We launched a platinum open access overlay neuroscience journal (Neurons, Behavior, Data Analysis, and Theory – NBDT). After 30 articles accepted, we are now ready for inclusion in Pubmed Central (PMC). This requires providing the full text of articles in an XML format that conforms to an acceptable journal article DTD (Document Type Definition). The following pages provide detailed information about PMC’s technical requirements:
How to Include a Journal in PMC.
This section details all of our data sample requirements.
See the PMC file specifications at: http://www.ncbi.nlm.nih.gov/pmc/pub/filespec/.
This page details the XML and image file requirements, and describes how these files must be named and packaged for delivery.
The minimum criteria for evaluation of sample data can be found at: http://www.ncbi.nlm.nih.gov/pmc/pub/min_requirements/.
At the moment papers are submitted to NBDT in latex format.
NBDT is hosted by Scholastica, and they have already something in place for archiving in XML: Why archiving is essential for open access journals and how to get started. We can certainly start from there, but it would be good to have an independent streamline in case we decide to change platform.
Planned effort: Approximately 175 hours
Intended skill level: Intermediate, Advanced
Project effort: Half-time
Pre-requisite skills: Latex, XML, Python, Html
Lead mentor: Daniele Marinazzo @Daniele_Marinazzo (Ghent University) – CET timezone
Co-mentor: Konrad Kording @Konrad_Kording (University of Pennsylvania) – EST timezone
Project aims and tasks:
We describe the project structure and approximate work as follows
- Create a pipeline to convert latex papers in xml, this can be a good start Tools for Converting LaTeX to XML (45 hours)
- Adapt the final format to PMC requirements (see above) (30 hours)
- Integrate with the current Scholastica platform (30 hours)
- Explore and prototype a standalone platform (70 hours)
Tech keywords: Latex, XML, Python, Html, DTD (Document Type Definition)