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:
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.
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 |