How to search IntAct

Basic IntAct search

Searching for interactions in IntAct is very simple (Figure 18): Open the Search tab [A] and just paste the name or accession of your molecule(s) of interest in the search bar and press "Search". In this example, we use a list of proteins and we give their UniProtKB accessions.

The IntAct search page

Figure 18. The IntAct search page. [A] Search bar. [B] Quick search. [C] Ontology Search. [D] Other searches.

Different ways of searching in IntAct shown in the figure above:

[A]  The Search bar can be accessed using the search tab.

[B]  The Search tab view allows the use of the normal quick search.

[C]  Ontology Search: can be used  to search using more advanced features such as terms from the different controlled vocabularies that IntAct uses, such as the Gene Ontology or the PSI-MI ontology.

[D] Other Searches: can be used to do searches like a chemical search, in which we can look for interacting partners of a particular chemical substance or structure.

You can also use filters to refine your search, which we will describe next.

Advanced IntAct Search

Advanced searches in IntAct can be performed using the filtering options (Figure 19).

Advanced filtering search for a particular organism or method

Figure 19. Advanced filtering search for a particular organism or method.

 

In the search bar, look for the “Fields” link [A].

Using this link we can use specific fields to filter our search for a particular organism or method.

Once the search is performed, additional filters can be added to refine our search results.

Here we will show you how to use advanced search to filter your search with a particular organism and biological role.

Steps

 

  1. On the homepage open the advanced search option as shown
  2. In the 'Field' box select 'organism' and type in 'human' in the next box. You can now search for all human protein interactions in IntAct and other databases by clicking the 'Add and Search' button.
  3. To add more options in the advanced search, type 'species: human' in the main 'Search' box, open the 'Show Advanced Fields' and select the 'And' button.
  4. Now you can choose  'biological role' from the Field box and type 'enzyme' in the next box.

 

 

Next, we will describe how to search using the Molecular Interaction Query Language (MIQL).

Searching with MIQL

You can also build complex queries using the Molecular Interaction Query Language (MIQL). Press the "MIQL syntax reference" link to obtain a detailed description of the field aliases that you can use to build your MIQL search (Figure 20). The operators "NOT", "AND" and "OR" can be used to filter for more than one field and different fields can be grouped using parentheses. 

For example, imagine that you need to look for all the interactions involving the human protein HTT (Huntingtin) and any other human protein, but you want only those interactions detected using two-hybrid methodologies. You could use the following query:

                                       (alias:(htt) AND (taxidA:9606 AND taxidB:9606)) AND detmethod:”two hybrid*” 

 

An example of a MIQL query

Figure 20. Example of a MIQL query (boxed text) and the MIQL syntax summary that you can use to construct a MIQL query.

Next, we will show how to download your results.