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1.  Improvements to services at the European Nucleotide Archive 
Nucleic Acids Research  2009;38(Database issue):D39-D45.
The European Nucleotide Archive (ENA; is Europe’s primary nucleotide sequence archival resource, safeguarding open nucleotide data access, engaging in worldwide collaborative data exchange and integrating with the scientific publication process. ENA has made significant contributions to the collaborative nucleotide archival arena as an active proponent of extending the traditional collaboration to cover capillary and next-generation sequencing information. We have continued to co-develop data and metadata representation formats with our collaborators for both data exchange and public data dissemination. In addition to the DDBJ/EMBL/GenBank feature table format, we share metadata formats for capillary and next-generation sequencing traces and are using and contributing to the NCBI SRA Toolkit for the long-term storage of the next-generation sequence traces. During the course of 2009, ENA has significantly improved sequence submission, search and access functionalities provided at EMBL–EBI. In this article, we briefly describe the content and scope of our archive and introduce major improvements to our services.
PMCID: PMC2808951  PMID: 19906712
2.  Non-redundant patent sequence databases with value-added annotations at two levels 
Nucleic Acids Research  2009;38(Database issue):D52-D56.
The European Bioinformatics Institute (EMBL-EBI) provides public access to patent data, including abstracts, chemical compounds and sequences. Sequences can appear multiple times due to the filing of the same invention with multiple patent offices, or the use of the same sequence by different inventors in different contexts. Information relating to the source invention may be incomplete, and biological information available in patent documents elsewhere may not be reflected in the annotation of the sequence. Search and analysis of these data have become increasingly challenging for both the scientific and intellectual-property communities. Here, we report a collection of non-redundant patent sequence databases, which cover the EMBL-Bank nucleotides patent class and the patent protein databases and contain value-added annotations from patent documents. The databases were created at two levels by the use of sequence MD5 checksums. Sequences within a level-1 cluster are 100% identical over their whole length. Level-2 clusters were defined by sub-grouping level-1 clusters based on patent family information. Value-added annotations, such as publication number corrections, earliest publication dates and feature collations, significantly enhance the quality of the data, allowing for better tracking and cross-referencing. The databases are available format:
PMCID: PMC2808894  PMID: 19884134
3.  IPD—the Immuno Polymorphism Database 
Nucleic Acids Research  2009;38(Database issue):D863-D869.
The Immuno Polymorphism Database (IPD) ( is a set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of Killer-cell Immunoglobulin-like Receptors, IPD-MHC, is a database of sequences of the Major Histocompatibility Complex of different species; IPD-human platelet antigens, alloantigens expressed only on platelets and IPD-ESTDAB, which provides access to the European Searchable Tumour cell-line database, a cell bank of immunologically characterised melanoma cell lines. The data is currently available online from the website and ftp directory.
PMCID: PMC2808958  PMID: 19875415
4.  Web services at the European Bioinformatics Institute-2009 
Nucleic Acids Research  2009;37(Web Server issue):W6-W10.
The European Bioinformatics Institute (EMBL-EBI) has been providing access to mainstream databases and tools in bioinformatics since 1997. In addition to the traditional web form based interfaces, APIs exist for core data resources such as EMBL-Bank, Ensembl, UniProt, InterPro, PDB and ArrayExpress. These APIs are based on Web Services (SOAP/REST) interfaces that allow users to systematically access databases and analytical tools. From the user's point of view, these Web Services provide the same functionality as the browser-based forms. However, using the APIs frees the user from web page constraints and are ideal for the analysis of large batches of data, performing text-mining tasks and the casual or systematic evaluation of mathematical models in regulatory networks. Furthermore, these services are widespread and easy to use; require no prior knowledge of the technology and no more than basic experience in programming. In the following we wish to inform of new and updated services as well as briefly describe planned developments to be made available during the course of 2009–2010.
PMCID: PMC2703973  PMID: 19435877
5.  Development of Danish version of child oral-health-related quality of life questionnaires (CPQ8–10 and CPQ11–14) 
BMC Oral Health  2009;9:11.
The Child Perceptions Questionnaire (CPQ) is a self-reported questionnaire developed to measure oral health-related quality of life in children. The CPQ aims to improve the description of children's oral health, while taking into consideration the importance of psychological aspects in the concept of health. The CPQ exists in two versions: the CPQ8–10 for children aged 8–10 years and the CPQ11–14 for those aged 11–14 years. The aim of this study was to develop a Danish version of the CPQ8–10 and the CPQ11–14 and to evaluate its validity for use among Danish-speaking children.
The instruments were translated from English into Danish in accordance with a recommended translation procedure. Afterwards, they were tested among children aged 8–10 (n = 120) and 11–14 years (n = 225). The validity was expressed by the correlation between overall CPQ scores and i) self-reported assessment of the influence of oral conditions on everyday life (not at all, very little, some, a lot, very much) and ii) the self-reported rating of oral health. Furthermore, groups of children with assumed decreased oral health-related quality of life were compared with children with healthy oral conditions. Finally, we examined the internal consistency.
The correlation between overall CPQ scores and global assessments of the influence of oral conditions on everyday life showed Spearman correlation coefficients of 0.45, P < 0.001 for CPQ8–10 and 0.50, P < 0.001 for CPQ11–14. The correlation between overall CPQ scores and the self-reported rating of oral health showed Spearman correlation coefficients of 0.45, P < 0.001 for CPQ8–10 and 0.17, P = 0.010 for CPQ11–14.
The median overall CPQ8–10 scores were 7 for individuals with healthy oral conditions, 5 for individuals with cleft lip and palate, and 15 for individuals with rare oral diseases. The median overall CPQ11–14 scores were 9 for individuals with healthy oral conditions, 9 for individuals with cleft lip and palate, 17.0 for individuals with rare oral diseases, and 22.0 for individuals with fixed orthodontic appliances. There were statistically significant differences between the groups of children with healthy oral conditions and each of the subgroups, except for children with cleft lip and palate.
Chronbach'α were 0.82 for CPQ8–10 and 0.87 for CPQ11–14.
The results of this study reveal that the Danish CPQ8–10 and CPQ11–14, seem to be valid instruments for measuring oral health-related quality of life in children although its ability to discriminate between children with cleft lip and palate and healthy children seem to be limited.
PMCID: PMC2679003  PMID: 19383176

Results 1-5 (5)