Pathema Community
Outreach

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 • 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

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 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

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

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 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