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mechanisms are widely implicated in species-specific adaptation and the etiology of disease. This initiative culminated in the formation of an international consortium of like-minded scientists dedicated to accomplishing this task. The RegCreative jamboree was the first opportunity for these groups to meet to be able to accurately assess the current state of knowledge in gene regulation and to begin to develop standards by which to curate regulatory information.
175:. Within these annotations, one new dataset was added to ORegAnno; 274 human enhancers were programmatically annotated by Maximillian Haessler, Institute Alfred Fessard, from Visel et al., Nucleic Acids Research, 2006. In total, 130 scientific studies were examined in depth. The annotated papers were pre-selected from expert-curated publications in the ORegAnno queue that had full-text available through
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in facilitating regulatory annotation. Sessions were led by Dr. Lynette
Hirschman, MITRE, and Dr. Martin Krallinger, CNIO, to formulate where text-mining can help. A short term object of text-mining based analyses was formulated around both populating the ORegAnno queue and using the expert-curated
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As of
December 20, 2006, ORegAnno contained 4220 regulatory sequences (excluding deprecated records) for 2190 transcription factor binding sites, 1853 regulatory regions (enhancers, promoters, etc.), 170 regulatory polymorphisms, and 7 regulatory haplotypes for 17 different organisms (predominantly
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There exists an immediate need for improved data standardization and development of associated ontologies. Specifically, this should include the open access development and integration of transcription factor naming conventions and sequence, cell type, cell line, tissue, and evidence ontologies.
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Prior to the RegCreative
Jamboree, attendees were asked to participate in an interannotator agreement assessment. Two ORegAnno mirrors were established with identical sets of publications to be annotated in their queue. In total, 33 redundant annotations from 18 publications were collected. (79
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in that order). These records were obtained by manual curation of 828 publications by 45 ORegAnno users from the gene regulation community. The ORegAnno publication queue contained 4215 publications of which 858 were closed, 34 were in progress (open status), and 3321 were awaiting annotation
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Griffith OL, Montgomery SB, Bernier B, Chu B, Kasaian K, Aerts S, Mahony S, Sleumer MC, Bilenky M, Haeussler M, Griffith M, Gallo SM, Giardine B, Hooghe B, Van Loo P, Blanco E, Ticoll A, Lithwick S, Portales-Casamar E, Donaldson IJ, Robertson G, Wadelius C, De Bleser P, Vlieghe D, Halfon MS,
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The RegCreative jamboree was stimulated by a community initiative to curate in perpetuity the genomic sequences which have been experimentally determined to control gene expression. This objective is of fundamental importance to evolutionary analysis and translational research as regulatory
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Hands-on annotation activities occurred during the first 2 days of the 3-day workshop. In total, 39 researchers contributed 184 TFBS and 317 Regulatory
Regions from 96 papers. Many of these researchers were also trained on the ORegAnno system, significantly increasing its experienced-user
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Learning-based ontology development was widely regarded as an essential feature of the annotation process. Such that, annotators are not restricted from annotating based on the limitations of the controlled vocabulary and that these exceptions can be used to further develop the backbone
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Transcription factor naming issues were addressed through discussion of integration of transcription factor prediction pipelines, such as DBD or flyTF, which have been supplemented with manual curation versus solely manual curated implementations like
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In total, 44 researchers attended the workshop from 9 different countries and 23 institutions. Funding was also obtained from ENFIN, the BioSapiens
Network, FWO Research Foundation, Genome Canada and Genome British Columbia.
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Ontology development should be decentralized from the ORegAnno annotation framework. Specifically, it is planned that the ORegAnno evidence ontology will be removed and made available to broader community
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annotations for 31 papers and 60 annotations for 21 papers were collected on servers 1 and 2, respectively.) This effort was used as a baseline from which to establish annotator efficiency.
243:"ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation"
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within ORegAnno. This allows the researcher to analyze regulatory data using their own conditions as to the suitability of the supporting evidence.
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Lesurf R, Cotto KC, Wang G, Griffith M, Kasaian K, Jones SJ, Montgomery SB, Griffith OL, Open
Regulatory Annotation Consortium (2016).
24:) is designed to promote community-based curation of regulatory information. Specifically, the database contains information about
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portion of the ORegAnno queue to validate text-mining-based publication acquisition. The latter objectives are being led by Dr.
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Montgomery SB, Griffith OL, Sleumer MC, Bergman CM, Bilenky M, Pleasance ED, Prychyna Y, Zhang X, Jones SJ (2006).
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122:(pending status). ORegAnno is continually updated and therefore current database contents should be obtained from
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The groundwork for addressing and prioritizing these needs was accomplished in several ways during the meeting:
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from existing ORegAnno and REDfly database conventions within the framework being developed as part of the
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community. The contribution of these annotations to individual species was 339 annotations in
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Wasserman W, Hardison R, Bergman CM, Jones SJ, Open
Regulatory Annotation Consortium (2008).
171:, 6 annotations in Halocynthia roretzi, 2 annotations in Ciona savignyi and 2 annotations in
92:- all data and all software that is produced in the project can be freely accessed and used.
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track. Furthermore, each entry is associated with its experimental evidence, embedded as an
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Renewed focus on integrating species-specific resources with annotation framework.
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279:"ORegAnno: an open-access community-driven resource for regulatory annotation"
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322:"ORegAnno 3.0: a community-driven resource for curated regulatory annotation"
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72:. The information within ORegAnno is regularly mapped and provided as a
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201:. A preliminary version of these improvements can be found on the
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The specific outcomes of the RegCreative meeting to date are:
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A specific focus of the workshop was addressing the role of
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52:For each entry, cross-references are maintained to
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18:Open Regulatory Annotation Database
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260:10.1093/bioinformatics/btk027
289:(Database issue): D107–13.
35:, regulatory variants, and
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199:Open Biomedical Ontologies
66:the NCBI Taxonomy database
375:RegCreative Jamboree 2006
130:RegCreative Jamboree 2006
84:Software and data access
230:, University of Leuven.
161:Drosophila melanogaster
103:Drosophila melanogaster
326:Nucleic Acids Research
283:Nucleic Acids Research
115:Caenorhabditis elegans
390:Biological databases
167:, 14 annotations in
163:, 24 annotations in
159:, 72 annotations in
155:, 42 annotations in
30:transcription factor
338:10.1093/nar/gkv1203
74:UCSC Genome Browser
295:10.1093/nar/gkm967
165:Ciona intestinalis
26:regulatory regions
195:Sequence Ontology
169:Rattus norvegicus
119:Rattus norvegicus
96:Database contents
78:Evidence Ontology
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124:www.oreganno.org
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332:(D1): D126-32.
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157:Mus musculus
153:Homo sapiens
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111:Mus musculus
107:Homo sapiens
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228:Stein Aerts
223:text mining
209:ontologies.
191:Marc Halfon
90:open source
62:Entrez Gene
384:Categories
235:References
37:haplotypes
370:ORegAnno
356:26578589
313:18006570
269:16397004
43:Overview
22:ORegAnno
347:4702855
304:2239002
54:EnsEMBL
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58:dbSNP
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