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 (free text 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 detmethod:P12345 OR type:P12345 OR interaction_id:P12345 OR xref:P12345 OR pxref:P12345 OR bioeffect:P12345 OR causalstatement:P12345
MIQL Fields
| Field Name | Searches on | Implicit* | Example |
| idA | Identifier A | No | idA:P74565 |
| idB | Identifier B | No | idB:P74565 |
| id | Identifiers (A or B) | No | id:P74565 |
| alias | Aliases (A or B) | No | alias:(KHDRBS1 HCK) |
| identifiers | Identifiers and Aliases undistinctively | Yes | identifier:P74565 |
| pubauth | Publication 1st author(s) | Yes | pubauth:scott |
| pubid | Publication Identifier(s) | Yes | pubid:(10837477 12029088) |
| taxidA | Tax ID interactor A: the tax ID or the species name | No | taxidA:mouse |
| taxidB | Tax ID interactor B: the tax ID or species name | No | taxidB:9606 |
| species | Species. Tax ID A or Tax ID B | Yes | species:human |
| type | Interaction type(s) | Yes | type:"physical interaction" |
| detmethod | Interaction Detection method(s) | Yes | detmethod:"two hybrid*" |
| interaction_id | Interaction identifier(s) | Yes | interaction_id:EBI-761050 |
| pbioroleA | Biological role A | No | pbioroleA:ancillary |
| pbioroleB | Biological role B | No | pbioroleB:"MI:0684" |
| pbiorole | Biological roles (A or B) | No | pbiorole:enzyme |
| ptypeA | Interactor type A | No | ptypeA:protein |
| ptypeB | Interactor type B | No | ptypeB:"gene" |
| ptype | Interactor types (A or B) | No | pbiorole:"small molecule" |
| pxrefA | Interactor xref A (or Identifier A) | No | pxrefA:"GO:0003824" |
| pxrefB | Interactor xref B (or Identifier B) | No | pxrefB:"GO:0003824" |
| pxref | Interactor xrefs (A or B or Identifier A or Identifier B) | Yes | pxref:"catalytic activity" |
| xref | Interaction xrefs (or Interaction identifiers) | Yes | xref:"nuclear pore" |
| annot | Interaction annotations and tags | No | annot:"internally curated" |
| udate | Update date | No | udate:[20100101 TO 20120101] |
| negative | Negative interaction boolean | No | negative:true |
| complex | Complex expansion | No | complex:"spoke expanded" |
| ftypeA | Feature type of participant A | No | ftypeA:"sufficient to bind" |
| ftypeB | Feature type of participant B | No | ftypeB:mutation |
| ftype | Feature type of participant A or B | No | ftype:"binding site" |
| pmethodA | Participant identification method A | No | pmethodA:"western blot" |
| pmethodB | Participant identification method B | No | pmethodB:"sequence tag identification" |
| pmethod | Participant identification methods (A or B) | No | pmethod:immunostaining |
| stc | Stoichiometry (A or B). Only true or false, just to be able to filter interaction having stoichiometry available | No | stc:true |
| param | Interaction parameters. Only true or false, just to be able to filter interaction having parameters available | No | param:true |
| bioeffectA | Biological effect of participant A | No | bioeffectA:"kinase activity" |
| bioeffectB | Biological effect of participant B | No | bioeffectB:"antioxidant activity" |
| bioeffect | Biological effect of participant A or B | Yes | bioeffect:"molecular carrier activity" |
| causalmechanism | The indirect causal regulatory mechanism between participants A and B | No | causalmechanism:"MI:2245" |
| causalstatement | The causal statement describing the effect of participant A on participant B | Yes | causalstatement:"up regulates" |
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 your 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.