Europe PubMedCentral API

[blahah]

The EUPMC API provides fulltextXML in JATS format, as well as zipped 'supplementary files' which in my experience include full-sized figure images.

The only way to access the files is via the zipped archive, meaning we can't simply refer out to an external image to show previews during search results - we'll have to pull the data and extract it.

Easy to get with getpapers:

getpapers --query 'some query' --xml --supp --outdir somedir

[blahah]

OK, this is looking like the most promising of the bunch.

I've found that in addition to providing the files as a .zip, europepmc has a predictable URL structure for thumbnails of figures.

They look like this:

is

http://europepmc.org/articles/PMC1318471/bin/1471-2105-6-281-2.gif

[blahah]

So the thumbnail URL for a given figure is:

http://europepmc.org/articles/#{article_id}/bin/#{figure_id}.gif

[blahah]

I now have this working!

Example slide generated:

---
title: The larval nervous system of the penis worm Priapulus caudatus (Ecdysozoa).
authorString: 'Martín-Durán JM, Wolff GH, Strausfeld NJ, Hejnol A.'
pmcid: PMC4685585
pmid: '26598729'
abstract: 'The origin and extreme diversification of the animal nervous system is a central question in biology. While most of the attention has traditionally been paid to those lineages with highly elaborated nervous systems (e.g. arthropods, vertebrates, annelids), only the study of the vast animal diversity can deliver a comprehensive view of the evolutionary history of this organ system. In this regard, the phylogenetic position and apparently conservative molecular, morphological and embryological features of priapulid worms (Priapulida) place this animal lineage as a key to understanding the evolution of the Ecdysozoa (i.e. arthropods and nematodes). In this study, we characterize the nervous system of the hatching larva and first lorica larva of the priapulid worm Priapulus caudatus by immunolabelling against acetylated and tyrosinated tubulin, pCaMKII, serotonin and FMRFamide. Our results show that a circumoral brain and an unpaired ventral nerve with a caudal ganglion characterize the central nervous system of hatching embryos. After the first moult, the larva attains some adult features: a neck ganglion, an introvert plexus, and conspicuous secondary longitudinal neurites. Our study delivers a neuroanatomical framework for future embryological studies in priapulid worms, and helps illuminate the course of nervous system evolution in the Ecdysozoa.'
tags:
  - eupmc
  - figure
doi: 10.1098/rstb.2015.0050
thumb_url: 'http://europepmc.org/articles/PMC4685585/bin/rstb20150050-g1.gif'
figure_no: 1
---
<img src='http://europepmc.org/articles/PMC4685585/bin/rstb20150050-g1.jpg' style='max-height: 400px'>
### Figure 1
<p style='font-size: 10px;'><p>Localization of acetylated tubulin in <italic>P. caudatus</italic> larvae. (<italic>a–e</italic>) Maximal <italic>z</italic>-projections of confocal stacks of whole mount larvae stained against acetylated tubulin (AcTub, in grey) and counterstained with the nuclear marker Sytox Green (red, in <italic>a</italic> and <italic>c</italic>). (<italic>a</italic>) The hatching larva of <italic>P. caudatus</italic> shows a circumoral brain (yellow arrows) and neural commissures at the neck region (neck ganglion; blue arrowheads). The oral scalids and the posterior sensory trunk tubuli are also innervated. (<italic>b</italic>) Detail of the region indicated by a dashed rectangle in (<italic>a</italic>). Thin neural fibres (white arrowheads) project from the sensory trunk tubuli towards the introvert. (<italic>c</italic>) After the first moult, a well-developed ventral nerve cord (green arrowheads) connects the circumoral brain (yellow arrows) with the posterior region of the trunk. The neck ganglion (blue arrowheads) appears more distinct. (<italic>d</italic>) The introvert region of the first lorica larva is rich in neural fibres, with a dense innervation of the scalids from the brain area (black dashed circle; main ventral nerve indicated by green arrowheads and the neck commissures by blue arrowheads). (<italic>e</italic>) Similar to the anterior scalids, the posterior lorica tubuli are strongly innervated, with thin fibres (white arrowheads) projecting from them longitudinally towards the anterior region and posteriorly towards the anal opening, where they meet with the ventral nerve (green arrowheads). In all cases, the asterisk indicates the position of the mouth. (<italic>a,b</italic>) are lateral views, and (<italic>c–e</italic>) are ventral views. lt, lorica tubulus; nt, neck tubulus; sc, scalids; tt, trunk tubulus. Scale bars, 25 µm in (<italic>a,b,d,e</italic>); 50 µm in (<italic>c</italic>).</p></p>

[blahah]

improved version:

---
name: 26598729_fig1
title: The larval nervous system of the penis worm Priapulus caudatus (Ecdysozoa).
authorString: 'Martín-Durán JM, Wolff GH, Strausfeld NJ, Hejnol A.'
pmcid: PMC4685585
pmid: '26598729'
abstract: 'The origin and extreme diversification of the animal nervous system is a central question in biology. While most of the attention has traditionally been paid to those lineages with highly elaborated nervous systems (e.g. arthropods, vertebrates, annelids), only the study of the vast animal diversity can deliver a comprehensive view of the evolutionary history of this organ system. In this regard, the phylogenetic position and apparently conservative molecular, morphological and embryological features of priapulid worms (Priapulida) place this animal lineage as a key to understanding the evolution of the Ecdysozoa (i.e. arthropods and nematodes). In this study, we characterize the nervous system of the hatching larva and first lorica larva of the priapulid worm Priapulus caudatus by immunolabelling against acetylated and tyrosinated tubulin, pCaMKII, serotonin and FMRFamide. Our results show that a circumoral brain and an unpaired ventral nerve with a caudal ganglion characterize the central nervous system of hatching embryos. After the first moult, the larva attains some adult features: a neck ganglion, an introvert plexus, and conspicuous secondary longitudinal neurites. Our study delivers a neuroanatomical framework for future embryological studies in priapulid worms, and helps illuminate the course of nervous system evolution in the Ecdysozoa.'
tags:
  - eupmc
  - figure
doi: 10.1098/rstb.2015.0050
thumb_url: 'http://europepmc.org/articles/PMC4685585/bin/rstb20150050-g1.gif'
figure_no: 1
---
<img src='http://europepmc.org/articles/PMC4685585/bin/rstb20150050-g1.jpg' style='max-height: 300px'>
### Figure 1
<p style='font-size: 10px;'>Localization of acetylated tubulin in *P. caudatus* larvae. (*a–e*) Maximal *z*-projections of confocal stacks of whole mount larvae stained against acetylated tubulin (AcTub, in grey) and counterstained with the nuclear marker Sytox Green (red, in *a* and *c*). (*a*) The hatching larva of *P. caudatus* shows a circumoral brain (yellow arrows) and neural commissures at the neck region (neck ganglion; blue arrowheads). The oral scalids and the posterior sensory trunk tubuli are also innervated. (*b*) Detail of the region indicated by a dashed rectangle in (*a*). Thin neural fibres (white arrowheads) project from the sensory trunk tubuli towards the introvert. (*c*) After the first moult, a well-developed ventral nerve cord (green arrowheads) connects the circumoral brain (yellow arrows) with the posterior region of the trunk. The neck ganglion (blue arrowheads) appears more distinct. (*d*) The introvert region of the first lorica larva is rich in neural fibres, with a dense innervation of the scalids from the brain area (black dashed circle; main ventral nerve indicated by green arrowheads and the neck commissures by blue arrowheads). (*e*) Similar to the anterior scalids, the posterior lorica tubuli are strongly innervated, with thin fibres (white arrowheads) projecting from them longitudinally towards the anterior region and posteriorly towards the anal opening, where they meet with the ventral nerve (green arrowheads). In all cases, the asterisk indicates the position of the mouth. (*a,b*) are lateral views, and (*c–e*) are ventral views. lt, lorica tubulus; nt, neck tubulus; sc, scalids; tt, trunk tubulus. Scale bars, 25 µm in (*a,b,d,e*); 50 µm in (*c*).</p>