Ten days ago I mentioned a paper by Zhiyong Lu that gives an overview over the available web tools to search the biomedical literature. Most of these tools enhance the PubMed service, and Zhiyong Lu in fact works for the NCBI, the developer of PubMed. In this post I want to take a more detailed look at the available tools. A good starting point is the companion webpage to the paper, listing 28 services.
Zhiyong Lu recently published an excellent overview of the web tools that are currently available to search the biomedical literature. The article has also a companion web page that allows user to filter for the features they are interested in, and to report new tools. The author describes 28 tools developed specifically for the biomedical domain. The tools are grouped based on their most important features into 1. Ranking search results 2.
On Monday I gave a presentation about ORCID, based on the ORCID Principles. The slides are hopefully a good introduction to ORCID and the current status of the initiative. A good in-person update of the ORCID initiative is the next ORCID Participant Meeting that takes place May 18 in Boston. Registration is free and everybody interested in unique identifiers for scholarly authors is invited to attend. More information at the ORCID website.
The recent tragic events in Japan have made it difficult or impossible for many Japanese scientists to continue their work. The newly launched Nippon Science Support Network has therefore established a database of positions and stipends in other countries for Japanese students, research fellows and scientific personnel.
We are all familiar with digital object identifiers (DOIs) provided by CrossRef to identify (and link to) journal articles. Some of us are familiar with the DOIs issued by DataCite to link to datasets. But most of us don’t know that CrossRef is also providing component DOIs that can provide persistent links to a particular table or figure in a paper.
Version 2.1 of the reference manager Zotero was released last Friday. The biggest change for me is the support of Citation Style Language (CSL) 1.0. CSL is an open XML-based standard for citations and bibliographies. Older versions of Zotero used CSL 0.8.1, but the improved CSL 1.0 was released a year ago.
The history of HTML begins 1989 at CERN, the European Laboratory for Particle Physics in Geneva. Tim Berners-Lee, Robert Cailliau and colleagues invented HTML (as well as the transport protocol HTTP and the web browser) to facilitate collaboration between CERN physicists. HTML was originally invented for scholarly communication, but of course by the mid-1990s was also used by everybody else.
The best and quickest discussions of a scientific paper now sometimes happen in science blogs rather than in the peer-reviewed literature. Whereas we have a number of scholarly databases that track citations between papers, we don’t have the same tools for science blogs.
The reference management software Papers has been a regular topic on this blog.
The bibliography of a scholarly paper is interesting and important reading material. You can see whether the authors have cited the relevant literature, and you often find references to interesting papers you didn’t know about. Bibliographies are obviously also needed to count citations, and then do all kinds of useful and not so useful things with them. Unfortunately almost all bibliographies are in the wrong format.
One of the annoyances with bibliographies as we use them for scholarly papers is that is usually unclear why a particular paper was cited. It is often possible for readers to gather this information by looking at the citation in the context of the surrounding text, but this is very difficult to automate.