Search queries

Here you can learn how to build your search queries.

Search by string

Retrieve documents containing a specific string. Example: insulin

Search by document label

Find documents tagged with specific label and value.

Boolean example: label:isSevere:true

Enum example: label:severity:high

Search by entity type

Retrieve all documents containing at least one entity that belongs to the given entity type. Example: entity:disease, retrieves all documents with at least one entity of the type disease.

If you add a term, e.g. entity:disease:cancer, you can find all documents containing at least one entity using that term.


Only by using the entity type id, you can also perform more advanced queries as:

  • count e.g. count_e_1:[2 TO *]): retrieve documents with at least 2 annotations of the type e_1.
  • norms_count_uniq e.g. norms_count_uniq_e_1:[2 TO *] retrieve documents with at least 2 annotations of the type e_1 that are normalized to different unique names (e.g Rezulin and Romozin - same diabetic drug sold under different commercial names - would be normalized to troglitazone, so it would count 1 unique entity normalized, not 2).

Search by normalization

Retrieve all documents containing at least one entity that normalizes to the given normalization. Example: entity:genes:HER2, retrieves all documents with at least one entity gene that normalizes to HER2.

Search by date

Retrieve all documents imported or updated in a given time frame.

created: documents imported in a given time frame. Examples: created:2018, created:2018-03, created:2018-03-06, created:[2013 to NOW], created:[2016-12 TO 2017-02], created:[NOW-1DAY TO NOW] - documents imported since the previous day.

updated: documents updated in a given time frame. Examples: updated:2018, updated:2018-03, updated:2018-03-06, updated:[2013 to NOW], updated:[2016-12 TO 2017-02], updated:[NOW-1DAY TO NOW] - documents updated since the previous day.

Search confirmed documents

You can search which documents are confirmed with query: anncomplete:true.

You can search which documents are not confirmed with query: anncomplete:false.

Wildcard search

To perform a single character wildcard search use ?. Example: entity:gene:P?2649.

To perform a multiple character wildcard search use *. Example: "Kepler-2*", "Kepler-4*c".

Fuzzy search

Find similar terms (string based search) based on the Levenshtein Distance, or Edit Distance algorithm. Use ~ at the end of a single word term. Example: roam~ will also find terms as foam.

You can fine tune the similarity level by adding, at the end, a number between 0 (less similar) and 1 (more similar). Example: roam~0.8.

Proximity search

Finding words (string based search) within a specific distance away. Example: "diabetes insulin"~10, to search documents with the terms diabetes and insulin within 10 words of each other.

Boolean operators

Search queries can be combined using the operators AND, OR, NOT and -. Some examples:

  • entity:GGP AND entity:Mutation search for documents that contain GGP entities and Mutation entities.
  • "type 1 diabetes" OR insulin search for documents that contain "type 1 diabetes" or "insulin".
  • "type 1 diabetes" NOT insulin search for documents that contain "type 1 diabetes" but not "insulin". This operator cannot be used with just one term.
  • -entity:GGP search for documents that don't contain mentions of genes, i.e. GGP entities.

Escaping Special Characters

To escape these special characters use the \ before the character. For example to search for PD-L1 use the query: PD\-L1.

Experimental search query fields

These are currently valid for scientific articles.

Field Example Description
language language:fre Retrieve all documents written in the language specified
orgs orgs:university of Finland Retrieve all documents, which were written by authors with affiliations related to the term specified
authors_full authors_full:mueller
authors_key authors_key:"t goldberg"
publication publication:nature Retrieve all documents, which were written by the specified journal
published published:2018 published:2018-03-06 published:[2013 to NOW] Retrieve all documents published in a specified time frame.