The NIF search box now can be used to search not just the full text of papers but also to restrict search to individual sections, e.g., methods, discussion, acknowledgements. For example, users looking for papers that used antibodies to a particular protein or resource providers who want to see who is using their database or tool can restrict search to just the methods section (see Figures 1 and 2 below). We encourage users to play with this feature. Be mindful that this is a filter, so turning it off before moving onto a new search may be required to get the expected result set. Refreshing the entire page will also turn off the filter.
The job of NIF is to connect researchers to resources. Over the past few years, NIF has been providing Pub Med with a list of link outs from individual papers to data, materials and tools using their Link Out feature. Now, these link outs can be viewed directly within NIF literature. For example, this paper dealing with pigeon calcium binding proteins, lists 3 antibodies as LinkOuts (Figure 3). These exact antibodies were used in the paper.
A preview of the new NIF annotation function for the literature is now available. Using this feature, NIF users will be able to create and store annotations on top of the open access papers using the DOMEO tool (documentation available here http://annotationframework.org/). These annotations will be used to make it easier for users within MyNIF to keep track of their papers, but more importantly, will help make the NIF better by allowing us to link these annotations to additional information like resources. We will be hosting several in depth tutorials on NIF annotation at the upcoming Society for Neuroscience meeting in October. In the meanwhile, feel free to play with the tool. Here is a brief tutorial:
Clicking the annotate button will open the DOMEO tool in a default NIFuser that makes all of the annotations public (Figure 4).
DOMEO annotations are viewable by clicking on the right hand side yellow tab, and they can be made by selecting text and clicking on either the text mine button or the annotate button. Text mining will give a suggestion for the section text mined (Figure 5 shows the results for chemokine receptor that can now be given a thumbs up or down).
Annotations can be thought of as notes. These annotations will be made available to anyone viewing this paper in DOMEO and in a few weeks also through the NIF interface and PubMed as LinkOuts.