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The kabob-query project provides a command-line interface (CLI) for querying kabob via a collection of predefined query templates. These queries are meant to be representative of common queries a user may be interested in submitting. The query templates are by no means an exhaustive representation of the kinds of information available in kabob.

Note: In the future, the kabob-query CLI will be self-documenting, however while that functionality is under construction this page will be used to demonstrate/document example queries supported by the CLI.

KaBOB Query CLI examples

All participants for a biological process

• Input: a Gene Ontology biological process concept, e.g. obo:GO_0001525

• CLI command example:

  $ java -jar target/kabob-query-0.1.0-SNAPSHOT-standalone.jar \
    kabob-query/cli \
   -q sparql/process/participants \
   -a "[\"obo:GO_0001525\"]" \
   -p "{:db-url \"http://repository_url:port\" :repository-name \"kabob-dev\" :username \"USER\" :password \"*****\"}"

• Sample output:

  process_id, ext_participant_ids
  obo:GO_0001525, pr:A0JPN4;refseq:NP_001071139;refseq:XP_006238927;uniprot:A0JPN4
  obo:GO_0001525, uniprot:C9JCL2
  obo:GO_0001525, uniprot:J3QRR7
  

All biological processes for a given participant protein

• Input: a protein identifier, e.g. uniprot:P24941

• CLI command example:

  $ java -jar target/kabob-query-0.1.0-SNAPSHOT-standalone.jar \
    kabob-query/cli \
   -q sparql/protein/processes \
   -a "[\"uniprot:P24941\"]" \
   -p "{:db-url \"http://repository_url:port\" :repository-name \"kabob-dev\" :username \"USER\" :password \"*****\"}"

• Sample output:

  source_id, bp, label
  uniprot:P24941, obo:GO_0007265, Ras protein signal transduction
  uniprot:P24941, obo:GO_0006468, protein phosphorylation
  uniprot:P24941, obo:GO_0016572, histone phosphorylation
  

All cellular component locations for a given protein

• Input: a protein identifier, e.g. uniprot:P24941

• CLI command example:

  $ java -jar target/kabob-query-0.1.0-SNAPSHOT-standalone.jar \
    kabob-query/cli \
   -q sparql/protein/cellular-components \
   -a "[\"uniprot:P24941\"]" \
   -p "{:db-url \"http://repository_url:port\" :repository-name \"kabob-dev\" :username \"USER\" :password \"*****\"}"

• Sample output:

  source_id, cc, label
  uniprot:P24941, obo:GO_0005737, cytoplasm
  uniprot:P24941, obo:GO_0005813, centrosome
  uniprot:P24941, obo:GO_0005815, microtubule organizing center
  

All binary interaction partners for given protein

• Input: a protein identifier, e.g. uniprot:P24941

• CLI command example:

  $ java -jar target/kabob-query-0.1.0-SNAPSHOT-standalone.jar \
    kabob-query/cli \
   -q sparql/protein/binary-interaction-partners \
   -a "[\"uniprot:P24941\"]" \
   -p "{:db-url \"http://repository_url:port\" :repository-name \"kabob-dev\" :username \"USER\" :password \"*****\"}"

• Sample output:

  ext_source_id, interaction_label, ext_partner_ids
  uniprot:P24941, physical association, irefweb:39428984;pr:P29144;refseq:NP_003282;uniprot:P29144
  uniprot:P24941, physical association, irefweb:98817308;pr:P27708;refseq:NP_001293008;refseq:NP_004332;uniprot:F8VPD4;uniprot:P27708
  uniprot:P24941, physical association, irefweb:20082085;pr:P78396;refseq:NP_001104515;refseq:NP_001104516;refseq:NP_001104517;refseq:NP_003905;refseq:XP_011533596;refseq:XP_011533597;refseq:XP_011533598;refseq:XP_011533599;uniprot:P78396
  

The label(s) for given bio-entity

• Input: a bio-entity identifier, e.g. drugbank:DB01076

• CLI command example:

  $ java -jar target/kabob-query-0.1.0-SNAPSHOT-standalone.jar \
    kabob-query/cli \
   -q sparql/label/bioentity-label \
   -a "[\"drugbank:DB01076\"]" \
   -p "{:db-url \"http://repository_url:port\" :repository-name \"kabob-dev\" :username \"USER\" :password \"*****\"}"

• Sample output:

  entity_id, label
  drugbank:DB01076, Atorvastatin
  

The protein targets for a given drug

• Input: a drug identifier, e.g. drugbank:DB01076

• CLI command example:

  $ java -jar target/kabob-query-0.1.0-SNAPSHOT-standalone.jar \
    kabob-query/cli \
   -q sparql/drug/protein-targets \
   -a "[\"drugbank:DB01076\"]" \
   -p "{:db-url \"http://repository_url:port\" :repository-name \"kabob-dev\" :username \"USER\" :password \"*****\"}"

• Sample output:

  drugbank:DB05739, irefweb:55726284;irefweb:90401684;pr:P30556;refseq:NP_000676;refseq:NP_004826;refseq:NP_033611;refseq:NP_114038;uniprot:D3DNG8;uniprot:P30556;uniprot:Q53YY0;uniprot:Q6NUP5
  drugbank:DB05739, irefweb:113488704;pr:P50052;refseq:NP_000677;refseq:XP_011535835;uniprot:P50052
  

The drugs that target a given protein

• Input: a protein identifier, e.g. uniprot:Q6NUP5

• CLI command example:

  $ java -jar target/kabob-query-0.1.0-SNAPSHOT-standalone.jar \
    kabob-query/cli \
   -q sparql/protein/targeted-by-drug \
   -a "[\"uniprot:Q6NUP5\"]" \
   -p "{:db-url \"http://repository_url:port\" :repository-name \"kabob-dev\" :username \"USER\" :password \"*****\"}"

• Sample output:

  ext_source_id, ext_drug_ids
  uniprot:Q6NUP5, binding_db:50049186;chebi:9927;chemspider:54833;dpd:11702;dpd:2244781;drugbank:DB00177;drugcodedirectory:0078-0360-34;guide_to_pharmacology:3937;iuphar:3937;kegg:D00400;pharmgkb:PA451848;pubchem_compound:60846;pubchem_substance:46509000;wikipedia:Valsartan
  uniprot:Q6NUP5, binding_db:50049209;chemspider:117146;drugbank:DB01342;pharmgkb:PA164776845;pubchem_compound:132706;pubchem_substance:46505698
  uniprot:Q6NUP5, chebi:4814;dpd:11894;dpd:2243942;drugbank:DB00876;kegg:C07467;kegg:D04040;pharmgkb:PA449481;pubchem_compound:5281037;pubchem_substance:46506765;wikipedia:Eprosartan