Nucleic Acids Research, 2007, Vol. 35, Web Server issue W23 Figure 1. Schema of operations of iHOP web services. Each box is a web service, and double boxes are the recommended starting points for workﬂows. Links show some suggested ﬂows between services that are useful for workﬂow building. Green links represent bi-directional ﬂow, and black arrowed blue lines mean uni-directional ﬂow. Grey thick lines illustrate bidirectional external access and orange dashed lines are accesses to the iHOP core (http://www.ihop-net.org/). Taverna 1.4 and 1.5 are discouraged, because SOAP services results are pruned. Taverna 1.5.1 solves these and other issues, and it is recommended. Older versions, like Taverna 1.3.1, also work, but they have many limitations related to BioMOBY services. RESULTS AND DISCUSSION A proof for the functionality, completeness and usefulness of the iHOP web service APIs are a number of collab- orative projects that make programmatic use of iHOP content. Table 3 contains a brief list of the projects where iHOP web services have been used, and Figure 3 shows a CARGO (Cases et al., submitted to NAR-WEB 2007) widget using information provided by iHOP CGI-XML services. In the context of the use of iHOP as a web service it is necessary to be aware of the current limitations of biological text mining. BioCreAtIvE (12) and other blind community assessments (13) have clearly shown that name identiﬁcation and in particular matching gene/name in the literature with the corresponding database entries is a hard problem and the best systems are still far from perfect (14). Our own evaluation of iHOP in 2005 (15) shows that in model organisms the average precision is around 94% and the recall around 87%. Even if the inclusion of additional reﬁnements and dictionaries is producing continuous progress the poor adhesion of the community to naming standards (16) will continue creating problems in this area. Other obvious limitations of iHOP and all other current text mining systems are imposed by the limited availability of full text sources [main reason for the common use of