Vivisimo Customer Case Study

Capitalizing on the power of the Internet, the Houston Academy of Medicine-Texas Medical Center (HAM-TMC) Library is using search to reinvent itself in this digital age. By using the Vivisimo Velocity Search Platform to search its multiple repositories, the library has helped users find information they never knew existed as well as positioned the library as a thought leader in its community.

The sequence comparison index: A novel method for comparing proteins and proteomes

Historically morphological features were used as the primary means to classify organisms. However, the age of molecular genetics has allowed us to approach this field from the perspective of the organism's genetic code. Early work used highly conserved sequences, such as ribosomal RNA. The increasing number of complete genomes in the public data repositories provides the opportunity to look not only at a single gene, but at organisms' entire parts list. ^ Here the Sequence Comparison Index (SCI) and the Organism Comparison Index (OCI), algorithms and methods to compare proteins and proteomes, are presented. The complete proteomes of 104 sequenced organisms were compared. Over 280 million full Smith-Waterman alignments were performed on sequence pairs which had a reasonable expectation of being related. From these alignments a whole proteome phylogenetic tree was constructed. This method was also used to compare the small subunit (SSU) rRNA from each organism and a tree constructed from these results. The SSU rRNA tree by the SCI/OCI method looks very much like accepted SSU rRNA trees from sources such as the Ribosomal Database Project, thus validating the method. The SCI/OCI proteome tree showed a number of small but significant differences when compared to the SSU rRNA tree and proteome trees constructed by other methods. Horizontal gene transfer does not appear to affect the SCI/OCI trees until the transferred genes make up a large portion of the proteome. ^ As part of this work, the Database of Related Local Alignments (DaRLA) was created and contains over 81 million rows of sequence alignment information. DaRLA, while primarily used to build the whole proteome trees, can also be applied shared gene content analysis, gene order analysis, and creating individual protein trees. ^ Finally, the standard BLAST method for analyzing shared gene content was compared to the SCI method using 4 spirochetes. The SCI system performed flawlessly, finding all proteins from one organism against itself and finding all the ribosomal proteins between organisms. The BLAST system missed some proteins from its respective organism and failed to detect small ribosomal proteins between organisms. ^

Cost analysis of opt-in consent procedures for the Texas statewide immunization information system, ImmTrac

Background. Childhood immunization programs have dramatically reduced the morbidity and mortality associated with vaccine-preventable diseases. Proper documentation of immunizations that have been administered is essential to prevent duplicate immunization of children. To help improve documentation, immunization information systems (IISs) have been developed. IISs are comprehensive repositories of immunization information for children residing within a geographic region. The two models for participation in an IIS are voluntary inclusion, or "opt-in," and voluntary exclusion, or "opt-out." In an opt-in system, consent must be obtained for each participant, conversely, in an opt-out IIS, all children are included unless procedures to exclude the child are completed. Consent requirements for participation vary by state; the Texas IIS, ImmTrac, is an opt-in system.^ Objectives. The specific objectives are to: (1) Evaluate the variance among the time and costs associated with collecting ImmTrac consent at public and private birthing hospitals in the Greater Houston area; (2) Estimate the total costs associated with collecting ImmTrac consent at selected public and private birthing hospitals in the Greater Houston area; (3) Describe the alternative opt-out process for collecting ImmTrac consent at birth and discuss the associated cost savings relative to an opt-in system.^ Methods. Existing time-motion studies (n=281) conducted between October, 2006 and August, 2007 at 8 birthing hospitals in the Greater Houston area were used to assess the time and costs associated with obtaining ImmTrac consent at birth. All data analyzed are deidentified and contain no personal information. Variations in time and costs at each location were assessed and total costs per child and costs per year were estimated. The cost of an alternative opt-out system was also calculated.^ Results. The median time required by birth registrars to complete consent procedures varied from 72-285 seconds per child. The annual costs associated with obtaining consent for 388,285 newborns in ImmTrac's opt-in consent process were estimated at $702,000. The corresponding costs of the proposed opt-out system were estimated to total $194,000 per year. ^ Conclusions. Substantial variation in the time and costs associated with completion of ImmTrac consent procedures were observed. Changing to an opt-out system for participation could represent significant cost savings. ^