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Molecular Interaction Query Language (MIQL) reference extended to MITAB 2.7
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Updated Jul 17, 2013 by mdumouss...@yahoo.com

MIQL 2.7

The Molecular Interactions Query Language (MIQL) defines a way to allow more powerful and flexible queries by using a specific syntax when doing searches. If we have a common way to access the data (PSICQUIC), we need a common way to write the search queries. In most cases, searches are done for a specific identifier or group of identifiers. However, the service is not limited to these. For instance, there are ways to search for specific organisms, interaction detection methods or publication identifiers. The MIQL defines how these kind of queries can be done.

MIQL is a consensus between the different databases, so you should be able to use the same query across different repositories. It is based on the PSIMITAB 2.7 format and allows to search for data in specific columns, by using the fields explained in the next section.

The MIQL syntax is based on Lucene's syntax. A query is broken into terms and operators:

  • Terms: single words or phrases (group of words surrounded by quotes). E.g. brca2 or "pull down"
  • Fields: used to search in a specific column. See the next section for the specific field names. E.g. species:human
  • Term modifiers: wildcard searches, fuzzy searches, proximity and range searches. E.g. brc*
  • Operands: OR (or space), AND, NOT, +, -. E.g. brca2 AND rpa1 or brca2 NOT mouse or +brca2 –mouse –complex:spoke
  • Grouping and field grouping: brca2 AND (mouse "in vitro")

Fields

The following table shows the available standard fields that can be used in PSICQUIC searches:

Field Name Searches on MITAB 2.7 Columns Example
idA Identifier A 1 idA:P74565
idB Identifier B 2 idB:P74565
id Identifiers (A or B) 1..4 id:P74565
alias Aliases (A or B) 5, 6 alias:(KHDRBS1 OR HCK)
identifier Identifiers (A or B) or Alternatives (A or B) Aliases (A or B) 1..6 identifier:P74565
pubauth Publication 1st author(s) 8 pubauth:scott
pubid Publication Identifier(s) 9 pubid:(10837477 OR 12029088)
taxidA Tax ID interactor A: be it the tax ID or the species name 10 taxidA:mouse
taxidB Tax ID interactor B: be it the tax ID or species name 11 taxidB:9606
species Species. Tax ID A and Tax ID B 10, 11 species:human
type Interaction type(s) 12 type:"physical association"
detmethod Interaction Detection method(s) 7 detmethod:"two hybrid*"
interaction_id Interaction identifier(s) 14 interaction_id:EBI-761050
pbioroleA Biological role A 17 pbioroleA:ancillary
pbioroleB Biological role B 18 pbioroleB:"MI:0684"
pbiorole Biological roles (A or B) 17, 18 pbiorole:enzyme
ptypeA Interactor type A 21 ptypeA:protein
ptypeB Interactor type B 22 ptypeB:"gene"
ptype Interactor types (A or B) 21, 22 pbiorole:"small molecule"
pxrefA Interactor xref A (or Identifier A) 23, 1 pxrefA:"GO:0003824"
pxrefB Interactor xref B (or Identifier B) 24, 2 pxrefB:"GO:0003824"
pxref Interactor xrefs (A or B or Identifier A or Identifier B) 23, 24, 1, 2 pxref:"catalytic activity"
xref Interaction xrefs (or Interaction identifiers) 25, 14 xref:nuclear pore
annot Interaction annotations and tags 26 annot:"internally curated"
udate Update date 32 udate:[20100101 TO 20120101]
negative Negative interaction boolean 36 negative:true
complex Complex expansion 16 complex:"spoke expanded" or complex:"MI:1060"
ftypeA Feature type of participant A 37 ftypeA:"sufficient to bind"
ftypeB Feature type of participant B 38 ftypeB:mutation
ftype Feature type of participant A or B 37, 38 ftype:"binding site"
pmethodA Participant identification method A 41 pmethodA:"western blot"
pmethodB Participant identification method B 42 pmethodB:"sequence tag identification"
pmethod Participant identification methods (A or B) 41, 42 pmethod:immunostaining
stc Stoichiometry (A or B). Only true or false, just to be able to filter interaction having stoichiometry available 39, 40 stc:true
param Interaction parameters. Only true or false, just to be able to filter interaction having parameters available 30 param:true


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