FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization

Single nucleotide polymorphism (SNP) prioritization based on the phenotypic risk is essential for association studies. Assessment of the risk requires access to a variety of heterogeneous biological databases and analytical tools. FASTSNP (function analysis and selection tool for single nucleotide polymorphisms) is a web server that allows users to efficiently identify and prioritize high-risk SNPs according to their phenotypic risks and putative functional effects. A unique feature of FASTSNP is that the functional effect information used for SNP prioritization is always up-to-date, because FASTSNP extracts the information from 11 external web servers at query time using a team of web wrapper agents. Moreover, FASTSNP is extendable by simply deploying more Web wrapper agents. To validate the results of our prioritization, we analyzed 1569 SNPs from the SNP500Cancer database. The results show that SNPs with a high predicted risk exhibit low allele frequencies for the minor alleles, consistent with a well-known finding that a strong selective pressure exists for functional polymorphisms. We have been using FASTSNP for 2 years and FASTSNP enables us to discover a novel promoter polymorphism. FASTSNP is available at

Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma genes Online)

BACKGROUND: The significant advances in microarray and proteomics analyses have resulted in an exponential increase in potential new targets and have promised to shed light on the identification of disease markers and cellular pathways. We aim to collect and decipher the HCC-related genes at the systems level. RESULTS: Here, we build an integrative platform, the Encyclopedia of Hepatocellular Carcinoma genes Online, dubbed EHCO , to systematically collect, organize and compare the pileup of unsorted HCC-related studies by using natural language processing and softbots. Among the eight gene set collections, ranging across PubMed, SAGE, microarray, and proteomics data, there are 2,906 genes in total; however, more than 77% genes are only included once, suggesting that tremendous efforts need to be exerted to characterize the relationship between HCC and these genes. Of these HCC inventories, protein binding represents the largest proportion (~25%) from Gene Ontology analysis. In fact, many differentially expressed gene sets in EHCO could form interaction networks (e.g. HBV-associated HCC network) by using available human protein-protein interaction datasets. To further highlight the potential new targets in the inferred network from EHCO, we combine comparative genomics and interactomics approaches to analyze 120 evolutionary conserved and overexpressed genes in HCC. 47 out of 120 queries can form a highly interactive network with 18 queries serving as hubs. CONCLUSION: This architectural map may represent the first step toward the attempt to decipher the hepatocarcinogenesis at the systems level. Targeting hubs and/or disruption of the network formation might reveal novel strategy for HCC treatment

From Wrapping to Knowledge

One the most challenging problems for Enterprise Information Integration is to deal with heterogeneous information sources on the Web. The reason is that they usually provide information that is in human-readable form only, which makes it difficult for a software agent to understand it. Current solutions build on the idea of annotating the information with semantics. If the information is unstructured, proposals such as S-CREAM, MnM, or Armadillo may be effective enough since they rely on using natural language processing techniques; furthermore, their accuracy can be improved by using redundant information on the Web, as C-PANKOW has proved recently. If the information is structured and closely related to a back-end database, Deep Annotation ranges among the most effective proposals, but it requires the information providers to modify their applications; if Deep Annotation is not applicable, the easiest solution consists of using a wrapper and transforming its output into annotations. In this paper, we prove that this transformation can be automated by means of an efficient, domain-independent algorithm. To the best of our knowledge, this is the first attempt to devise and formalize such a systematic, general solution.Comisión Interministerial de Ciencia y Tecnología TIC2003-02737-C02-0

Reconfigurable Web Wrapper Agents for Web Information Integration

In this paper, we presented a tool to exploit online Web data sources using reconfigurable Web wrapper agents. We described how these agents can be rapidly generated and executed based on the script language WNDL and extraction rule generator IEPAD. WNDL is an XML-based language that provides a representation of a Web browsing session. A WNDL script describes how to locate the data, extract the data and combine the data. By executing different WNDL scripts, user can automate virtually all types of Web browsing sessions. We also describe IEPAD, a data extractor based on pattern discovery techniques. IEPAD allows our software agents to automatically discover the extraction rules to extract the contents of a structurally formatted Web page without the need to label a Web page to train a wrapper. With a programming-by-example authoring tool, a user can generate a complete Web wrapper agent by browsing the target Web sites. We have built a variety of applications to demonstrate the feasibility of our approach.

Reconfigurable Web Wrapper Agents for Web Information Integration

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