Ross Mounce

How best to link the figure, to the paper & the underlying data?

Whilst visiting EBI, Hinxton yesterday, [Robert
Hanson](http://www.stolaf.edu/people/hansonr/) (computational chemist)
reminded me of an interesting hack you can do to embed data in images.

Back in 2010 it was [widely reported that people were using Flickr to
transmit data (secretly) in
images](http://www.newscientist.com/article/dn19284-hiding-files-in-flickr-pics-will-fool-web-censors.html).

This general technique is called
**[Steganography](http://en.wikipedia.org/wiki/Steganography).**

Turns out I can use this hack in my project too...

As a proof of concept, I've uploaded one recent PLOS ONE phylogeny
figure to my 'plosone-phylo' flickr account:

<https://www.flickr.com/photos/123621741@N08/14385231987/in/photostream/>

In this special file, I've embedded the nexus, NeXML & Bibtex file from
[TreeBASE](http://treebase.org/treebase-web/search/study/summary.html?id=15461) that
correspond to the image. This
[website](http://wiki.linuxquestions.org/wiki/Embed_a_zip_file_into_an_image)
has cross-platform instructions -- it's remarkably simple.

So now if you download that special file I put on Flickr (this hack
*only* works if you download the original, not resized versions) and
'unzip' the image file you'll reveal the hidden data embedded in the
image:  nexus, NeXML & Bibtex.  
**Try it!**

<figure id="attachment_1445" class="wp-caption alignleft"
aria-describedby="caption-attachment-1445" style="width: 774px">
<a
href="http://rossmounce.co.uk/wp-content/uploads/2014/07/2014-07-04-134429_794x890_scrot.png"><img
src="http://rossmounce.co.uk/wp-content/uploads/2014/07/2014-07-04-134429_794x890_scrot.png"
class="size-full wp-image-1445" loading="lazy" decoding="async"
srcset="https://rossmounce.co.uk/wp-content/uploads/2014/07/2014-07-04-134429_794x890_scrot.png 774w, https://rossmounce.co.uk/wp-content/uploads/2014/07/2014-07-04-134429_794x890_scrot-300x232.png 300w"
sizes="(max-width: 774px) 100vw, 774px" width="774" height="600"
alt="Screenshot showing what to click to download the original image" /></a>
<figcaption>Screenshot showing what to click to download the original
image</figcaption>
</figure>

 

This certainly isn't the 'optimal' way of doing things. But it is a nice
way of keeping everything together in ONE file. Maybe you might have a
use for this hack too?


<strong>
 How best to link the figure, to the paper &amp; the underlying data?
</strong>
Whilst visiting EBI, Hinxton yesterday, Robert Hanson (computational chemist) reminded me of an interesting hack you can do to embed data in images. Back in 2010 it was widely reported that people were using Flickr to transmit data (secretly) in images.


Steganography, phylogenetics and Flickr

I'm proud to announce an interesting public output from my BBSRC-funded
postdoc project:  
**PLUTo: Phyloinformatic Literature Unlocking Tools. Software for making
published phyloinformatic data discoverable, open, and reusable**

<figure id="attachment_1391" class="wp-caption alignleft"
aria-describedby="caption-attachment-1391" style="width: 590px">
<a
href="http://rossmounce.co.uk/wp-content/uploads/2014/05/2014-05-07-172932_1163x965_scrot.png"><img
src="http://rossmounce.co.uk/wp-content/uploads/2014/05/2014-05-07-172932_1163x965_scrot-1024x671.png"
class="size-large wp-image-1391" loading="lazy" decoding="async"
srcset="https://rossmounce.co.uk/wp-content/uploads/2014/05/2014-05-07-172932_1163x965_scrot-1024x671.png 1024w, https://rossmounce.co.uk/wp-content/uploads/2014/05/2014-05-07-172932_1163x965_scrot-300x196.png 300w, https://rossmounce.co.uk/wp-content/uploads/2014/05/2014-05-07-172932_1163x965_scrot.png 1153w"
sizes="(max-width: 590px) 100vw, 590px" width="590" height="386"
alt="MOAR PHYLOGENY!" /></a>
<figcaption>Screenshot of some of the PLOS ONE phylogeny figure
collection on Flickr</figcaption>
</figure>

 

 

 

 

 

 

 

 

 

 

 

 

 

 

I've made openly available my first-pass filter of PLOS ONE phylogeny
figures (I'm not in any way claiming this is \*all\* of them).

This curated & tagged image collection is on Flickr for easy browsing:
<http://bit.ly/PLOStrees>

As well as on Github for version control, open archiving, and
collaboration (I have remote collaborators):

<https://github.com/rossmounce/P1-phylo-part1>

<https://github.com/rossmounce/P1-phylo-part2>

<https://github.com/rossmounce/P1-phylo-part3>

<https://github.com/rossmounce/P1-phylo-part4>

(Github doesn't like repositories over 1GB so I've had to split-up the
content between 4 separate repositories)

 

**Why?**

The aim of the PLUTo project is to re-extract & liberate phylogenetic
data & associated metadata from the research literature. Sadly, [only
\~4% of modern published phylogenetic analysis studies make their
underlying data
available](http://www.biomedcentral.com/1756-0500/5/574). Another study
finds that [if you ask the authors for this data, only 16% will be kind
enough to reply with the requested
data](http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001636)!

This particular data type is a cornerstone of modern evolutionary
biology. You'll find phylogenetic analyses across a whole host of
journal subjects -- medical, ecological, natural history,
palaeontology... There are also many different ways in which this data
can be re-used e.g.
[supertrees](http://en.wikipedia.org/wiki/Supertree)  & [comparative
cladistics](http://onlinelibrary.wiley.com/doi/10.1111/j.1096-0031.2009.00265.x/abstract).
Not to mention, simple validation studies &/or analyses which
extend-upon or map new data on to a phylogeny. It's really useful data
and we should be archiving it for future re-use and re-analysis. To my
great delight, this is what I'm being paid to attempt to do for my first
postdoc; on a grant I co-wrote -- finding & liberating phylogenetic data
*for everyone*!

 

**Why PLOS ONE?**

 

-  It's a BOAI-compliant open access journal that publishes most
  articles under [CC BY](http://creativecommons.org/licenses/by/4.0/),
  with a few under [CC0](http://creativecommons.org/choose/zero/).



- This means I can openly re-publish figures online (provided sufficient
  attribution is given) --- no need to worry about DMCA takedown notices
  or 'getting sued'! This makes the process of research much easier.
  Private, non-public, access-restricted repositories for collaboration
  are a hassle I'd rather do without.



- It's a high-volume 'megajournal' publishing \~200 articles per day,
  many of which include phylogenetic analyses.
  - Thus its worthwhile establishing a regular daily or weekly method
    for parsing-out phylogenetic tree figures from this journal



- *Killer feature:* as far as I know, PLOS are the only publisher to
  embed rich metadata inside their figure image files.
  - This makes satisfying the CC BY licence trivially easy ---
    sufficient attribution metadata is already embedded in the file.
    Just ensure that wherever you're uploading the file to doesn't wipe
    this embedded data, hence why I chose Flickr as my initial upload
    platform.

 

**What does this enable or make easier?**

 

On it's own, this collection doesn't do much, this is still an early
stage -- but it gives us an important insight into the prevalence of
certain types of visual display-style that researchers are using:

'radial' phylogenies

<https://www.flickr.com/search?user_id=123621741%40N08&sort=relevance&text=radial>

<figure id="attachment_1400" class="wp-caption alignleft"
aria-describedby="caption-attachment-1400" style="width: 300px">
<a
href="http://rossmounce.co.uk/wp-content/uploads/2014/05/14130299804_7b1a739cd3_z.jpg"><img
src="http://rossmounce.co.uk/wp-content/uploads/2014/05/14130299804_7b1a739cd3_z-300x300.jpg"
class="wp-image-1400 size-medium" loading="lazy" decoding="async"
srcset="https://rossmounce.co.uk/wp-content/uploads/2014/05/14130299804_7b1a739cd3_z-300x300.jpg 300w, https://rossmounce.co.uk/wp-content/uploads/2014/05/14130299804_7b1a739cd3_z-150x150.jpg 150w, https://rossmounce.co.uk/wp-content/uploads/2014/05/14130299804_7b1a739cd3_z.jpg 640w"
sizes="(max-width: 300px) 100vw, 300px" width="300" height="300"
alt="Source: Zerillo et al 2013 PLOS ONE. Carbohydrate-Active Enzymes in Pythium and Their Role in Plant Cell Wall and Storage Polysaccharide Degradation" /></a>
<figcaption>Source: Zerillo et al 2013 PLOS ONE. Carbohydrate-Active
Enzymes in Pythium and Their Role in Plant Cell Wall and Storage
Polysaccharide Degradation</figcaption>
</figure>

 

 

 

 

 

 

 

 

 

 

 

 

 

'geophylogeny' (phylogeny displayed relative to a map of some sort, 2D
or 3D)

<https://www.flickr.com/search?user_id=123621741%40N08&sort=relevance&text=geophylogeny>

<figure id="attachment_1399" class="wp-caption alignleft"
aria-describedby="caption-attachment-1399" style="width: 300px">
<a
href="http://rossmounce.co.uk/wp-content/uploads/2014/05/14120122712_24551a9ea3_b.jpg"><img
src="http://rossmounce.co.uk/wp-content/uploads/2014/05/14120122712_24551a9ea3_b-300x181.jpg"
class="wp-image-1399 size-medium" loading="lazy" decoding="async"
srcset="https://rossmounce.co.uk/wp-content/uploads/2014/05/14120122712_24551a9ea3_b-300x181.jpg 300w, https://rossmounce.co.uk/wp-content/uploads/2014/05/14120122712_24551a9ea3_b.jpg 1024w"
sizes="(max-width: 300px) 100vw, 300px" width="300" height="181"
alt="Source: Guo et al 2012 PLOS ONE. Evolution and Biogeography of the Slipper Orchids: Eocene Vicariance of the Conduplicate Genera in the Old and New World Tropics" /></a>
<figcaption>Source: Guo et al 2012 PLOS ONE. Evolution and Biogeography
of the Slipper Orchids: Eocene Vicariance of the Conduplicate Genera in
the Old and New World Tropics</figcaption>
</figure>

 

 

 

 

 

 

 

 

 

 

'timescaled' (phylogenies where the branch lengths are proportional to
units of time or geological periods)  
<https://www.flickr.com/search?user_id=123621741%40N08&sort=relevance&text=timescaled>

<figure id="attachment_1398" class="wp-caption alignleft"
aria-describedby="caption-attachment-1398" style="width: 300px">
<a
href="http://rossmounce.co.uk/wp-content/uploads/2014/05/14124910962_70b9bf6d69_z.jpg"><img
src="http://rossmounce.co.uk/wp-content/uploads/2014/05/14124910962_70b9bf6d69_z-300x185.jpg"
class="wp-image-1398 size-medium" loading="lazy" decoding="async"
srcset="https://rossmounce.co.uk/wp-content/uploads/2014/05/14124910962_70b9bf6d69_z-300x185.jpg 300w, https://rossmounce.co.uk/wp-content/uploads/2014/05/14124910962_70b9bf6d69_z.jpg 640w"
sizes="(max-width: 300px) 100vw, 300px" width="300" height="185"
alt="Source: Pol et al 2014 PLOS ONE. A New Notosuchian from the Late Cretaceous of Brazil and the Phylogeny of Advanced Notosuchians" /></a>
<figcaption>Source: Pol et al 2014 PLOS ONE. A New Notosuchian from the
Late Cretaceous of Brazil and the Phylogeny of Advanced
Notosuchians</figcaption>
</figure>

 

 

 

 

 

 

 

 

 

'splitstrees'

<https://www.flickr.com/search?user_id=123621741%40N08&sort=relevance&text=splitstree>

<figure id="attachment_1397" class="wp-caption alignleft"
aria-describedby="caption-attachment-1397" style="width: 300px">
<a
href="http://rossmounce.co.uk/wp-content/uploads/2014/05/split.png"><img
src="http://rossmounce.co.uk/wp-content/uploads/2014/05/split-300x216.png"
class="wp-image-1397 size-medium" loading="lazy" decoding="async"
srcset="https://rossmounce.co.uk/wp-content/uploads/2014/05/split-300x216.png 300w, https://rossmounce.co.uk/wp-content/uploads/2014/05/split-1024x740.png 1024w"
sizes="(max-width: 300px) 100vw, 300px" width="300" height="216"
alt="Source: McDowell et al 2013 PLOS ONE. The Opportunistic Pathogen Propionibacterium acnes: Insights into Typing, Human Disease, Clonal Diversification and CAMP Factor Evolution" /></a>
<figcaption>Source: McDowell et al 2013 PLOS ONE. The Opportunistic
Pathogen Propionibacterium acnes: Insights into Typing, Human Disease,
Clonal Diversification and CAMP Factor Evolution</figcaption>
</figure>

 

 

 

 

 

 

 

 

 

 

 

Arguably it also facilitates complex searches for specific types of
phylogeny

e.g. analyses using cytochrome b  
[https://www.flickr.com/search/?w=123621741@N08&q=%22cyt%20b%22%20OR%20%22cytochrome%20b%22  
](https://www.flickr.com/search/?w=123621741@N08&q=%22cyt%20b%22%20OR%20%22cytochrome%20b%22)(you
could use PLOS's API to do this, particularly their figure/table caption
search field --- but you'd get a lot of false positives --- this is an
expert-curated collection that has filtered-out non-phylo figures)

In my initial roadmap, the plan is to do PLOS ONE, the other PLOS
journals, then BMC journals, then possibly Zootaxa & Phytotaxa (Magnolia
Press). There will be a Github-based website for the project soon, lots
still to do...!

 

**Want to know more / collaborate / critique ?**

Conferences:

I've got an accepted lightning talk at [iEvoBio](http://ievobio.org/) in
Raleigh, NC later this year about the PLUTo project.

As well as an accepted lightning talk at the [Bioinformatics Open Source
Conference](http://www.open-bio.org/wiki/BOSC_2014) (BOSC) in Boston,
MA.

Elsewise, contact me via twitter @rmounce , the comment section on this
blog post, or email ross dot mounce \<at\> gmail dot com

I’m proud to announce an interesting public output from my BBSRC-funded postdoc project:
<strong>
 PLUTo: Phyloinformatic Literature Unlocking Tools. Software for making published phyloinformatic data discoverable, open, and reusable
</strong>
Screenshot of some of the PLOS ONE phylogeny figure collection on Flickr


Rogue Scholar Beiträge

Steganography, phylogenetics and Flickr

PLOS ONE PHYLOGENY