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The Intermine API
Nicolas Coutin
May 14, 2015
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The PathQuery API

InterMine installations accept queries over their data in a custom format known as Path-Queries. This is a graph-based query format which inherits some of its semantics and terminology from SQL.

Paths

The core concept of Path-Queries is naturally enough the Path, examples of which are:

  • Gene: A plain root
  • Gene.symbol: A root and an attribute
  • Gene.chromosomeLocation: A reference to a complex attribute (a reference)
  • Gene.organism.name: A chain from a root to an attribute through one or more references.
  • Gene.pathways.identifier: A path may potentially match multiple values - there may be several pathway identifiers that match this path for any given gene.
  • Protein.gene.homologues.homologue.alleles.alleleClass: Paths may be of arbitrary length.

In the XML serialization of path-queries, all paths must be completely qualified. In the JSON format a prefix can be specified with the from or root property.

query()

  • model = "genomic"
  • view = "Organism.name Organism.taxonId"
  • name = "the name of the query"
  • sortOrder = "Gene.secondaryIdentifier ASC"
  • constraintLogic = "A and B"

join()

  • path = "a.path"
  • style = "OUTER"

constraint()

  • path = ""
  • type = ""
  • op = ""
  • value = ""
  • extraValue = ""
  • code = ""

data used in this study

In D. melanogaster, the Karpen group used ChIP-chip and ChIP-seq to assay the binding sites of chromatin binding and modification proteins in four fly cell lines: S2, BG3, Kc and Cl.8.

  • i.e. from Gary Karpen's lab @ Lawrence Berkeley National Laboratory.