NaCTeM

KLEIO

The query syntax used in KLEIO is summarised below. KLEIO's searching functions are implemented based on Lucene and the query syntax is the subset of Lucene.

Word Query:

Query TypeExampleComment
One word plain text query IL-2 The query will return all documents containing at least one occurrence of the word in their content.
Compound-word plain text query "ID card" The query will return all documents containing at least one occurrence of the compound word sequence formed by
Multi-word plain text query ID card The query will return all documents containing at least one occurrence of the sequence formed by the multi-words.

Boolean query:

Query TypeExampleComment
AND word-A AND word-B Returns all documents containing both word-A and word-B.
OR word-A OR word-B Returns all documents containing at least either word-A or word-B.
NOT word-A NOT word-B Returns all documents where word-A appears and word-B does not appear.
Note: You cannot use a NOT operater with just one term
(i.e. NOT word-A returns no results)
.

Query with a field:

Query TypeExampleComment
AUTHOR: AUTHOR:"Smith J" Returns all documents where "Smith J" appears as an author.
PUBLICATIONTYPE: PUBLICATIONTYPE:"Journal Article" Returns all documents of which the publication types include "Journal Article".
PUB_DATE:[20050101 TO 20061231] Returns all documents of which the published date is between 01/01/2005 and 31/12/2006
Note: Some articles have only year and month information as a publication date, for the articles. the day is set to 01. (e.g. "Jul, 2008" is converted into 20080701)

Semantic query:

Query TypeExampleComment
ACRONYM,
PROTEIN,
GENE,
METABOLITE,
DISEASE,
SYMPTOM,
ORGAN,
DIAG_PROC,
THERAPEUTIC_PROC,
GENERAL_PHENOM,
HUMAN_PHENOM,
NATURAL_PHENOM,
INDICATOR
PROTEIN:IL-2

DISEASE:"atopic eczema"
Using these operators it is possible to retrieve an entity of a given type.
Note: All operators should stay capitalised.
  • ACRONYM: recognised acronyms with AcroMine
  • PROTEIN, GENE: Annotated based on BioThesaurus and Genia corpus
  • METABOLITE: Annotated based on HMDB, DrugBank
  • The following entities are annotated based on UMLS Metathesaurus:
    • DISEASE, SYMPTOM, ORGAN,
    • DIAG_PROC, THERAPEUTIC_PROC,
      (diagnostic/therapeutic procedure, e.g. MRI, "cerebral blood flow")
    • GENERAL_PHENOM, HUMAN_PHENOM, NATURAL_PHENOM,
      (Medical phenomenon or process, e.g. "UV radiation" )
    • INDICATOR (Reagent or diagnostic aid, e.g. "hydrogen peroxide", "sulfhydryl reagent")

Combining query:

Query TypeExampleComment
- PROTEIN:IL-2 AND PUB_DATE:[20050101 TO 20061231] It is possible to combine different operators in a query to narrow down the retrieved results.