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REGULATORY HAPLOTYPE: 7 entries. |
AN OPEN ACCESS DATABASE FOR GENE REGULATORY ELEMENT AND POLYMORPHISM ANNOTATIONThe Open REGulatory ANNOtation database (ORegAnno) is an open database for the curation of known regulatory elements from scientific literature. Annotation is collected from users worldwide for various biological assays and is automatically cross-referenced against PubMED, Entrez Gene, EnsEMBL, dbSNP, the eVOC: Cell type ontology, and the Taxonomy database, where appropriate, with information regarding the original experimentation performed (evidence). ORegAnno further provides an open validation process for all regulatory annotation in the public domain. Assigned validators receive notification of new records in the database and are able to cross-reference the citation to ensure record integrity. Validators have the ability to modify any record (deprecating the old record and creating a new one) if an error is found. Further, any contributor to the database can comment on any annotation by marking errors, or adding special reports into function as they see fit. These features of ORegAnno ensure that the collection is of the highest quality and uniquely provides a dynamic view of our changing understanding of gene regulation in the various genomes. As a first step, we recommend reading through our Help page. The ORegAnno data and web application are all LGPL open-source to encourage the development and maintenance of the database to new information and experimentation techniques. Please use our current citation information when referring to ORegAnno data in publication. We encourage interested contributors to send email to the ORegAnno mailing list at oreganno@bcgsc.ca or visit the mailing-list archives or email obig@bcgsc.ca.
INCORPORATED DATASETSORegAnno provides the ability to incorporate well-established datasets and provide relevant citation and ongoing maintenance functionality for these sets. For more information read the help pages on datasets or our citation page.
WHY ANOTHER GENE REGULATION DATABASE?Many databases and datasets exist that annotate regulatory elements in general or from niche areas of gene regulation. We provide a list on the Other Resources page. While these databases provide insight into gene regulation, certain challenges exist with each. In all cases, the data are static or maintained internally, and few or no mechanisms exist in which a community of researchers can add value to the annotations. Also, in some cases, like TRANSFAC, the latest data does not exists in the public domain. In some cases, like TRRD, the data are difficult to find or access in any convenient way. In MPromDB, the data are limited to human, mouse, and rat, and are not accessible programatically. EPD, SCPD, PlantCARE, HemoPDB, and OPD are examples of databases that target only certain types of promoters. In dbQSNP, existing functional variation is ignored, despite it contributing new insight into candidate promoter polymorphisms. In every database, negative controls are disregarded; no information is supplied on regions searched, or instances where annotation was unsuccessfully tested for transcription-affecting properties. This is problematic when the development of sophisticated computational biology techniques depends on being able to access this information. To address these issues we have created an open annotation and open source database initiative that promotes the development of a unified resource for this information. ORegAnno uses advanced programming techniques and APIs suchs as Hibernate, Lucene, JAAS, MD5, Axis Web Services, Struts, and JSPs to deliver its data either graphically through this website or programatically through Web Services to any location in the world. |
Questions or comments to oreganno@bcgsc.ca. (Archived here)
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