The new world of scholarly communication and e-scholarship is potentially a confusing one, with much opinion about where it should go at this point, but perhaps with little empirical evidence to back up claims. This is a first in a series of blogs where we provide some explanation and useful matrials on various topics under the tag: Scholarly Communication 101. These are not meant to be exhaustive, just useful. As always, feel free to add your own, and comment as needed.

1) Thesaurus, ontology? What do these terms mean?

Controlled vocabularies, ontologies, thesauri, taxonomies;  all are at the core of attempts to structure and integrate information within information systems, and, increasingly, within articles and other forms of unstructured information.  Often, many of these terms are used interchangeably, and trying to define them precisely usually leads to some debate, but essentially they are means by which we structure human knowledge in a form that is more amenable for use within information systems. We know that the richness of language and its exquisite expressiveness is a boon in writing literature, but a nightmare when we are trying to find information. Many words mean the same thing; the same words can mean many different things. Sometimes an information system doesn't have the exact thing I am looking for, but something closely related. By providing human knowledge in a structured form, machines can perform some of the same types of retrieval and inferencing operations that humans do.  A glossary of terms associated with terminological resources can be found here.  It's a little old but still useful.

2) What is green access?  Gold access? Clear access?  What do these colors of open access mean?

Open Access can be delivered in two ways:

• 'green': the author can self-archive at the time of submission of the publication (the 'green' route) whether the publication is grey literature (usually internal non-peer-reviewed), a peer-reviewed journal publication, a peer-reviewed conference proceedings paper or a monograph
• 'gold': the author or author institution can pay a fee to the publisher at publication time, the publisher thereafter making the material available 'free' at the point of access (the 'gold' route). The two are not, of course, incompatible and can co-exist.
• Clear OA – content where both the cost and permissions barriers have been removed (e.g., libre OA)

The 'green' route makes publications available freely in parallel with any publication system but is not, itself, publishing. The 'gold' route is one example of electronic publishing. At present it is much more common to have non-OA electronic access to publications in a publisher's database for a subscription fee. (the above was taken from:  Jeffreys:  Open Access.  An Introduction)

3) Is all open access the same?

Not exactly.  We often think that open access means that I can read the article without having to have a subscription, but there are (of course) more issues at stake:  reader rights, reuse rights, copyright, author posting rights, automatic posting and machine readibility.  A more in depth treatment can be found in Peter Suber's articles.  He has just written a book about open access, which, ironically, isn't open access (although it will be after one year).   To help standardize some of the terminology and in recognition that Open Access-Closed Access is actually a continuum, SPARC, PLoS and OASPA are publishing a guide to open access publishing.  A draft of the guide is available for review. Peter Murray Rust also has a blog on the topic. 

4) Who is Ingelfinger and why does he have his own rule?  Publishing original research.

As scientists, we are taught by our mentors that we can't publish the same original research in more than one place.  In the age of the internet, this practice has led to lots of confusion and argument about whether scientists can use publically available data within new publications, and whether they can release pre-prints on the web before they are published in journals.  Apparently, this practice dates back to Franz J Ingelfinger, editor of the New England Journal of Medicine, in 1969.  According to Wikipedia, the "Ingelfinger Rule" stipulates that a scientist may not publish the same original research in two different outlets.  It was created as an effort to prevent NEJM from losing originality, and the rule was subsequently adopted by several other scientific journals. It has shaped scientific publishing ever since. 

Of course, like many practices adopted and adapted during the "Guttenberg era" (Harnad, 2000), this rule is being questioned by many as to whether it is good for science and perhaps needs to be reconsidered in the Age of the Internet.