ChickVD: a sequence variation database for the chicken genome

Working in parallel with the efforts to sequence the chicken (Gallus gallus) genome, the Beijing Genomics Institute led an international team of scientists from China, USA, UK, Sweden, The Netherlands and Germany to map extensive DNA sequence variation throughout the chicken genome by sampling DNA from domestic breeds. Using the Red Jungle Fowl genome sequence as a reference, we identified 3.1 million non-redundant DNA sequence variants. To facilitate the application of our data to avian genetics and to provide a foundation for functional and evolutionary studies, we created the ‘Chicken Variation Database’ (ChickVD). A graphical MapView shows variants mapped onto the chicken genome in the context of gene annotations and other features, including genetic markers, trait loci, cDNAs, chicken orthologs of human disease genes and raw sequence traces. ChickVD also stores information on quantitative trait loci using data from collaborating institutions and public resources. Our data can be queried by search engine and homology-based BLAST searches. ChickVD is publicly accessible at http://chicken.genomics.org.cn

Search and Discovery Tools for Astronomical On-line Resources and Services

A growing number of astronomical resources and data or information services are made available through the Internet. However valuable information is frequently hidden in a deluge of non-pertinent or non up-to-date documents. At a first level, compilations of astronomical resources provide help for selecting relevant sites. Combining yellow-page services and meta-databases of active pointers may be an efficient solution to the data retrieval problem. Responses generated by submission of queries to a set of heterogeneous resources are difficult to merge or cross-match, because different data providers generally use different data formats: new endeavors are under way to tackle this problem. We review the technical challenges involved in trying to provide general search and discovery tools, and to integrate them through upper level interfaces.Comment: 7 pages, 2 Postscript figures; to be published in A&A

Promoting the digital literacy of undergraduate historians using digitised historic newspapers

Mass digitisation offers new possibilities for learning and teaching in higher education by making primary sources such as newspapers much more accessible for teaching. However, as Hawkins & Gildart (2010) report, in practice promoting the digital literacy of historians can be very challenging. However, the more recent experience of the author using Chronicling America for undergraduate Level 6 teaching suggests that students engage more enthusiastically with digitised historic newspapers and have a more positive experience when in particular searching functionality (i.e. the functionality of the search engine) is designed to optimise user engagement

A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms

We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms ( SNPs). This map is based on a comparison of the sequences of three domestic chicken breeds ( a broiler, a layer and a Chinese silkie) with that of their wild ancestor, red jungle fowl. Subsequent experiments indicate that at least 90% of the variant sites are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about five SNPs per kilobase for almost every possible comparison between red jungle fowl and domestic lines, between two different domestic lines, and within domestic lines - in contrast to the notion that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100 kilobases

The uncertain representation ranking framework for concept-based video retrieval

Concept based video retrieval often relies on imperfect and uncertain concept detectors. We propose a general ranking framework to define effective and robust ranking functions, through explicitly addressing detector uncertainty. It can cope with multiple concept-based representations per video segment and it allows the re-use of effective text retrieval functions which are defined on similar representations. The final ranking status value is a weighted combination of two components: the expected score of the possible scores, which represents the risk-neutral choice, and the scores’ standard deviation, which represents the risk or opportunity that the score for the actual representation is higher. The framework consistently improves the search performance in the shot retrieval task and the segment retrieval task over several baselines in five TRECVid collections and two collections which use simulated detectors of varying performance

Automatic Discovery and Ranking of Synonyms for Search Keywords in the Web

Search engines are an indispensable part of a web user's life. A vast majority of these web users experience difficulties caused by the keyword-based search engines such as inaccurate results for queries and irrelevant URLs even though the given keyword is present in them. Also, relevant URLs may be lost as they may have the synonym of the keyword and not the original one. This condition is known as the polysemy problem. To alleviate these problems, we propose an algorithm called automatic discovery and ranking of synonyms for search keywords in the web (ADRS). The proposed method generates a list of candidate synonyms for individual keywords by employing the relevance factor of the URLs associated with the synonyms. Then, ranking of these candidate synonyms is done using co-occurrence frequencies and various page count-based measures. One of the major advantages of our algorithm is that it is highly scalable which makes it applicable to online data on the dynamic, domain-independent and unstructured World Wide Web. The experimental results show that the best results are obtained using the proposed algorithm with WebJaccard