Pathema Community Outreach

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Conference: Annual BRC Meeting (BRC6), Oct 28-29, 2008 in Ft. Lauderedale, Florida.
Presenter: Tanja Davidsen

Published in: Technology, Education
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Pathema Community Outreach

  1. 1. Pathema Community Outreach
  2. 2. Pathema Community
  3. 3. Pathema Workshops • Clade-specific Pathema Workshops On JCVI Campus  2 Days Hands On – – Live/Archived Webinar Broadcast – 4 Workshops Conducted, one per clade Organism Specific Meetings  4 Hours Hands On – – 5 Workshops Conducted • Prokaryotic Annotation & Analysis Course 4 times each year at JCVI  General annotation, not specific to an organism clade 
  4. 4. Pathema Annotation Jamborees • 3 day Jamborees held at JCVI • First day teaches our annotation methodologies • Follow up days allow the community to annotate with aid from our expert curators • Excellent participation and feedback from our participants
  5. 5. Pathema Annotation Jamborees • Entamoeba • Burkholderia Total Contributions: Total Contributions:   14 Participants 9 Participants   1022 Functional Names 502 Functional Names   2019 GO Terms 1480 GO Terms   43 Gene Structures 86 Gene Structures   285 Literature References 11 Literature References   120 Paralogous Families 10 Burkholderia genomes   4 Continued Collaborations
  6. 6. Presentations and Posters • Last two years, focus on clade specific meetings ASM Biodefense  Microbial Genomes  International Conference on Microbial Genomics  Genome Medicine and Environment (GME)  International Biocuration Meeting  Genome Informatics  IBRCC  The World Melioidosis Conference  Workshop on Amoebiasis  Functional Genomics of Gram+ Microorganisms  Bacillus ACT Meeting 
  7. 7. Collaborative Data Exchange • Gene model and functional curation 7 Bacillus anthracis strains  1 Bacillus cereus strain  1 Bacillus pumilus strain  11 Clostridium botulinum strains  4 Burkholderia pseudomallei strains  • Clostridium toxin curation • Burkholderia mobile elements
  8. 8. Annotation Services • JCVI’s prokaryotic annotation pipeline is available for any genome • Offered for the past 7 years • Currently processing 9 genomes a month with over 100 delivered so far in 2008 • Offered in conjunction with our 3 day class • IGS also offers an annotation service called the IGS Annotation Engine
  9. 9. GenBank Annotation Updates GenBank Annotation Submission Updates db_xref Product Gene Gene Genome project EC# link name symbol model C.perfringens ATCC 13124 2899 16 11 9 0 C.botulinum E3 str Alaska 3264 65 4 3 0 E43 C.botulinum NCTC 2916 3747 153 14 14 0 C.botulinum A ATCC 1939 7 3598 68 13 14 0 E.histolytica HM-1:IMS S 8161 1381 18 16 1301 Total 21669 1683 60 56 1301
  10. 10. Additional Outreach • Clade-specific Manuals & Tutorials • Glossary of Terms • Frequently Asked Questions • Integration of Informational Icons • 24 hour Response Helpdesk • Publications and Presentation Page • Wiki Bug Reporting and Tracking System
  11. 11. Pathema Usage Statistics http://www.google.com/analytics/ Visitor Overview: 16,500 unique users 2,700 unique users per month 25,800 visits 14,000 page hits Visitor Loyalty: 5:46 average time 10:00 direct users Traffic Sources: 38% search engines 32% direct traffic 30% referred sites Top Referral Sites: Google, Wikipedia & NCBI

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