AskOmics aims to provide a simple interface able to create complex queries on linked entities.
The query interface is customized based on available (both personal and public) integrated data.

Starting point¶

Any entity integrated with the starting entity type can be used to start a query. Other entities can still be queried through a linked entity.
The starting entity will start with its label already set to 'visible'.

Once the start entity is chosen, the query builder is displayed.

On the left-side of the query builder is the entity graph. Nodes (circles) represent entities and links represent relations between entities.
The currently selected entity is surrounded by a red circle. Dotted links and entities are not yet instantiated.

Filtering on attributes¶

The selected entity's attributes are shown as attribute boxes on the right of the graph.

Various filters are available to further refine the query, with each attribute type having its own filter:

• Entity URI, entity label, and String attribute type: exact match or regular expression (equal or not equal)
• Numeric attribute type, FALDO start, FALDO end: comparison operators
• Category attribute type, FALDO reference, FALDO strand: Value selection among a list
• Date attribute type: comparison operators with a date picker
• Boolean attribute type: "True" or "False" selector

Additional customization¶

In addition to the filter, several customization options are available for each attribute box. Depending on the attribute type, not all options will be available.

From left to right :

• : Mark the attribute as a form attribute. More information here.
• : Link this attribute to another (on a different entity or the same one).
  • This will filtrer based on the linked attribute value, with an optional modifier (See note).
• : Show all values for this attribute, including empty values.
• : Exclude one or more categories, instead of including.
  • Select where the attribute is not XXX.
• : Display the attribute value in the results.

Filtering on related entities¶

To query on a linked entity, simple click on a suggested node. The linked node will be surrounded in a red circle, and the list of attributes on the right-hand side will change to show the new node's attributes.

Explicit relations¶

Explicit relations between entities (defined by the "@" symbol in CSV files, and the "Parents"/"Derives_from" relations from GFF files) will appears between related entities. If the relation is a symetric relation, it will appear twice between entities.

FALDO relations¶

All FALDO entities will be linked by an implicit Included in relation. This relation is slightly different than explicit relations: it relies on the FALDO attributes of both entities for the query, instead of a direct link. This relation can be customized to either Included in, Overlap with, or Distant from.

FALDO entities are represented with a green circle and FALDO relations have a green arrow.

Filtering displayed relations¶

If there are too many related entities displayed, it can be difficult to select the entity you wish to link to. It is possible to filter the displayed relations on either the name of the entity, or the name of the link.

Simply type out the name you want to filter in either the "Filter links" or the "Filter nodes" fields on the top of the graph.

Removing instanciated relations¶

At any point, you can remove an instanciated node (and any node linked to it), by selecting the node you wish to remove, and using the Remove Node button at the top of the interface.

MINUS and UNION subqueries¶

Minus and Union nodes are an additional way of querying on relations. Both nodes are applied to an entity as an additional filter.

• Minus nodes remove results based on a subquery
  • Show all genes except those that match XXX
• Union nodes act as a "OR" between multiple subqueries
  • Show all genes that match either XXX or YYY

Both type of nodes can be integrated in a bigger query

• List genes linked to a mRNA, except mRNA linked to another entity
• List genes linked to a mRNA with either attribute A set to XXX, or attribute B set to YYY

MINUS nodes¶

Minus nodes remove from the results any instance that match a specific subquery.

• Display all genes that are not linked to an mRNA
• Display all genes that are not linked to an mRNA whose reference is XXX

The generated SPARQL query will look like this:

# Listing all genes NOT related to an mRNA by the 'Parent' relation.

SELECT DISTINCT ?gene1_Label
WHERE {
    ?gene1_uri rdf:type <http://askomics.org/data/gene> .
    ?gene1_uri rdfs:label ?gene1_Label .
    {
        MINUS {
        ?mRNA31_uri <http://askomics.org/data/Parent> ?gene1_uri .
        ?mRNA31_uri rdf:type <http://askomics.org/data/mRNA> .
        }
    }
}   

UNION node¶

UNION nodes implement the conditional OR.

• Display transcripts that are either
  • Linked to a 3′-UTR
  • Linked to a 5′-UTR

The generated SPARQL query will look like this:

# List all genes with an ortholog who has either the attribute "organism" set to "Arabidopsis thaliana", or the "reference" attribute set to "Chra01"
# Two sub-queries linked with an UNION

SELECT DISTINCT ?gene1_Label ?gene3_Label ?gene4_Label
WHERE {
    ?gene1_uri rdf:type <http://askomics.org/data/gene> .
    ?gene1_uri rdfs:label ?gene1_Label .
    {
        {
            ?gene1_uri <http://askomics.org/data/ortholog_of> ?gene26_uri .
            ?gene26_uri rdf:type <http://askomics.org/data/gene> .
            ?gene26_uri rdfs:label ?gene3_Label .
            ?gene26_uri faldo:location/faldo:begin/faldo:reference ?gene26_chromosomeCategory .
            VALUES ?gene26_chromosomeCategory { <http://askomics.org/data/Chra01> }
        }
        UNION {
            ?gene1_uri <http://askomics.org/data/ortholog_of> ?gene64_uri .
            ?gene64_uri rdf:type <http://askomics.org/data/gene> .
            ?gene64_uri rdfs:label ?gene4_Label .
            ?gene64_uri <http://askomics.org/data/organism> ?gene64_organismCategory .
            VALUES ?gene64_organismCategory { <http://askomics.org/data/Arabidopsis%20thaliana> }
        }
    }
}

Removing special nodes¶

Much like a "normal" node, you can remove special nodes (and any node linked to it) at any time by selecting it, and using the Remove Node button.

Launching queries¶

Once you are satisfied with your query, you can either:

• Preview the results (at most 30 rows) with Run & Preview
• Send a full query with Run & save

In the case of a full query, you will be able to access the query results (and more) on the results page