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Title	The wiki-based transcription factor encyclopedia and a model for robust community participation
Creator	Wasserman, Wyeth W.
Date Issued	2011-10-27
Description	This session took place on October 27, 2011 in the Lillooet Room of the Irving K. Barber Learning Centre at the University of British Columbia. This presentation can be found at 55:56 – 01:10:31 in the recording.
Genre	Presentation
Type	Text
Language	eng
Series	Open Access Week
Date Available	2011-12-15
Provider	Vancouver : University of British Columbia Library
Rights	Attribution-NonCommercial-NoDerivatives 4.0 International
DOI	10.14288/1.0077854
URI	http://hdl.handle.net/2429/39745
Affiliation	Medicine, Faculty of Medical Genetics, Department of
Peer Review Status	Unreviewed
Scholarly Level	Faculty
Rights URI	http://creativecommons.org/licenses/by-nc-nd/4.0/
AggregatedSourceRepository	DSpace

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The wiki-based Transcription Factor Encyclopedia  and a model for robust community participation Wyeth W. Wasserman 30 November 2010 http://www.cisreg.ca/tfe 2 3 4 Transcription Factors at the Centre of the Universe 5 Transcription Factors 101  Diverse set of proteins sharing common functional role in the regulation and production of RNA transcripts  Present in all species  For the purpose of today’s talk, TF will refer to the subset of the proteins that bind to DNA in a sequence-specific manner 6 Wiki-in-the-classroom 7 8 9TFe Goal: create an online encyclopedic collection of reviews about well-studied TFs, combining a mixture of expert-curated and automatic content. http://www.cisreg.ca/tfe Reader Interface 10 11 Authoring Interface 12 Author Recruitment  Stage 1 (alpha)  Friends  Friends of Friends  ~10  Stage 2 (beta)  PubMed mining to identify experts (> 10 published articles about a TF) with email solicitation  ~100 13 TFe Authors 14 +1 Australia ~15% of contacted experts agreed to participate ~60% of participants completed an entry Author Motivation  Sponsoring Journal  Scientists more willing to commit time and effort to projects that give authorships  Progress Scores  Many people are competitive and like to see their work achieve the best possible grade  Peer Review  Respect of peers and fixing weaknesses 15 TFe Article Scoring Procedure 16 17 PDFs 18 Lessons Learned  Motivation for authors – Sponsor Journals  Simple interfaces with extremely short learning periods to keep authors’ attention  Dedicated manager to engage authors, suggest changes and resolve issues  Focus allows the system to be tailored to the needs of the field 19 20 Thanks! • National Institutes of Health • Genome Canada / Genome BC •  Canadian Institutes for Health Research •  Canada Foundation for Innovation • Dimas Yusuf • Elodie Portales-Casamar • Warren Cheung • Stefanie Butland • Magdalena Swanson •  Virginie Bernard •  Rebecca Hunt-Newbury •  Andrew Kwon •  Miroslav Hatas •  David Arenillas •  Jonathan Lim •  Dora Pak  •And many alumni THE LAB THE APPRECIATED FUNDERS! • Phil Bradley and Amy Ticoll (FHCRC) • Frances Sladek (UC – Riverside) •~100 TFe Authors COLLABORATORS 21 Transcription Factors 102  Act cooperatively with other TFs to confer specific patterns of gene activity in response to developmental, physiological and environmental conditions  Much of their function is defined by protein- protein interactions  Understanding TFs is key to understanding developmental and tissue differentiation 22 Resources for the Study of TFs 23 Reader Interface -2 24 Authoring Interface - 2 25 Authoring Interface - 3 26 Authoring Interface - 4 27 TFBS Data Submission 28 Data within TFe 29 URL-based Data Extraction 30 System Map 31 Data Sources  PDB  Pfam  PAZAR  Gene Ontology  PubChem  BioGRID  MeSH  Entrez Gene  GeneRIF  MeSHOP  UCSC Genome Browser  Allen Brain Atlas  PubMed 32 PDF Generator - 2 33 Other Features  Predicted Binding Domain Structures (Phil Bradley, FHCRC)  MeSH Over-representation Profiles – Attribute Clouds (Warren Cheung)  TF Binding Site Profiles (Elodie Portales- Casamar)  Parent-Child Relationships (inherit ortholog content if no species-specific version) 34 Sustainability  Unclear if it can be sustained – not proven  Continuing journal sponsorships to motivate authors to update articles (or for new authors to take on abandoned articles)  Focused TF Family-based papers (e.g. Nuclear Receptors) 35

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