The feedback we had when we spoke to some friends at caBIG was that this was no big surprise as their efforts had been directed at the US biomedical enterprise and they had not made any serious investment in promoting their offering in Europe...
We thought the headline of the article ("European cancer researchers failing to use research tools") might raise a few eyebrows with other friends of ours at research institutes across the UK who most certainly are using research tools - so we thought we'd set about finding out what tools are available in Europe and who is using what.
First stop, the European Bioinformatics Institute - OK, so they don't focus on cancer, but the tools they offer clearly have an application in various aspects of cancer research - in their own words, the most popular of them "include tools for the analysis and comparison of nucleotide and protein sequences, data from functional genomics experiments, text mining of the scientific literature and tools for determination and visualisation of macromolecular structures. All these tools can be accessed over the web and most provide Web Services interfaces using SOAP orREST APIs."
For more detail, see the EBI tools page - but in summary, they offer tools covering:
- Nucleotide sequence searches x2 (across various database including EMBL-Bank, Coding Sequences, immunoglobulins and High throughput cDNA)
- Protein sequence searches x2 (across database including UniProtKB, sequences derived from macro molecular structures, immunoglobulins and sequences from patents)
- Multiple sequence alignment tools x5!
- Pairwise sequence alignment tools x2
- Functional genomics tools x3
- Potein function analysis tools x4
- Molecular structural analysis tools x2
- Scientific literature text mining tools x2
- And five data retrieving and ID mapping services: