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Saturday, February 09, 2019

Comparing Research Journals Quality #1: FAIRness of journal articles

What a traditional research article
looks like. Nice layout, hard to
reuse the knowledge from.
Image: CC BY-SA 4.0.
After Plan S was proposed, there finally was a community-wide discussion on the future of publishing. Not everyone is clearly speaking out if they want open access or not, but there's a start for more. Plan S aims to reform the current model. (Interestingly, the argument that not a lot of journals are currently "compliant" is sort of the point of the Plan.) One thing it does not want to reform, is the quality of the good journals (at least, I have not seen that as one of the principles). There are many aspects to the quality of a research journal. There are also many things that disguise themselves as aspects of quality but are not. This series discusses quality of a journal. We skip the trivial ones, like peer review, for now, because I honestly do not believe that the cOAlition S funders want worse peer review.

We start with FAIRness (doi:10.1038/sdata.2016.18). This falls, if you like, under the category of added value. FAIRness does not change the validness of the conclusions of an article, it just improves the rigor of the knowledge dissemination. To me, a quality journal is one that takes knowledge dissemination seriously. All journals have a heritage of being printed on paper, and most journals have been very slows in adopting innovative approaches. So, let's put down some requirements of the journal of 2020.

First the about the article itself:

About findable

  • uses identifiers (DOI) at least at article level, but possibly also for figures and supplementary information
  • provides data of an article (including citations)
  • data is actively distributed (PubMed, Scopus, OpenCitations, etc)
  • maximizes findability by supporting probably more than one open standard
About accessible
  • data can be accessed using open standards (HTTP, etc)
  • data is archived (possibly replicated by others, like libraries)
About interoperable
  • data is using open standards (RDF, XML, etc)
  • data uses open ontologies (many open standards exist, see this preprint)
  • uses linked data approaches (e.g. for citations)
About reusable
  • data is as complete as possible
  • data is available under an Open Science compliant license
  • data is uses modern and used community standards
Pretty straightforward. For author, title, journal, name, year, etc, most journals apply this. Of course, bigger publishers that invested in these aspects many moons ago can be compliant much easier, because they already were.

Second, what about the content of the article? There we start seeing huge differences.

About findable
  • important concepts in the article are easily identified (e.g. with markup)
  • important concepts use (compact) identifiers
Here, the important concepts are entities like cities, genes, metabolites, species, etc, etc. But also reference data sets, software, cited articles, etc. Some journals only use keywords, some journals have policies about use of identifiers for genes and proteins. Using identifiers for data and software is rare, sadly.

About accessible
  • articles can be retrieved by concept identifiers (via open, free standards)
  • article-concept identifier links are archived
  • table and figure data is annotated with concept identifiers
  • table and figure data can be accessed in an automated way
Here we see a clear problem. Publishers have been actively fighting this for years, even to today. Text miners and projects like Europe PMC are stepping in, but severely hampered by copyright law and publishers not wishing to make exception.

About interoperable
  • concept are describes common standards (many available)
  • table and figure data is available as something like CSV, RDF
Currently, the only serious standard used by the majority of (STM?) journals are MeSH terms for keywords and perhaps CrossRef XML for citations. Table and figures are more than just a graphical representations. Some journals are experimenting with this.

About reusable
  • the content of the article has a clear licence, Open Science compliant
  • the content is available with relevant standards of now
This is hard. These community standards are a moving target. For example, how we name concepts changes over time. But also identifiers themselves change over time. But a journal can be specific and accurate, which ensures that even 50 years from now, the context of the content can be determined. Of course, with proper Open Science approaches, translation to then modern community standards is simplified.

There are tons of references I can give here. If you really like these ideas, I recommend:
  1. continue reading my blog with many, many pointers
  2. read (and maybe sign) our Open Science Feedback to the Guidance on the Implementation of Plan S (doi:10.5281/zenodo.2560200), where many of these ideas are part of


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