| 1. |
- Backofen, Rolf, et al.
(författare)
-
Requirements and specification of bioinformatics use cases
- 2005
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- This deliverable specifies use cases based on bioinformatics research carried out by members ofA2. The use cases involve the use of rules to reason over ontologies and pathways (Dresden,Edinburgh, Paris, Linköping) and rules to specify workflows to integrate bioinformatics data (Lisbon, Skövde, Jena, Bucharest). The use cases are designed as a reference point to foster the take up of A2 use cases by I-work packages. Most notably, many of the use cases specify the need for querying and reactivity with languages like Xcerpt (I4), Erus (I5) and Prova (I5). The use cases range from basic research applications to fully deployed software with an international user base.
|
|
| 2. |
|
|
| 3. |
- Backofen, Rolf, et al.
(författare)
-
Usage of bioinformatics tools and identification of information sources
- 2005
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Bioinformatics is an important application area for semantic web technologies as much of the data is online and accessible in XML format, as some sites already support web services, and as ontologies are widely used to annotate data. In this deliverable, we give a survey over 18 of the most important bioinformatics resources and discuss their availability and accessibility, which are two of the main criteria for these resources to act as bases for later demonstrators.
|
|
| 4. |
|
|
| 5. |
- Bastian, Patrick J., et al.
(författare)
-
Insignificant Prostate Cancer and Active Surveillance: From Definition to Clinical Implications
- 2009
-
Ingår i: European Urology. - : Elsevier BV. - 1873-7560 .- 0302-2838. ; 55:6, s. 1321-1332
-
Forskningsöversikt (refereegranskat)abstract
- Context: Due to early detection strategies, prostate cancer is diagnosed early in its natural history. It remains unclear whether all patients diagnosed with prostate cancer warrant radical treatment or may benefit from delayed intervention following active surveillance. Objective: A systematic review of active surveillance protocols to investigate the inclusion criteria for active surveillance and the outcome of treatment. Evidence acquisition: Medline was searched using the following terms: prostate cancer, active surveillance and expectant management for dates up to October 2008. Further studies were chosen on the basis of manual searches of reference lists and review papers. Evidence synthesis: Numerous studies on active surveillance were identified. The recent inclusion criteria of the studies are rather similar. Keeping the short follow-up of all studies in mind, the majority of men stay on active surveillance, and the percentage of patients receiving active treatment is as high as 35% of all patients. Once a patients requires active treatment, most patients still present with curable prostate cancer. Furthermore, only few deaths due to prostate cancer have occurred. Conclusions: Active surveillance is an alternative option to immediate treatment of men with presumed insignificant prostate cancer. It seems that criteria used to identify men with low-risk prostate cancer are rather similar, and immediate treatment of men meeting these criteria may result in an unnecessary number of treatments in these highly selected patients. Data from randomised trials comparing active surveillance and active treatment will provide additional insight into outcome and follow-up strategies. (C) 2009 Published by Elsevier B.V. on behalf of European Association of Urology.
|
|
| 6. |
|
|
| 7. |
- Doms, Andreas, et al.
(författare)
-
Ontologies and Text Mining as a Basis for a Semantic Web for the Life Sciences
- 2006
-
Ingår i: Reasoning Web, Second International Summer School. - Berlin, Heidelberg : Springer Berlin/Heidelberg. - 9783540384090 ; , s. 164-183
-
Bokkapitel (refereegranskat)abstract
- This book presents thoroughly arranged tutorial papers corresponding to lectures given by leading researchers at the Second International Summer School on Reasoning Web in Lisbon, Portugal, in September 2006. Building on the predessor school held in 2005 and published as LNCS 3564, the ten tutorial lectures presented provide competent coverage of current topics in semantic Web research and development.
|
|
| 8. |
- Jakonienė, Vaida, 1974-
(författare)
-
Integration of Biological Data
- 2006
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Data integration is an important procedure underlying many research tasks in the life sciences, as often multiple data sources have to be accessed to collect the relevant data. The data sources vary in content, data format, and access methods, which often vastly complicates the data retrieval process. As a result, the task of retrieving data requires a great deal of effort and expertise on the part of the user. To alleviate these difficulties, various information integration systems have been proposed in the area. However, a number of issues remain unsolved and new integration solutions are needed.The work presented in this thesis considers data integration at three different levels. 1) Integration of biological data sources deals with integrating multiple data sources from an information integration system point of view. We study properties of biological data sources and existing integration systems. Based on the study, we formulate requirements for systems integrating biological data sources. Then, we define a query language that supports queries commonly used by biologists. Also, we propose a high-level architecture for an information integration system that meets a selected set of requirements and that supports the specified query language. 2) Integration of ontologies deals with finding overlapping information between ontologies. We develop and evaluate algorithms that use life science literature and take the structure of the ontologies into account. 3) Grouping of biological data entries deals with organizing data entries into groups based on the computation of similarity values between the data entries. We propose a method that covers the main steps and components involved in similarity-based grouping procedures. The applicability of the method is illustrated by a number of test cases. Further, we develop an environment that supports comparison and evaluation of different grouping strategies.The work is supported by the implementation of: 1) a prototype for a system integrating biological data sources, called BioTRIFU, 2) algorithms for ontology alignment, and 3) an environment for evaluating strategies for similarity-based grouping of biological data, called KitEGA.
|
|
| 9. |
- Schroeder, Kari B., et al.
(författare)
-
Haplotypic background of a private allele at high frequency in the Americas
- 2009
-
Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 26:5, s. 995-1016
-
Forskningsöversikt (refereegranskat)abstract
- Recently, the observation of a high-frequency private allele,the 9-repeat allele at microsatellite D9S1120, in all sampledNative American and Western Beringian populations has been interpretedas evidence that all modern Native Americans descend primarilyfrom a single founding population. However, this inference assumedthat all copies of the 9-repeat allele were identical by descentand that the geographic distribution of this allele had notbeen influenced by natural selection. To investigate whetherthese assumptions are satisfied, we genotyped 34 single nucleotidepolymorphisms across 500 kilobases (kb) around D9S1120 in 21Native American and Western Beringian populations and 54 otherworldwide populations. All chromosomes with the 9-repeat alleleshare the same haplotypic background in the vicinity of D9S1120,suggesting that all sampled copies of the 9-repeat allele areidentical by descent. Ninety-one percent of these chromosomesshare the same 76.26 kb haplotype, which we call the "AmericanModal Haplotype" (AMH). Three observations lead us to concludethat the high frequency and widespread distribution of the 9-repeatallele are unlikely to be the result of positive selection:1) aside from its association with the 9-repeat allele, theAMH does not have a high frequency in the Americas, 2) the AMHis not unusually long for its frequency compared with otherhaplotypes in the Americas, and 3) in Latin American mestizopopulations, the proportion of Native American ancestry at D9S1120is not unusual compared with that observed at other genomewidemicrosatellites. Using a new method for estimating the timeto the most recent common ancestor (MRCA) of all sampled copiesof an allele on the basis of an estimate of the length of thegenealogy descended from the MRCA, we calculate the mean timeto the MRCA of the 9-repeat allele to be between 7,325 and 39,900years, depending on the demographic model used. The resultssupport the hypothesis that all modern Native Americans andWestern Beringians trace a large portion of their ancestry toa single founding population that may have been isolated fromother Asian populations prior to expanding into the Americas.
|
|
| 10. |
- Wächter, Thomas, et al.
(författare)
-
A Corpus-driven Approach for Design, Evolution and Alignment of Ontologies
- 2006
-
Ingår i: Winter Simulation Conference,2006. - 9781424405008 ; , s. 1595-, s. 1595-1602
-
Konferensbidrag (refereegranskat)abstract
- Bio-ontologies are hierarchical vocabularies, which are used to annotate other data sources such as sequence and structure databases. With the wide use of ontologies their integration, design, and evolution becomes an important problem. We show how textmining on relevant text corpora can be used to identify matching ontology terms of two separate ontologies and to propose new ontology terms for a given term. We evaluate these approaches on the GeneOntology.
|
|
