Consolidated Database for the Harvard PGP

In order to facilitate ease of access, some of the information available through Harvard Personal Genome Project page and the GET-Evidence site has been consolidated into a small SQLite database (~120Mb uncompressed). This is a web page front end that gives some canned visualizations of the data and allows you to create your own. This website, along with the data files it uses, resides in an Arvados collection. Feel free to browse the contents.

The Harvard PGP SQLite database is available here:

For convenience, the individual tables are also available as tab-separated text files that can be downloaded individually:

There are participant surveys available through Personal Genome Project website but they've been collected here for convenience as well:

The schema for the SQLite database is split between two files and is available as well:

Custom Visualization

Each row should have an x field followed by any number of labelled y fields. The results will be grouped by each row. See the examples on the lower right for some canned queries.

SQLite Database Schema

table field type example
survey id int 123
human_id string hu826751
date datetime 2015-06-23 10:30:01
phenotype_category string Participant_Survey:Age
phenotype string 30-39 years
uploaded_data id int 123
human_id string hu826751
date string 2015-06-23 10:30:01
data_type string Complete Genomics
source string PGP
name string CGI sample: GS03052-DNA_B01
download_description string (101.3 MB)
download_url string http://evidence.pgp-hms.org/genome_download.php?download_genome_id=8e2fb8975d5a05735c56505e1697ad1fa1df73ab&download_nickname=CGI+sample%3A+GS03052-DNA_B01
report_description string male 2,743,807,495 positions covered ref. b37
report_url string http://evidence.pgp-hms.org/genomes?display_genome_id=8e2fb8975d5a05735c56505e1697ad1fa1df73ab
allergies id int 123
human_id string hu826751
name string Honey Bee Venom Protein
severity string MILD
start_date string 2000-08-01
end_date string 2010-05-01
conditions id int 123
human_id string hu826751
name string Chest Pain
start_date string 2001-08-06
end_date string 2010-03-01
demographics id int 123
human_id string hu826751
date_of_birth string 1968-11-01 (46 years old)
gender string Female
weight string 145lbs (66kg)
height string 5ft 10in (177cm)
blood_type string A+
race string White
immunizations id int 123
human_id string hu826751
name string Tetanus/Diphtheria/Pertussis (Tdap) Vaccine
date string 2008-08-13
medications id int 123
human_id string hu826751
name string Viibryd
dosage string 50 Milligram (mg)
frequency string Take 1, 2 Times Daily
start_date string 2013-01-01
end_date string 2013-02-01
procedures id int 123
human_id string hu826751
name string ELECTROCARDIOGRAM
date string 2011-10-20
test_results id int 123
human_id string hu826751
name string Height
result string 77 inches
date string 2009-07-01
suff_record id int 123
json_record string ["benign","0.000114142",4,"Low","Uncertain","OFD1-Q545R",true,"benign","Homozygous",-1]
human_suff_record_map id int 123
uploaded_data_id int 465
suff_record_index int 89
insuff_record id int 123
json_record string ["","0.000",1,"","","ACOT2-M455V",false,"","Heterozygous",-1]
human_insuff_record_map id int 123
uploaded_data_id int 465
insuff_record_index int 130

Query examples