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Automated Annotation and Probe Update System for Cancer Center Microarrays

DESCRIPTION

This system annotates microarray probes using databases like Entrez Gene and UniGene for cancer research. It automatically updates annotations, allows web-based and API queries, and aims for caGRID compliance. Utilizes caCORE SDK for code generation. Data sources include UniSTS, Gene Ontology, dbSNP, and more. Limitations include slow PubMed curation, non-optimized complex searches, and lack of meta-data storage in caArray.

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Automated Annotation and Probe Update System for Cancer Center Microarrays

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  1. caFE Server Siteman Cancer Center

  2. Introduction • Annotate probes on microarrays using publicly available biomedical databases • Automatically update annotations on a regular basis • Web-based and API based query search • Uses caCORE SDK (version 1.0.3) generated code • Working towards caGRID compliance

  3. Data Sources • Entrez Gene • UniGene • Gene Ontology • dbSNP • UniSTS • HomoloGene • PubMed

  4. Annotation Interlinks Microarrays caArray Custom Entrez Gene UniGene GenBank Gene ID UniGene ClusterID Accession Number HomoloGene dbSNP PubMed Gene Ontology Orthologus genes RefSNP ID Pubmed relationship GO terms

  5. Limitations • Initial run of PubMed data curation takes 2-3 months • APIs generated using caCORE SDK • Not optimized for complex searches • Performing searches that involves complex computations. • For example, searching for literature correlation with depth 2 or more • Meta-information of caArray is not stored

  6. Demo

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