Search Tips

To do a search you can use the Molecular Interaction Query Language which is based on Lucene's syntax.

  • Use OR or space ' ' to search for ANY of the terms in a field
  • Use AND if you want to search for those interactions where ALL of your terms are found
  • Use quotes (") if you look for a specific phrase (group of terms that must be searched together) or terms containing special characters that may otherwise be interpreted by our query engine (eg. ':' in a GO term)
  • Use parenthesis for complex queries (e.g. '(XXX OR YYY) AND ZZZ')
  • Wildcards (*,?) can be used between letters in a term or at the end of terms to do fuzzy queries,
    but never at the beginning of a term
  • Optionally, you can prepend a symbol in from of your term.
    • + (plus): include this term. Equivalent to AND. e.g. +P12345
    • - (minus): do not include this term. Equivalent to NOT. e.g. -P12345
    • Nothing in front of the term. Equivalent to OR. e.g. P12345
  • Implicit fields are used when no field is specified (simple search). For instance, if you put 'P12345' in the simple query box, this will mean the same as identifier:P12345 OR pubid:P12345 OR pubauth:P12345 OR species:P12345 OR type:P12345 OR detmethod:P12345 OR interaction_id:P12345

MIQL Fields

Field NameSearches onImplicit*Example
idAIdentifier ANoidA:P74565
idBIdentifier BNoidB:P74565
idIdentifiers (A or B)Noid:P74565
aliasAliases (A or B)Noalias:(KHDRBS1 HCK)
identifiersIdentifiers and Aliases undistinctivelyYesidentifier:P74565
pubauthPublication 1st author(s)Yespubauth:scott
pubidPublication Identifier(s) ORYespubid:(10837477 12029088)
taxidATax ID interactor A: the tax ID or the species nameNotaxidA:mouse
taxidBTax ID interactor B: the tax ID or species nameNotaxidB:9606
speciesSpecies. Tax ID A or Tax ID BYesspecies:human
typeInteraction type(s)Yestype:"physical interaction"
detmethodInteraction Detection method(s)Yesdetmethod:"two hybrid*"
interaction_idInteraction identifier(s)Yesinteraction_id:EBI-761050
pbioroleABiological role AYespbioroleA:ancillary
pbioroleBBiological role BYespbioroleB:"MI:0684"
pbioroleBiological roles (A or B)Yespbiorole:enzyme
ptypeAInteractor type AYesptypeA:protein
ptypeBInteractor type BYesptypeB:"gene"
ptypeInteractor types (A or B)Yespbiorole:"small molecule"
pxrefAInteractor xref A (or Identifier A)YespxrefA:"GO:0003824"
pxrefBInteractor xref B (or Identifier B)YespxrefB:"GO:0003824"
pxrefInteractor xrefs (A or B or Identifier A or Identifier B)Yespxref:"catalytic activity"
xrefInteraction xrefs (or Interaction identifiers)Yesxref:"nuclear pore"
annotInteraction annotations and tagsYesannot:"internally curated"
udateUpdate dateYesudate:[20100101 TO 20120101]
negativeNegative interaction booleanYesnegative:true
complexComplex expansionYescomplex:"spoke expanded"
ftypeAFeature type of participant AYesftypeA:"sufficient to bind"
ftypeBFeature type of participant BYesftypeB:mutation
ftypeFeature type of participant A or BYesftype:"binding site"
pmethodAParticipant identification method AYespmethodA:"western blot"
pmethodBParticipant identification method BYespmethodB:"sequence tag identification"
pmethodParticipant identification methods (A or B)Yespmethod:immunostaining
stcStoichiometry (A or B). Only true or false, just to be able to filter interaction having stoichiometry availableYesstc:true
paramInteraction parameters. Only true or false, just to be able to filter interaction having parameters availableYesparam:true

Interaction clustering

This application allows you to query PSICQUIC services and browse their respective interactions. However these dataset can feature multiple evidence of two molecule interacting together, not only within one service but also across several. The same, redundant information may have been separately curated by multiple resources. The clustering feature will allow you to bring under a single binary interaction all evidences for that given pair of molecules. All details such as experimental methods, publications, source database, scoring will be aggregated in the resulting interaction.

How do we cluster your query

The method we are using is clustering together molecular interactions that are found to be between the same pair of molecules. That is, whenever the molecules are described using the same identifier from the following ordered list of public databases:

The order of the molecules, whether A-B or B-A does not matter and results in the same final data.

How to build a clustered query

First of all you need to build your query via the usual means, that is, typing a MIQL query in the search box and press the search button). On the right hand side of the services list should appear a button labelled 'Cluster this query'. So far the button will only be available if the sum of all interactions available for your query is no higher than 5000 interactions (we are working on relaxing these constraints in the future). Once you have pressed the button, a job will be created to process your request. The list of your jobs should appear above the button. The displayed status of each job can be as follows:

  • QUEUED: your job has been submitted but no work has yet been carried out,
  • RUNNING: your clustered query is being built,
  • COMPLETED: your clustered query is now ready to be used,
  • FAILED: the processing of you request has failed.

At any time, you can remove your job from the list by clicking the 'remove' link.

How to browse your clustered query

Once your job's status is set to COMPLETED, you can click on the 'view' link to open the set of interactions. The display is similar to the one you use to view the data of a given PSICQUIC service. Please note that the search functionality is disabled while browsing a clustered dataset. Should you want to return to the complete list of PSICQUIC services, you only need press the link 'back to all services' positioned at the top left of the interaction table.