This interface is designed for an easier and more comprehensive exploration of a set of publications from PubMed and other sources in the context of the RIMICIA project. It allows revising the articles sorting them by different criteria, classifying in subgroups, highlighting important information or exploring their citation network, among other things.
The interface is divided in four main sections:
(top-left)
The table lists all papers within the set, one per row. Click on any row to display the details for this paper in the "Details" section (see below). The fields (columns) are:
The table can be sorted by any field clicking the corresponding column header (press the header again to reverse the sort order). This is useful, for example, to have at the top of the list the highly cited papers, the reviews, the newer articles, ... etc.
(top-right)
This section displays the title and abstract of a given article. Relevant MeSH terms are highlighted coloring them according with the following schema: diseases, chemical compounds, microorganisms, other MeSH categories relevant for the project (right now "foods", "body parts and fluids" and "age"). Additionally generic terms of interest (either belonging to the MeSH vocabulary or not) can be entered by the user and they will be highlighted in purple. (See "Enter new highlighted terms" below).
Although MeSH terms are only associated to PubMed articles, instances of them mentioned in articles from other sources are also highlighted. Similarly, for a particular PubMed entry, all mentions in its title/abstract of any MeSH of the whole set are highlighted, irrespective of whether they are indexed for that particular article or not.
This section also includes at the top the reference and the type of article, as well as the article ID, which is a link to the article record in the corresponding database. At the bottom, links to clinical trial databases are included if available, which lead to the corresponding record in these databases with all the details on the clinical trial associated to the publication.
(bottom-left)
This table contain the whole list of MeSH terms associated to the PubMed articles in the set, as well as the terms introduced by the user (See "Enter new highlighted terms" below).
Mesh terms are sorted by their frequencies in the set of articles where they are indexed. The user-introduced terms always appear at the top of the table irrespective of their frequencies. For each term, the following information is shown:
(bottom-right)
This section shows the network of internal citations between the papers. Only PubMed articles are include here.
Each node represents a paper and each arrow a citation, going from the citing paper to the cited paper. Nodes are colored by the number of internal citations received, from dark blue (less) to yellow (more). Papers that don't participate in any internal citation (either citing or getting cited) are not included in the network.
Use the mouse wheel to zoom in/out the network. Drag the mouse in the background (outside any node) to pan/move the representation. It is possible to move the nodes to different places dragging them with the mouse.
Use the "[+]" menu to change the layout of the network. Note: this can "freeze" for large networks. Use this feature for small networks only (~<2000 nodes).
You can left-click on any node to show the details of the corresponding paper on the Details section (see above). Selected nodes, whose details are shown in the Details Box, are circled in pink . Articles selected in the "article list" or "MeSH terms" sections (see above) are also highlighted in this network. You can right-click on any node to highlight its connections: blue for incoming citations and red for outgoing citations. Left-click in any part of the network to clear the highlighting.
This functionality allows the user to assign tags to papers. These will be shown in the "Tag" field of the Article List. To tag papers select one or more items from the Article List by checking the corresponding box(es) in the "Sel." column. Then you can either tag these articles as important or use custom tags:
Note: You can click in the "Tag" field from the papers table header to sort the papers by tag.
This tool allows the user to (temporary) remove papers from the Article List.
First, select the paper(s) you want to delete by checking the corresponding box(es) in the "Sel." column, and then press "Del. selection". These papers will disappear from the table. To see the list of "deleted" papers, press "Go to deleted->". In this new table you can select deleted papers and press "Undelete selection" to move them back to the Article List. Press "<-Return" to leave this deleted papers table and return to the main Article List.
This tool allows the user to enter new terms that will be highlighted in purple.
For that, press "Enter new terms" to display a new dialog box and there, write the new terms in the text box. You can enter them one by one, pressing "Add" after writing each of the new terms, or you can enter many at once, separated by ";". You can also delete the list of user terms by pressing "Clear". After making all the changes (either adding or deleting), it's necessary to press "Save changes". Press "Enter new terms" again to hide the dialog box.
Any word that contains one of the user terms will be colored in purple. User terms must be at least three characters long. Terms written in lower case will match either upper case, lower case or mixed, but terms written in upper case will only match upper case. When entering acronyms, it's recommended to write them in upper case, to avoid unwanted matches (e.g. the term "RNA" should be enter in upper case to avoid matching words that contain "rna" such as "alternative").
Note: Make sure your new terms are colored in purple in the "Added" list. If not, you might have forgotten to press "Save changes".
Use your web browser "Save page" functionality to save the current work session as a HTML file. Select "web page COMPLETE" option if available. For example, in Firefox, go to "Menu > Save page as" and make sure the "Web page, complete" option is selected.
To recover a saved session, just open the corresponding HTML file.