Saturday, December 19, 2009

ORCID -- an international research identification system?

From the Nature news article titled "Credit where credit is due" in (462:7275, p. 825 on December 17, 2009), I came cross the ORCID initiative:
Name ambiguity and attribution are persistent, critical problems imbedded in the scholarly research ecosystem. The ORCID Initiative represents a community effort to establish an open, independent registry that is adopted and embraced as the industry’s de facto standard. Our mission is to resolve the systemic name ambiguity, by means of assigning unique identifiers linkable to an individual's research output, to enhance the scientific discovery process and improve the efficiency of funding and collaboration.
Overall, I think it is a good idea. If properly implemented and widely adopted, ORCID could help solve lots of issues associated with various ways of spelling a person's name due to, e.g., cultural differences. For example, put Chinese way, one's family name comes before one's given name, just the opposite of the western convention. Additionally, when a given name has two characters (quite common), there are could be a space or a hyphen (as I normally put in Xiang-Jun) or nothing in between. Combined with possible first name initials, there are already many ways to spell out a Chinese name.

The above Nature article, “Credit Where Credit is Due”, helps introduce the ORCID Initiative. As an specific example, it points to another article on page 843, where Nature profiles a research group trying to "complete the reference human genome sequence, which is still full of errors nearly a decade after the first draft was announced in 2000." Nature acknowledges that "It is essential work", "But it is also work that offers few academic rewards beyond the satisfaction of a job well done — it is unlikely to result in a high profile publication." Hopefully, by adopting the ORCID system, contributions of such types (e.g., software support and maintenance) would be more properly acknowledged by the scientific community.

Given the high profile of the founding parties, I am hopeful that the ORCID initiative would move forward as promised. I will keep an eye on it and see how it evolves.

Friday, December 18, 2009

Ribosomal structure: it helps to know some background information

This year's Nobel Prize in Chemistry has been awarded to Venki Ramakrishnan, Tom Steitz, and Ada Yonath "for studies of the structure and function of the ribosome."

My connection with ribosomal structure began with the 50S large subunit of Haloarcula marismortui solved by Tom Steitz's group. Ever since the fully refined crystal structure at 2.4 Å resolution was published in 2001 (PDB entry: 1jj2; NDB code: rr0033), I have been using it to check 3DNA's applicability. In the two 3DNA papers (2003 NAR and 2008 NP), 1jj2 was used as an example to illustrate how find_pair can identify higher-order base-associations in complicated RNA containing structures. At the time, though, my understanding of the ribosomal RNA structure was purely geometrical: for quite a while, I got overwhelmed by the various biological terminologies, including the various S-es: 50S large ribosomal subunit vs. the 23S and 5S rRNA; and of course, the 30S small subunit vs. 16S rRNA.

Over the past year or so, I have become more interested in RNA structures. After reading a lot of related articles, gradually I feel things are becoming clearer than before. Nevertheless, there is something still missing, since my focus has (mostly) been on recent X-ray crystal structure-related work. My understanding of the ribosomal structure was finally put into context, thanks to following two recent publications:
These two papers not only summarized the significance of work of the three Nobel laureates — "the atomic resolution structures of the ribosomal subunits provide an extraordinary context for understanding one of the most fundamental aspects of cellular function: protein synthesis" — but also provided background information of decades of work from other players, including Harry Noller, Peter Moore, and Joachim Frank. Solving the ribosomal structure serves as a good example of how the fact that scientific research is both cooperative and competitive in nature.