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. 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. 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. 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. 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. 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. 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. 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. 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