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