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Automated data pipelines at the rat genome database
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![Automated Data Pipelines for Loading, Integrating, Annotating and Quality Control of Data at the Rat Genome Database Abstract As the richness and diversity of biological data increase, model organism databases are confronted with the problem of quickly and efficiently populating their databases as well as providing timely updates to the information that they store. The Rat Genome Database (RGD, http://rgd.mcw.edu) provides comprehensive rat genetic, genomic and biological data through both manual and automated curation processes. A series of automated data pipelines have been implemented to acquire various data types from multiple sources, integrate them with existing data and provide comprehensive quality control data in order to maximize data coverage and reserve manual processes for targeted curation projects for data unavailable anywhere except the literature. Data acquired through these pipelines include 1) basic genomic elements such as genes and accompanying map, sequence and external database identifiers, protein information, genomic positions of exons and coding regions, 2) orthologs and ortholog relationships, 3) nomenclature alerts and reviews, 4) Gene Ontology annotations for human and mouse orthologs stored in RGD as well as appropriate annotations to rat genes, 5) ontology terms and relationships for GO, Mammalian Phenotype Ontology and Pathway Ontology. The pipelines at RGD are run with either incremental updates or delete-and-reload mechanisms and are run weekly to keep data up to date and synchronized with originating data sources. Pipeline mechanisms, quality control measures, and the methods to time and synchronize multiple pipelines will be presented along with the data types acquired and integrated and the process for resolving data errors and conflicts discovered during the QC processes. Fig 1. Synchronization of multiple pipelines at RGD assures data consistency while weekly runs providing timely updates. Fig 2. RGD pages are populated by multiple automated pipelines for various data types. Fig 3. Entrez Gene Pipelines automatically query the NCBI databases for gene records that have been modified during last week and make the necessary updates to RGD genes. ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],2. Orthologs and Nomenclature QC at RGD ,[object Object],[object Object],[object Object],Fig 4. Pipeline web report pages show the results and summaries from the last runs. A set of flags is assigned to every record (gene) processed, so curator can quickly jump to group of records of interest. Fig 7. RGD Nomenclature Curation Software 1. Gene QC at RGD Fig 6. RGD Nomenclature Pipeline ensures nomenclature QC via proposing necessary nomenclature changes every time the tool is opened. Nomenclature Pipeline, Manual Curation GOA and Mouse and Human GO Annotation Pipelines, Manual Curation Ortholog Relationship Pipeline Entrez Gene Pipelines Entrez Gene and UniProtKB Pipelines Nomenclature Pipeline ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],3. Assuring Gene Identity in Multiple RGD Pipelines Fig 8. The pipelines at RGD use cross referencing identifiers, which expedites data exchange between different resources and ensures gene identity. Entrez Gene Pipelines Fig 5. The curator can browse through particular class of conflicting records. The full hyperlinked XML representation of the incoming record is provided to allow for faster conflict resolution. Marek Tutaj, Mary Shimoyama, Elizabeth A. Worthey, Jennifer Smith, Rajni Nigam, Victoria Petri, Stan Laulederkind, Timothy F. Lowry, Tom Hayman, Shur-Jen Wang, Jeff De Pons, Pushkala Jayaraman, Weisong Liu, Diane Munzenmaier, Melinda Dwinell, Simon Twigger, Howard Jacob Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin Monday Tuesday Wednesday Thursday Friday Saturday Sunday Ontology Loading Pipeline ,[object Object],[object Object],[object Object],RGD Terms Reindexing (for search engine) GOC Annotations FTP Extract Entrezgene Pipeline (rat, human, mouse) Ortholog Loading UniProtKB sprot/trembl Process GOC Annotations GO Annotation Pipeline Mouse and Human GO Annotation UniSTS Pipeline Data Release Data Release (ctd.)](https://image.slidesharecdn.com/automateddatapipelinesattheratgenomedatabase-110112122254-phpapp02/85/Automated-data-pipelines-at-the-rat-genome-database-1-320.jpg)
