Biomedical subjects

Kexin Sun

Publications and source records attributed to Kexin Sun.

3 recordsLinked to original sources

PubMed2005

YPED: a proteomics database for protein expression analysis.

We have developed the Yale Protein Expression Database (YPED) to address the storage, retrieval, and integrated analysis of proteomics data generated by Yale's Keck Protein Chemistry and Mass Spectrometry Facility. YPED is Web-accessible and currently handles sample requisition, result reporting and sample comparison for ICAT, DIGE and MUDPIT samples. Sample descriptions are compatible with the evolving MIAPE standards. Peptides and proteins identified using Sequest or Mascot are validated with the Trans-Proteomic Pipeline developed at the Institute of Systems Biology and data from the resulting XML file are stored in the database. Researchers can view, subset and download their data through a secure Web interface.

Databases, Protein↗

PubMed2002

Metadata-driven creation of data marts from an EAV-modeled clinical research database.

Generic clinical study data management systems can record data on an arbitrary number of parameters in an arbitrary number of clinical studies without requiring modification of the database schema. They achieve this by using an Entity-Attribute-Value (EAV) model for clinical data. While very flexible for creating transaction-oriented systems for data entry and browsing of individual forms, EAV-modeled data is unsuitable for direct analytical processing, which is the focus of data marts. For this purpose, such data must be extracted and restructured appropriately. This paper describes how such a process, which is non-trivial and highly error prone if performed using non-systematic approaches, can be automated by judicious use of the study metadata-the descriptions of measured parameters and their higher-level grouping. The metadata, in addition to driving the process, is exported along with the data, in order to facilitate its human interpretation.

Breast Neoplasms↗

PubMed2002

Designing and implementing special-purpose databases: lessons from the pharmacogenetic network.

The Pharmacogenetics Research Network, which has the long-term goal of genotype-phenotype correlation related to pharmacotherapy, mandates timely electronic publication of results by participating research groups through submission to PharmGKB, the consortium's repository database. Because informatics expertise across groups varies, many groups need help in managing their own data and in generating electronic submissions. To assist these operations, we perform a needs assessment to determine an optimum database implementation strategy, which varies from standalone microcomputer database application to Web-based solutions, depending on the group and problem scope. Solution implementation is coupled with transfer of expertise through hands-on training, so as to reduce the groups' long-term dependence on us. Where multiple groups face common problems, such as managing genotyping data or clinical study support, we have devised generic software that can be reused in its entirety by individual groups, or customized with modest effort.

Computer Communication Networks↗