1. Anopheles gambiae PopGenBase Groundwork for a vector population genetics database UC Davis - UCLA

2. Anopheles gambiae s.l.  One of major vectors for malaria transmission in Africa  Different species and forms of An. gambiae s.l. are identical in morphology.  Researches have shown that different subpopulations of An. gambiae s.s. exhibit different response to important phenotype such as insecticide resistance.

3. Genetic markers are not randomly distributed. Mali

4. Distribution of the kdr SNP among An. gambiae s.s. in Mali Distribution of the kdr SNP among populations of the M and S molecular forms of An. gambiae at four sites in Mali at which the two forms occur in sympatry. The "rr" refers homozygote of kdr SNP; the "rs" refersheterozygotes; and "ss" refers wild-type homozygote. From Tripet et al. (2007)‏

5. Beginning  In 2004, our Anopheles gambiae population genetics study demanded a data repository tool that organizes population, geographical, ecological and genetic information.  Collaborators among multiple campuses desired a better way to share data than sending spreadsheet files.

6. Progress  Anopheles gambiae Population genomics DB (In-group DB)‏ Online data upload Summary pages for each country Query pages Interactive Google map of collection sites Chromosome Image links for verification Data output to fit into specific analysis programs Documentation regarding data structure and naming conventions

7. ER Diagram of in-group PopGenBase  Genetic data for each individual  A table for each experiment or protocol ScottTest Karyotype mos_id 2La 2Rj Species Mosquito id Researcher ID Name FaviaFanelloTest MicrosatData mos_id Length A Microsat ID Referencing attribute referenced attribute MicrosatList ID Collection site Collection date Tube num mos_id X Chrom form Researcher ID Last modified by Last_modified Sites village ID molecular form mos_id Researcher ID Precipitation Recording station ChromosomeImage file ID chromosome mos_id comment 2Rb 2Rc 2Rd chromosome Genebank name Length B Last_modified Last_modified by comment Last_modified Last_modified by comment Last_modified Last_modified by comment Lab Institution Position E-mail comment country latitude longitude elevation Meteorology Stations name ID country latitude longitude Recording date precipitation

8. Goals of PopGenBase  Provide encouragement to the vector population genetics community to use PopGenBase, much in the manner of many of the public data resources of NCBI and EMBL-EBI.  Bring some standardization of genetic markers and inter-study compatibility to the field of vector population genetics.  Directly link markers used in population studies with emerging knowledge of the genome, generating far more powerful population data sets.  Encourage studies in other areas of vector biology, like ecology, behavior and epidemiology, to incorporate genetic information, in order to identify genes affecting complex phenotypes.

9. Current Progress  https://grassi2.ucdavis.edu

10. [Current status] Query page

11. [Current status] Various query output format

12. [Current status] Chromosome Images

13. [Current status] GoogleMaps API

14. [Current status] Documentation

15. To Do List  Stage 2 PopGenBase Nov. 2008 – Jun. 2009 Incorporation of other genetic data such as microsatellite genotypes. A pilot “Work Bench” implementation and soliciting other research group as test groups. Improvement of GoogleMap API interface Define ‘Sample’ schema to aid cross-link among other vector databases.