Table Columns¶
The two important tables with the majority of the data are Study and SNP. In addition, phenotype data is stored in Phenotype and PhenoCats, population data is in Population, and platforms are in Platform.
Contents
Study¶
To query studies, it is recommended to use the query.get_studies() function.
Column | Description | Type |
---|---|---|
id | id | Integer |
pmid | PubmedID | String |
title | Study | String |
journal | Journal | String |
author | 1st_author | String |
grasp_ver | GRASPversion? | Integer |
noresults | No results flag | Boolean |
results | #results | Integer |
qtl | IsEqtl/meQTL/pQTL/gQTL/Metabolmics? | Boolean |
snps | Link to all SNPs in this study | relationship |
phenotype_id | ID of primary phenotype in Phenotype table | Integer |
phenotype | A link to the primary phenotype in the Phenotype table | relationship |
phenotype_cats | A link to all phenotype categories assigned in the PhenoCats table | relationship |
datepub | DatePub | Date |
in_nhgri | In NHGRI GWAS catalog (8/26/14)? | Boolean |
locations | Specific place(s) mentioned for samples | String |
mf | Includes male/female only analyses in discovery and/or replication? | Boolean |
mf_only | Exclusively male or female study? | Boolean |
platforms | Link to platforms in the Platform table. Platform [SNPs passing QC] | relationship |
snp_count | From “Platform [SNPs passing QC]” | String |
imputed | From “Platform [SNPs passing QC]” | Boolean |
population_id | Primary key of population table | Integer |
population | GWAS description, link to table | relationship |
total | Total Discovery + Replication sample size | Integer |
total_disc | Total discovery samples | Integer |
disc_pop_flag | A bitwise flag that shows presence/absence of discovery populations | Integer |
european | European | Integer |
african | African ancestry | Integer |
east_asian | East Asian | Integer |
south_asian | Indian/South Asian | Integer |
hispanic | Hispanic | Integer |
native | Native | Integer |
micronesian | Micronesian | Integer |
arab | Arab/ME | Integer |
mixed | Mixed | Integer |
unpecified | Unspec | Integer |
filipino | Filipino | Integer |
indonesian | Indonesian | Integer |
total_rep | Total replication samples | Integer |
rep_pop_flag | A bitwise flag that shows presence/absence of replication populations | Integer |
rep_european | European.1 | Integer |
rep_african | African ancestry.1 | Integer |
rep_east_asian | East Asian.1 | Integer |
rep_south_asian | Indian/South Asian.1 | Integer |
rep_hispanic | Hispanic.1 | Integer |
rep_native | Native.1 | Integer |
rep_micronesian | Micronesian.1 | Integer |
rep_arab | Arab/ME.1 | Integer |
rep_mixed | Mixed.1 | Integer |
rep_unpecified | Unspec.1 | Integer |
rep_filipino | Filipino.1 | Integer |
rep_indonesian | Indonesian.1 | Integer |
sample_size | Initial Sample Size, string description of integer population counts above. | String |
replication_size | Replication Sample Size, string description of integer population counts above. | String |
SNP¶
Column | Description | Type |
---|---|---|
id | NHLBIkey | BigInteger |
snpid | SNPid | String |
chrom | chr | String |
pos | pos | Integer |
pval | Pvalue | Float |
NHLBIkey | NHLBIkey | String |
HUPfield | HUPfield | String |
LastCurationDate | LastCurationDate | Date |
CreationDate | CreationDate | Date |
population_id | Primary | Integer |
population | Link | relationship |
study_id | Primary | Integer |
study | Link | relationship |
study_snpid | SNPid | String |
paper_loc | LocationWithinPaper | String |
phenotype_desc | Phenotype | String |
phenotype_cats | Link | relationship |
InGene | InGene | String |
NearestGene | NearestGene | String |
InLincRNA | InLincRNA | String |
InMiRNA | InMiRNA | String |
InMiRNABS | InMiRNABS | String |
dbSNPfxn | dbSNPfxn | String |
dbSNPMAF | dbSNPMAF | String |
dbSNPinfo | dbSNPalleles | String |
dbSNPvalidation | dbSNPvalidation | String |
dbSNPClinStatus | dbSNPClinStatus | String |
ORegAnno | ORegAnno | String |
ConservPredTFBS | ConservPredTFBS | String |
HumanEnhancer | HumanEnhancer | String |
RNAedit | RNAedit | String |
PolyPhen2 | PolyPhen2 | String |
SIFT | SIFT | String |
LSSNP | LS | String |
UniProt | UniProt | String |
EqtlMethMetabStudy | EqtlMethMetabStudy | String |
Phenotype¶
All available phenotypes are available on the Phenotypes wiki page
- id
- phenotype
- studies (link to Study table)
- snps (link to SNP table)
PhenoCats¶
All phenotype categories are available on the Phenotype Categories wiki page
- id
- population
- alias
- studies (link to Study table)
- snps (link to SNP table)
Population¶
- id
- population
- studies (link to Study table)
- snps (link to SNP table)
All population entries are available on the Populations wiki page