILE.pdf

I plan on packaging it, so that those who are interested can check it out
themselves (help wanted!). Currently, it only works on macOS.

What do you think of my approach? Which use cases should be added?

Cheers,
Manuel

On 3 Nov 2017, at 10:15, Christian Haider <[hidden email]> wrote:

Yes, reading PDFs is fine with PDFtalk, but what you want is more: Text extraction (there is a chapter in the spec about this).
This feature is not yet readily available. Some ground work has been done (content analysis), but for full text extraction more work is needed.

Cheers,
Christian

-----Ursprüngliche Nachricht-----
Von: Pharo-users [[hidden email]] Im Auftrag
von Stephane Ducasse
Gesendet: Freitag, 3. November 2017 09:46
An: Any question about pharo is welcome <[hidden email]>
Betreff: Re: [Pharo-users] LiteratureResearcher - where graphs, PDFs, and
BibTex happily live together

Hi manuel

thanks for the details. I think that the framework of christian haidler should
be able to read pdf.

Stef

On Thu, Nov 2, 2017 at 8:33 PM, Manuel Leuenberger
<[hidden email]> wrote:

Hi Stef,

The PDF integration consists of three parts:

1. CERMINE (https://github.com/CeON/CERMINE) is fed with the PDF and
outputs metadata as BibTex and a structured XML (title, authors,
affiliations, abstract, keyword, references, …). This is not perfect,
but way better than any other metadata extractor I could find.
2. From the metadata I generate hyperlinks that are anchored in the
PDF by a text key. pdf-linker (https://github.com/maenu/pdf-linker)
then searches for the anchors in the PDF text, using heuristics, as
PDF has a document model that is primarily intended for rendering and
printing, but not for processing. The hyperlinks are then inserted
using the awesome Apache PDFBox (https://pdfbox.apache.org/).
3. Those hyperlinks point to an URI like
“<a href="pharo://handle/clickReference.in.?args=1&amp;args=2" class="">pharo://handle/clickReference.in.?args=1&args=2” to represent a
reference 1 in the paper 2. Now comes the magic part: The OS allows
you to register custom handlers for custom URI schemes like pharo://.
For that I created a simple Objective-C app that handles the event and
passes it over as a HTTP message to a server running in Pharo
(https://github.com/maenu/PharoUriScheme). The OS will even start the
application if it is not yet running.

While the custom URI scheme approach is super powerful, it has
critical drawbacks. Any application can request to be the receiver of
a URI scheme, just as browser are for http://. Especially on mobile
devices with limited access to the OS, this opens up an attack point
for malware apps that replicate original apps that make use of schemes
like facebook:// and eavesdrop all interactions. If an original app
transmits any unencrypted secrets or user data encoded in those URIs,
malware can easily intercept it without the user noticing the leak. I
guess this is the reason why many PDF viewer just support the standard
http:// and mailto:// schemes. E.g., macOS Preview gives just an
audible beep when I click on a pharo:// link, Chromes viewer doesn’t
even bother giving any feedback. Only Adobe Acrobat allows you to
relax security settings to make them work (How could it be someone else

than Adobe, when it’s a security issue? ;).

I finished basic packaging today and will continue with some READMEs
and a nearly-all-in-one distribution tomorrow, I’ll keep you posted in
this thread.

Cheers,
Manuel

On 2 Nov 2017, at 18:08, Stephane Ducasse <[hidden email]>

wrote:

Hi manuel

this is super cool :)
Could you describe how you did the pdf integration?
And yes please package it :)
I want to try it.

Stef

On Wed, Nov 1, 2017 at 10:16 PM, Manuel Leuenberger
<[hidden email]> wrote:

Hi everyone,

I was experimenting in the last few weeks with my take on literature
research. For me, the corpus of scientific papers form an
interconnected graph, not those plain lists and tables we keep in our
bibliographies. So, here is the first prototype that has Google
Scholar integration for search, can fetch PDFs from IEEE and ACM,
extracts metadata from PDFs - all this results in hyperlinked PDFs!

See a demo here: https://youtu.be/EcK3Pt_WnEw Also slides from the

SCG

seminar here:
http://scg.unibe.ch/download/softwarecomposition/2017-10-31-

Leuenberge

r-ILE.pdf

I plan on packaging it, so that those who are interested can check it
out themselves (help wanted!). Currently, it only works on macOS.

What do you think of my approach? Which use cases should be added?

Cheers,
Manuel