Schema for ggLink
  Database: hgFixed    Primary Table: ggLink    Row Count: 1,322,485   Data last updated: 2017-06-05
Format description: hgcGeneGraph links between genes and enough info to draw a graph
On download server: MariaDB table dump directory
fieldexampleSQL type description
gene1 2varchar(255) Gene pair, symbol1 (first in alphabet)
gene2 C2varchar(255) Gene pair, symbol2 (second in alphabet)
linkTypes ppivarchar(255) comma-sep list of pwy (=pathway),ppi (=ppi-db), text. If ppi or pwy: low if low-throughput assay
pairCount 0int(11) text mining document count in gene1->gene2 direction
oppCount 0int(11) text mining document count in gene2->gene1 direction
docCount 0int(11) text mining document count for both directions
dbList ophid|hprdvarchar(255) |-separated list of databases that have curated this gene pair
minResCount 3int(11) minimum number of interactions assigned to any paper supporting this interaction. If this value is lower than X, the interaction is considered low-throughput-supported.
snippet  longblob if linkType contains 'text': selected sentence from text-mined results
context  longblob select document contexts (e.g. diseases or pathways)

Connected Tables and Joining Fields
        hg16.kgXref.geneSymbol (via ggLink.gene1)
      hg17.kgXref.geneSymbol (via ggLink.gene1)
      hg18.kgXref.geneSymbol (via ggLink.gene1)
      hg18.omimGeneMap.geneSymbol (via ggLink.gene1) Note: genome-wide queries are not available for this table.
      hg18.omimGeneMap2.geneSymbol (via ggLink.gene1) Note: genome-wide queries are not available for this table.
      hg19.kgXref.geneSymbol (via ggLink.gene1)
      hg19.omimGeneMap.geneSymbol (via ggLink.gene1) Note: genome-wide queries are not available for this table.
      hg19.omimGeneMap2.geneSymbol (via ggLink.gene1) Note: genome-wide queries are not available for this table.
      hg38.kgXref.geneSymbol (via ggLink.gene1)
      hg38.omimGeneMap.geneSymbol (via ggLink.gene1) Note: genome-wide queries are not available for this table.
      hg38.omimGeneMap2.geneSymbol (via ggLink.gene1) Note: genome-wide queries are not available for this table.
      hgFixed.ggGeneClass.gene (via ggLink.gene1)
      hgFixed.ggGeneName.gene (via ggLink.gene1)

Sample Rows
 
gene1gene2linkTypespairCountoppCountdocCountdbListminResCountsnippetcontext
2C2ppi000ophid|hprd3
2C3ppi000hprd8
2C4Bppi000hprd8
2C4BPAppi000ophid|hprd2
2C5ppi000hprd8
2CD46ppi000ophid|hprd3
2CFBppi000ophid|hprd3
2CR1ppi000ophid|hprd3
2EEF1A1ppi000ophid|hprd2
2MASP1ppi000hprd5

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.