Gobbledygook

Thank you PLOS

Starting next week I will work as the DataCite Technical Director, and I am excited about this new opportunity. But this is material for another post, here I want to reflect on the last three years working as Technical Lead for the PLOS Article-Level

doi

Component DOIs Revisited

Four years ago I wrote a blog post about component DOIs. It is time to revisit the topic, in particular since our approach to citing data associated with a publication has changed since 2011. Component DOIs are explained in the CrossRef Help System: DOIs

work

Why should we work where we live?

At the SciFoo Camp this weekend Erin McKiernan and I moderated an unconference session on the topic Why should we work where we live? This was a spontaneous idea after we had talked about this topic on Friday (Erin lives in Mexico with a

pid

Persistent Identifiers and URLs

Just like the rest of the internet, much of our scholarly infrastructure is built around the Hypertext Transfer Protocol (HTTP), increasingly HTTPS for security, and soon HTTP/2 for better performance. In this infrastructure Universal Resource Locators (URLs) are essential to locate resources (sic)

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Human-readable and machine-readable Persistent Identifiers

Yesterday Julie McMurry and co-authors published a preprint 10 Simple rules for design, provision, and reuse of persistent identifiers for life science data (McMurry et al., 2015). This is an important paper trying to address a fundamental problem: how can we make persistent identifiers

markdown

Introducing the Scholarly Markdown Bundle

Using Markdown to author scholarly documents is an attractive alternative to the standard authoring tools Microsoft Word and LaTeX. The feeling shared by many is that Scholarly Markdown is 80% there, and that more effort is needed for the remaining 20% - moving markdown

markdown

Blogging Beyond Jekyll

This blog has been on four different platforms since starting in 2007: a custom blogging engine and then Movable Type on Nature Network 2007-2010, Wordpress on the PLOS Blogs Network 2010-2013, and the static blogging engine Jekyll hosted on Github Pages since 2013. It

pandoc

Metadata in Microsoft Word documents

Metadata such as author, title, journal or persistent identifier are essential for scholarly documents, and some of us are spending a significant part of our time adding or fixing metadata. Unfortunately we sometimes don’t pay enough attention to the flow of metadata, i.

github

First analysis of software metrics

Last week I wrote about software.lagotto.io, an instance of the lagotto open source software collecting metrics for the about 1,400 software repositories included in Sciencetoolbox. In this post I want to report the first results analyzing the data. If you want

itunes

Why there is no iTunes for science papers

The iTunes Store was opened by Apple in 2003 to sell digital music and other digital assets. Since 2009 music purchased in the iTunes store is free of Digital Rights Management (DRM). Apple became the largest music vendor worldwide in 2010, and by 2013

software

Metrics for scientific software

One of the challenges of collecting metrics for scholarly outputs is persistent identifiers. For journal articles the Digital Object Identifier (DOI) has become the de-facto standard, other popular identifiers are the pmid from PubMed, the identifiers used by Scopus and Web of Science, and

citation

Manifests and Reference Lists

Last month at the Force15 conference in Oxford Ian Mulvany and I ran a workshop on data citation support in reference managers. The report of that workshop isn’t done yet, but I can say that it was a success - we now have

data

Data Citation Support in Reference Managers

This is the title of an upcoming workshop next Sunday organized by Ian Mulvany and myself. The workshop is a pre-conference event of the Force15 conference in Oxford. This blog post summarizes some of the issues and work that needs to be done. Data

citation

Webinar on Writing Zotero Translators

In a blog post two weeks ago I argued for the need for reference managers to properly support data citation, if we want data citation to become a standard activity. I am happy to announce two events working towards that goal. November 3rd: Webinar

barcamp

Let's do an unconference

This year’s SpotOn London conference takes place November 14-15 and the registration has opened this Monday. I am helping organize this conference since 2009, and I again look forward to the sessions, and - more importantly - the discussions with people in and

citation

Please keep it simple: citations, links and references

In my last post I wrote about the importance of keeping things simple in scholarly publishing, today I want to go into more detail with one example: citations in scholarly documents. LEGO scientists discuss how they can cite their dataCitations are an essential part

Please keep it simple

Doing scientific research is becoming increasingly complex, both in terms of the tools and technologies used, and in the collaboration across disciplines and locations that is increasingly commonplace. While the way we write up and publish research is of course also very different from

markdown

CommonMark and the Future of Scholarly Markdown

One of the important outcomes of the Markdown for Science workshop that took place in June 2013 was a decision on a name - Scholarly Markdown - and a brief definition: Markdown that supports the requirements of scientific textsMarkdown as format that glues open

word

Using Microsoft Word with git

One of the major challenges of writing a journal article is to keep track of versions - both the different versions you create as the document progresses, and to merge in the changes made by your collaborators. For most academics Microsoft Word is the

markdown

Introducing Rakali

In July and August I attended the Open Knowledge Festival and Wikimania. At both events I had many interesting discussions around open source tools for open access scholarly publishing, and I was part of a panel on that topic at Wikimania last Sunday. Some

visualization

Visualizing Scholarly Content

One topic I will cover this Sunday in a presentation on Open Scholarship Tools at Wikimania 2014 together with Ian Mulvany is visualization. Data visualization is all about telling stories with data, something that is of course not only important for scholarly content, but

doi

What is a DOI?

This Sunday Ian Mulvany and I will do a presentation on Open Scholarship Tools at Wikimania 2014 in London. From the abstract: This presentation will give a broad overview of tools and standards that are helping with Open Scholarship today.One of the four

doi

Fragment Identifiers and DOIs

Before all our content turned digital, we already used page numbers to describe a specific section of a book or longer document, with older manuscripts using the folio before that. Page numbers have transitioned to electronic books with readers such as the Kindle supporting

markdown

One Ring to Rule them All

One Ring to rule them all, One Ring to find them, One Ring to bring them all and in the darkness bind them.Yesterday 60 years ago the first volume of the Lord of the Rings trilogy by J.R.R. Tolkien was published.

citeproc

Don't Reinvent the Wheel

In a post last week I talked about roads and stagecoaches, and how work on scholarly infrastructure can often be more important than building customer-facing apps. One important aspect of that infrastructure work is to not duplicate efforts. Image by Cocoabiscuit on FlickrA good