Visualizing Social Networks in Open Notebooks
Increasing the role of automation in the scientific process has long been a fundamental objective of Open Notebook Science. The automatic discovery of new connections in open scientific work is potentially a very important contribution to this end.
Visualizing social networks within and between Open Notebooks is certainly a good first step. Luckily, our Reaction Attempts project has already abstracted the key elements of organic chemical reactions within a collection of Open Notebooks. This means that creating connection maps between people and chemicals can be attempted with reliable and semantically unambiguous database sources.
The Reaction Attempts database records the identity of reactants and products as ChemSpiderIDs for each reaction within a collection of notebooks. Also the name of the researcher, the solvent, the yield (when available) and a few more key identifiers are recorded.
We are very fortunate that Don Pellegrino, an IST student at Drexel, has selected the analysis of networks within Open Notebooks as part of his Ph.D. work. He has started to report his progress on our wiki and is eager to receive any feedback as the work progresses (his FriendFeed account is donpellegrino).
Don's first report is available here. He is using the Open Source software Gephi for visualization and has provided all of the data and code on the associated wiki page. (also see Tony Hirst's description of mapping ONS work which provided some very useful insights) Don has provided a detailed report of his findings but I think the most important can be seen in the global plot below.
This represents a map connecting people through chemicals. The large top right structure represents the connections within the UsefulChem project and the main circle represents the activity of graduate student Khalid Mirza who was the most active on this project. The crescent structure to the right of the circle represents other students - mainly undergraduates - who worked with the same chemicals as Khalid.