pathema community outreach
TRANSCRIPT
Pathema CommunityOutreach
Pathema Community
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
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
Pathema Annotation Jamborees
• Entamoeba Total Contributions: 14 Participants 1022 Functional Names 2019 GO Terms 43 Gene Structures 285 Literature References 120 Paralogous Families
• Burkholderia Total Contributions: 9 Participants 502 Functional Names 1480 GO Terms 86 Gene Structures 11 Literature References 10 Burkholderia genomes
4 Continued Collaborations
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
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
Annotation Services
• JCVI’s prokaryotic annotation pipeline isavailable 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
GenBank Annotation Updates
GenBank Annotation Submission Updates
Genome project db_xref
link Product
name EC#
Gene symbol
Gene model
C.perfringens ATCC 13124 2899 16 11 9 0
C.botulinum E3 str Alaska E 4 3
3264 65 4 3 0
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
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
Pathema Usage Statisticshttp://www.google.com/analytics/
Visitor Overview:16,500 unique users
2,700 unique users per month25,800 visits14,000 page hits
Visitor Loyalty:5:46 average time10:00 direct users
Traffic Sources:38% search engines32% direct traffic30% referred sites
Top Referral Sites:Google, Wikipedia & NCBI