Welcome. We have used our bioNerDS software to automatically extract database and software name mentions from the open access subset of PubMed Central. We then form pairs of these names based on their proximity in text. Combining all these pairs together across the literature, we form method networks of resources, which help to define the methods used within bioinformatics.
A paper which contains an analysis of the networks found on this site, and which further explains our methodology is now available:
Duck, G., Nenadic, G., Brass, A., Robertson, DL., and Stevens, R. Extracting patterns of database and software usage from the bioinformatics literature. Bioinformatics (2014). Link
In particular, the extracted resource data can be found here, the scripts used can be downloaded here, and the resulting networks can be found here.
Geraint Duck wrote the required scripts, and performs the required data analysis and pair extraction. Andy Brass provided statistical assistance, while Robert Stevens, Goran Nenadic and David Robertson helped supervise the project.