@article {Dietze2009GoWeb,
	title = {GoWeb: a semantic search engine for the life science web.},
	journal = {BMC bioinformatics},
	volume = {10 Suppl 10},
	number = {Suppl 10},
	year = {2009},
	pages = {S7+},
	abstract = {BACKGROUND: Current search engines are keyword-based. Semantic technologies promise a next generation of semantic search engines, which will be able to answer questions. Current approaches either apply natural language processing to unstructured text or they assume the existence of structured statements over which they can reason. RESULTS: Here, we introduce a third approach, GoWeb, which combines classical keyword-based Web search with text-mining and ontologies to navigate large results sets and facilitate question answering. We evaluate GoWeb on three benchmarks of questions on genes and functions, on symptoms and diseases, and on proteins and diseases. The first benchmark is based on the BioCreAtivE 1 Task 2 and links 457 gene names with 1352 functions. GoWeb finds 58\% of the functional GeneOntology annotations. The second benchmark is based on 26 case reports and links symptoms with diseases. GoWeb achieves 77\% success rate improving an existing approach by nearly 20\%. The third benchmark is based on 28 questions in the TREC genomics challenge and links proteins to diseases. GoWeb achieves a success rate of 79\%. CONCLUSION: GoWeb{\textquoteright}s combination of classical Web search with text-mining and ontologies is a first step towards answering questions in the biomedical domain. GoWeb is online at: http://www.gopubmed.org/goweb.},
	keywords = {it, ontologies, semantic-web},
	issn = {1471-2105},
	doi = {10.1186/1471-2105-10-S10-S7},
	url = {http://dx.doi.org/10.1186/1471-2105-10-S10-S7},
	author = {Dietze, Heiko and Schroeder, Michael}
}
@article {delaCalle2009BIRI,
	title = {BIRI: a new approach for automatically discovering and indexing available public bioinformatics resources from the literature.},
	journal = {BMC bioinformatics},
	volume = {10},
	number = {1},
	year = {2009},
	month = {October},
	pages = {320+},
	abstract = {BACKGROUND: The rapid evolution of Internet technologies and the collaborative approaches that dominate the field have stimulated the development of numerous bioinformatics resources. To address this new framework, several initiatives have tried to organize these services and resources. In this paper, we present the BioInformatics Resource Inventory (BIRI), a new approach for automatically discovering and indexing available public bioinformatics resources using information extracted from the scientific literature. The index generated can be automatically updated by adding additional manuscripts describing new resources. We have developed web services and applications to test and validate our approach. It has not been designed to replace current indexes but to extend their capabilities with richer functionalities. RESULTS: We developed a web service to provide a set of high-level query primitives to access the index. The web service can be used by third-party web services or web-based applications. To test the web service, we created a pilot web application to access a preliminary knowledge base of resources. We tested our tool using an initial set of 400 abstracts. Almost 90\% of the resources described in the abstracts were correctly classified. More than 500 descriptions of functionalities were extracted. CONCLUSION: These experiments suggest the feasibility of our approach for automatically discovering and indexing current and future bioinformatics resources. Given the domain-independent characteristics of this tool, it is currently being applied by the authors in other areas, such as medical nanoinformatics. BIRI is available at http://edelman.dia.fi.upm.es/biri/.},
	keywords = {bioinformatics, data-mining, it, text-mining},
	issn = {1471-2105},
	doi = {10.1186/1471-2105-10-320},
	url = {http://dx.doi.org/10.1186/1471-2105-10-320},
	author = {de la Calle, Guillermo and Garc\'{\i}a-Remesal, Miguel and Chiesa, Stefano and de la Iglesia, Diana and Maojo, Victor}
}
@article {Dudley2009Quick,
	title = {A quick guide for developing effective bioinformatics programming skills.},
	journal = {PLoS computational biology},
	volume = {5},
	number = {12},
	year = {2009},
	month = {December},
	pages = {e1000589+},
	publisher = {Public Library of Science},
	keywords = {it, methods, programming},
	issn = {1553-7358},
	doi = {10.1371/journal.pcbi.1000589},
	url = {http://dx.doi.org/10.1371/journal.pcbi.1000589},
	author = {Dudley, Joel T. and Butte, Atul J.}
}
@article {Pettifer2009Active,
	title = {An active registry for bioinformatics web services.},
	journal = {Bioinformatics (Oxford, England)},
	volume = {25},
	number = {16},
	year = {2009},
	month = {August},
	pages = {2090{\textendash}2091},
	abstract = {SUMMARY: The EMBRACE Registry is a web portal that collects and monitors web services according to test scripts provided by the their administrators. Users are able to search for, rank and annotate services, enabling them to select the most appropriate working service for inclusion in their bioinformatics analysis tasks. AVAILABILITY AND IMPLEMENTATION: Web site implemented with PHP, Python, MySQL and Apache, with all major browsers supported. (www.embraceregistry.net).},
	keywords = {bioinformatics, it, web},
	issn = {1367-4811},
	doi = {10.1093/bioinformatics/btp329},
	url = {http://dx.doi.org/10.1093/bioinformatics/btp329},
	author = {Pettifer, S. and Thorne, D. and McDermott, P. and Attwood, T. and Baran, J. and Bryne, J. C. and Hupponen, T. and Mowbray, D. and Vriend, G.}
}
