W24 Nucleic Acids Research, 2007, Vol. 35, Web Server issue abstract collections (17)] and the still limited possibilities to incorporate eﬀective Natural Processing Techniques for the extraction of additional features from biomedical text. A more detailed description of the status of this fast developing ﬁeld can be found in (18–20). Despite these general limitations in the ﬁeld, the iHOP web interface has become popular among biologists searching for information about the function and relation of the genes and proteins of their interest. To our knowledge, iHOP is the only large-scale text mining resource in biology that is oﬀered as an open web service, we therefore, expect that the novel possibilities described in this work will contribute to the use of iHOP as part of numerous high-throughput analysis environments. AVAILABILITY Information relevant to developers, like detailed docu- mentation of the iHOP web service XML ﬁle format, the URLs required to invoke the REST API, the WSDL document describing SOAP services and usage examples in Perl and Taverna are available at http://www.ihop-net. org/UniPub/iHOP/webservices/. Figure 2. This is a Taverna workﬂow diagram which takes as input some free text (e.g. ‘breast cancer’). The workﬂow fetches the gene and protein symbols related to the input free text, and it returns those symbols, their synonyms and all the abstracts with sentences where the symbols are showing interaction evidences with other protein or gene symbols. Table 2. Logical iHOP web services functionalities. These functionalities and the web services which implement them are focused on automation, so almost all functionalities have more than one input type. So, depending on the API model, some of these functionalities have been implemented more than once, based on each one of the possible input types. Functionality getRelatedSymbols getSymbolsFromReference guessSymbolIdFromSymbolText Inputs Free text (e.g. P53, breast cancer or BRCA2), and an optional NCBI TaxID. A biological database reference (e.g. UniProt accession, NCBI GENE). Free text, and an optional NCBI TaxID. guessSymbolIdFromReference A biological database reference getSymbolInfo getSymbolDeﬁnitions getSymbolInteractions Free text, and an optional NCBI TaxID,or an iHOP gene or protein symbol ID,or a biological database reference. Free text, and an optional NCBI TaxID,or an iHOP gene or protein symbol ID,or a biological database reference. Free text, and an optional NCBI TaxID,or an iHOP gene or protein symbol ID,or a biological database reference. getPubMed A PubMed PMID,or and iHOP abstract ID. Results A list of the possible iHOP identiﬁed gene or protein symbols, related to the input. The iHOP identiﬁed gene or protein symbol related to the input. The iHOP identiﬁed gene or protein symbol related to the input, chosen by na ı¨ve heuristics. The iHOP identiﬁed gene or protein symbol related to the input. The information available at the iHOP server about the iHOP identiﬁed gene or protein related to the input (name, organism, database references, synonyms, etc.). When free text is used, naı¨ ve heuristics have been used to choose the iHOP identiﬁed gene. The abstract sentences available at the iHOP server which uniquely deﬁne the iHOP identiﬁed gene or protein related to the input, along with their score, iHOP abstract ID, journal impact, etc. When free text is used, naı¨ ve heuristics have been used to choose the iHOP symbol. The abstract sentences available at the iHOP server which show evidences about interactions between the iHOP identiﬁed gene or protein symbol related to the input and other iHOP symbols, along with their score, iHOP abstract ID, journal impact, etc. When free text is used, naı¨ ve heuristics have been used to choose the iHOP symbol. iHOP analysed and enriched PubMed abstract associated to the input. All the abstract sentences are annotated, focusing on remarkable sentence elements (verbs, nouns, adjectives, gene or protein symbols, etc.).