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Jeffrey S. Grethe, Ph.D edited this page Jan 19, 2018 · 14 revisions

InterLex Services

Production services are available at scicrunch.org. You can test services (especially if you are writing data) at beta.scicrunch.org

*Note: All endpoints below reference the Beta server

Community Preferences

Services are available to retrieve information on community preferences

Retrieve Community Preferred Terms

In order to filter for ReproNim specific terms you need to first retrieve the Community annotated terms

  • Community Short Name: The short name (abbreviation) for the community (e.g. crnc)
  • API Key: Your API key from your SciCrunch user dashboard

Request

curl -sv 'https://beta.scicrunch.org/api/1/ilx/community/terms/[Community Short Name]?key=[API Key]'

Request Example

curl -sv 'https://beta.scicrunch.org/api/1/ilx/community/terms/scicrunch?key=[API Key]'

Returned Value

{"data":["tmp_0107497","tmp_0107423","tmp_0101839","tmp_0100612","tmp_0105405","tmp_0102514"],"success":true}

Elastic Search Term Search

Pass through service to access full ElasticSearch query API. Full reference available at https://www.elastic.co/guide/en/elasticsearch/reference/5.1/query-dsl.html

Example of a boolean query

This query uses information based on a set of preferred terms (i.e. tmp_0102410) and searches for cde's that refer to age.

  • API Key: Your API key from your SciCrunch user dashboard

Request Example

curl -XGET 'https://beta.scicrunch.org/api/1/elastic-ilx/scicrunch/term/_search?key=[API KEY]' -H 'Content-Type: application/json' -d'
{
  "query": {
    "bool": {
       "must" : [
       {  "term" : { "type" : "cde" } },
       { "term" : { "ancestors.ilx" : "tmp_0139029" } },
       { "multi_match" : {
         "query":    "age", 
         "fields": [ "label", "definition" ] 
       } }
	]
    }
  }
}
'

Returned Data

{"took":38,"timed_out":false,"_shards":{"total":5,"successful":5,"failed":0},"hits":{"total":216,"max_score":1.9569439,"hits":[{"_index":"scicrunch","_type":"term","_id":"tmp_0139542","_score":1.9569439,"_source":{"ilx":"tmp_0139542","label":"bpmt_q1 (ABCD Brief Problem Monitor-Teacher Form For Ages 6-18 (BPMT))","definition":"Acts too young for his\/her age.","comment":"","type":"cde","status":"0","synonyms":[{"literal":"","type":""}],"existing_ids":[{"curie":"ILX:0139542","iri":"http:\/\/uri.interlex.org\/base\/ilx_0139542","preferred":"1"}],"superclasses":[{"ilx":"tmp_0139535","label":"ABCD Brief Problem Monitor-Teacher Form For Ages 6-18 (BPMT)"}],"ancestors":[{"ilx":"tmp_0139535","label":"ABCD Brief Problem Monitor-Teacher Form For Ages 6-18 (BPMT)"},{"ilx":"tmp_0139029","label":"NIMH Data Archive Common Data Element"}],"relationships":[{"relationship_term_ilx":"","relationship_term_label":"subClassOf","term2_ilx":"tmp_0139535","term2_label":"ABCD Brief Problem Monitor-Teacher Form For Ages 6-18 (BPMT)"}],"annotations":[{"value":"required : Recommended","annotation_term_label":"ABCD Brief Problem Monitor-Teacher Form For Ages 6-18 (BPMT)","annotation_term_ilx":"tmp_0139535"},{"value":"condition : None","annotation_term_label":"ABCD Brief Problem Monitor-Teacher Form For Ages 6-18 (BPMT)","annotation_term_ilx":"tmp_0139535"},{"value":"filterElement : None","annotation_term_label":"ABCD Brief Problem Monitor-Teacher Form For Ages 6-18 (BPMT)","annotation_term_ilx":"tmp_0139535"},{"value":"type : Integer","annotation_term_label":"ABCD Brief Problem Monitor-Teacher Form For Ages 6-18 (BPMT)","annotation_term_ilx":"tmp_0139535"},{"value":"size : None","annotation_term_label":"ABCD Brief Problem Monitor-Teacher Form For Ages 6-18 (BPMT)","annotation_term_ilx":"tmp_0139535"},{"value":"valueRange : 0 ; 1 ; 2","annotation_term_label":"ABCD Brief Problem Monitor-Teacher Form For Ages 6-18 (BPMT)","annotation_term_ilx":"tmp_0139535"},{"value":"notes : 0 = Not True (as far as you know); 1 = Somewhat True; 2 = Very True","annotation_term_label":"ABCD Brief Problem Monitor-Teacher Form For Ages 6-18 (BPMT)","annotation_term_ilx":"tmp_0139535"},{"annotation_term_ilx":"","value":"","annotation_term_label":"Synonym"}],"ontologies":[]}},{"_index":"scicrunch","_type":"term","_id":"tmp_0139614","_score":1.856132,"_source":{"ilx":"tmp_0139614","label":"nihtbx_dr_agecorrpatterncomp (ABCD NIH TBX_ Demo Rescore)","definition":"NIH Toolbox Pattern Comparison Processing Speed Test Age 7+ v2.0 - (Age-Corrected Standard Score)","comment":"","type":"cde","status":"0","synonyms":[{"literal":"","type":""}],"existing_ids":[{"curie":"ILX:0139614","iri":"http:\/\/uri.interlex.org\/base\/ilx_0139614","preferred":"1"}],"superclasses":[{"ilx":"tmp_0139567","label":"ABCD NIH TBX_ Demo Rescore"}],"ancestors":[{"ilx":"tmp_0139567","label":"ABCD NIH TBX_ Demo Rescore"},{"ilx":"tmp_0139029","label":"NIMH Data Archive Common Data Element"}],"relationships":[{"relationship_term_ilx":"","relationship_term_label":"subClassOf","term2_ilx":"tmp_0139567","term2_label":"ABCD NIH TBX_ Demo Rescore"}],"annotations":[{"value":"required : Recommended","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"condition : None","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"filterElement : None","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"type : String","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"size : 30","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"valueRange : None","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"notes : None","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"annotation_term_ilx":"","value":"","annotation_term_label":"Synonym"}],"ontologies":[]}},{"_index":"scicrunch","_type":"term","_id":"tmp_0139628","_score":1.856132,"_source":{"ilx":"tmp_0139628","label":"nihtbx_dr_agecorrengvocab (ABCD NIH TBX_ Demo Rescore)","definition":"NIH Toolbox Picture Vocabulary Test Age 3+ v2.0 - (Age-Corrected Standard Score)","comment":"","type":"cde","status":"0","synonyms":[{"literal":"","type":""}],"existing_ids":[{"curie":"ILX:0139628","iri":"http:\/\/uri.interlex.org\/base\/ilx_0139628","preferred":"1"}],"superclasses":[{"ilx":"tmp_0139567","label":"ABCD NIH TBX_ Demo Rescore"}],"ancestors":[{"ilx":"tmp_0139567","label":"ABCD NIH TBX_ Demo Rescore"},{"ilx":"tmp_0139029","label":"NIMH Data Archive Common Data Element"}],"relationships":[{"relationship_term_ilx":"","relationship_term_label":"subClassOf","term2_ilx":"tmp_0139567","term2_label":"ABCD NIH TBX_ Demo Rescore"}],"annotations":[{"value":"required : Recommended","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"condition : None","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"filterElement : None","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"type : String","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"size : 30","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"valueRange : None","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"notes : None","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"annotation_term_ilx":"","value":"","annotation_term_label":"Synonym"}],"ontologies":[]}},{"_index":"scicrunch","_type":"term","_id":"tmp_0139618","_score":1.856132,"_source":{"ilx":"tmp_0139618","label":"nihtbx_dr_agecorrlistsort (ABCD NIH TBX_ Demo Rescore)","definition":"NIH Toolbox List Sorting Working Memory Test Age 7+ v2.0 - (Age-Corrected Standard Score)","comment":"","type":"cde","status":"0","synonyms":[{"literal":"","type":""}],"existing_ids":[{"curie":"ILX:0139618","iri":"http:\/\/uri.interlex.org\/base\/ilx_0139618","preferred":"1"}],"superclasses":[{"ilx":"tmp_0139567","label":"ABCD NIH TBX_ Demo Rescore"}],"ancestors":[{"ilx":"tmp_0139567","label":"ABCD NIH TBX_ Demo Rescore"},{"ilx":"tmp_0139029","label":"NIMH Data Archive Common Data Element"}],"relationships":[{"relationship_term_ilx":"","relationship_term_label":"subClassOf","term2_ilx":"tmp_0139567","term2_label":"ABCD NIH TBX_ Demo Rescore"}],"annotations":[{"value":"required : Recommended","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"condition : None","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"filterElement : None","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"type : String","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"size : 30","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"valueRange : None","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"notes : None","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"annotation_term_ilx":"","value":"","annotation_term_label":"Synonym"}],"ontologies":[]}},{"_index":"scicrunch","_type":"term","_id":"tmp_0139578","_score":1.8035917,"_source":{"ilx":"tmp_0139578","label":"nihtbx_demo_rescore_fail___5 (ABCD NIH TBX_ Demo Rescore)","definition":"Rescore Failure Information ( 4, Age missing)","comment":"","type":"cde","status":"0","synonyms":[{"literal":"","type":""}],"existing_ids":[{"curie":"ILX:0139578","iri":"http:\/\/uri.interlex.org\/base\/ilx_0139578","preferred":"1"}],"superclasses":[{"ilx":"tmp_0139567","label":"ABCD NIH TBX_ Demo Rescore"}],"ancestors":[{"ilx":"tmp_0139567","label":"ABCD NIH TBX_ Demo Rescore"},{"ilx":"tmp_0139029","label":"NIMH Data Archive Common Data Element"}],"relationships":[{"relationship_term_ilx":"","relationship_term_label":"subClassOf","term2_ilx":"tmp_0139567","term2_label":"ABCD NIH TBX_ Demo Rescore"}],"annotations":[{"value":"required : Recommended","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"condition : None","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"filterElement : None","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"type : Integer","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"size : None","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"valueRange : 0 ; 1","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"notes : 0 = No; 1 = Yes","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"annotation_term_ilx":"","value":"","annotation_term_label":"Synonym"}],"ontologies":[]}},{"_index":"scicrunch","_type":"term","_id":"tmp_0139626","_score":1.7501827,"_source":{"ilx":"tmp_0139626","label":"nihtbx_dr_computedengvocab (ABCD NIH TBX_ Demo Rescore)","definition":"NIH Toolbox Picture Vocabulary Test Age 3+ v2.0 - (Computed Score)","comment":"","type":"cde","status":"0","synonyms":[{"literal":"","type":""}],"existing_ids":[{"curie":"ILX:0139626","iri":"http:\/\/uri.interlex.org\/base\/ilx_0139626","preferred":"1"}],"superclasses":[{"ilx":"tmp_0139567","label":"ABCD NIH TBX_ Demo Rescore"}],"ancestors":[{"ilx":"tmp_0139567","label":"ABCD NIH TBX_ Demo Rescore"},{"ilx":"tmp_0139029","label":"NIMH Data Archive Common Data Element"}],"relationships":[{"relationship_term_ilx":"","relationship_term_label":"subClassOf","term2_ilx":"tmp_0139567","term2_label":"ABCD NIH TBX_ Demo Rescore"}],"annotations":[{"value":"required : Recommended","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"condition : None","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"filterElement : None","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"type : String","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"size : 30","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"valueRange : None","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"notes : None","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"annotation_term_ilx":"","value":"","annotation_term_label":"Synonym"}],"ontologies":[]}},{"_index":"scicrunch","_type":"term","_id":"tmp_0139623","_score":1.7404397,"_source":{"ilx":"tmp_0139623","label":"nihtbx_dr_agecorrengread (ABCD NIH TBX_ Demo Rescore)","definition":"NIH Toolbox Oral Reading Recognition Test Age 3+ v2.0 - (Age-Corrected Standard Score)","comment":"","type":"cde","status":"0","synonyms":[{"literal":"","type":""}],"existing_ids":[{"curie":"ILX:0139623","iri":"http:\/\/uri.interlex.org\/base\/ilx_0139623","preferred":"1"}],"superclasses":[{"ilx":"tmp_0139567","label":"ABCD NIH TBX_ Demo Rescore"}],"ancestors":[{"ilx":"tmp_0139567","label":"ABCD NIH TBX_ Demo Rescore"},{"ilx":"tmp_0139029","label":"NIMH Data Archive Common Data Element"}],"relationships":[{"relationship_term_ilx":"","relationship_term_label":"subClassOf","term2_ilx":"tmp_0139567","term2_label":"ABCD NIH TBX_ Demo Rescore"}],"annotations":[{"value":"required : Recommended","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"condition : None","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"filterElement : None","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"type : String","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"size : 30","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"valueRange : None","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"notes : None","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"annotation_term_ilx":"","value":"","annotation_term_label":"Synonym"}],"ontologies":[]}},{"_index":"scicrunch","_type":"term","_id":"tmp_0139609","_score":1.7404397,"_source":{"ilx":"tmp_0139609","label":"nihtbx_dr_agecorrpsm (ABCD NIH TBX_ Demo Rescore)","definition":"NIH Toolbox Picture Sequence Memory Test Age 8+ Form A v2.0 - (Age-Corrected Standard Score)","comment":"","type":"cde","status":"0","synonyms":[{"literal":"","type":""}],"existing_ids":[{"curie":"ILX:0139609","iri":"http:\/\/uri.interlex.org\/base\/ilx_0139609","preferred":"1"}],"superclasses":[{"ilx":"tmp_0139567","label":"ABCD NIH TBX_ Demo Rescore"}],"ancestors":[{"ilx":"tmp_0139567","label":"ABCD NIH TBX_ Demo Rescore"},{"ilx":"tmp_0139029","label":"NIMH Data Archive Common Data Element"}],"relationships":[{"relationship_term_ilx":"","relationship_term_label":"subClassOf","term2_ilx":"tmp_0139567","term2_label":"ABCD NIH TBX_ Demo Rescore"}],"annotations":[{"value":"required : Recommended","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"condition : None","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"filterElement : None","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"type : String","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"size : 30","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"valueRange : None","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"notes : None","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"annotation_term_ilx":"","value":"","annotation_term_label":"Synonym"}],"ontologies":[]}},{"_index":"scicrunch","_type":"term","_id":"tmp_0139625","_score":1.619553,"_source":{"ilx":"tmp_0139625","label":"nihtbx_dr_thetaengvocab (ABCD NIH TBX_ Demo Rescore)","definition":"NIH Toolbox Picture Vocabulary Test Age 3+ v2.0 - (Theta)","comment":"","type":"cde","status":"0","synonyms":[{"literal":"","type":""}],"existing_ids":[{"curie":"ILX:0139625","iri":"http:\/\/uri.interlex.org\/base\/ilx_0139625","preferred":"1"}],"superclasses":[{"ilx":"tmp_0139567","label":"ABCD NIH TBX_ Demo Rescore"}],"ancestors":[{"ilx":"tmp_0139567","label":"ABCD NIH TBX_ Demo Rescore"},{"ilx":"tmp_0139029","label":"NIMH Data Archive Common Data Element"}],"relationships":[{"relationship_term_ilx":"","relationship_term_label":"subClassOf","term2_ilx":"tmp_0139567","term2_label":"ABCD NIH TBX_ Demo Rescore"}],"annotations":[{"value":"required : Recommended","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"condition : None","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"filterElement : None","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"type : String","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"size : 30","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"valueRange : None","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"notes : None","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"annotation_term_ilx":"","value":"","annotation_term_label":"Synonym"}],"ontologies":[]}},{"_index":"scicrunch","_type":"term","_id":"tmp_0139631","_score":1.5867546,"_source":{"ilx":"tmp_0139631","label":"nihtbx_dr_agecorrfluid (ABCD NIH TBX_ Demo Rescore)","definition":"NIH Toolbox Cognition Fluid Composite - (Age-Corrected Standard Score)","comment":"","type":"cde","status":"0","synonyms":[{"literal":"","type":""}],"existing_ids":[{"curie":"ILX:0139631","iri":"http:\/\/uri.interlex.org\/base\/ilx_0139631","preferred":"1"}],"superclasses":[{"ilx":"tmp_0139567","label":"ABCD NIH TBX_ Demo Rescore"}],"ancestors":[{"ilx":"tmp_0139567","label":"ABCD NIH TBX_ Demo Rescore"},{"ilx":"tmp_0139029","label":"NIMH Data Archive Common Data Element"}],"relationships":[{"relationship_term_ilx":"","relationship_term_label":"subClassOf","term2_ilx":"tmp_0139567","term2_label":"ABCD NIH TBX_ Demo Rescore"}],"annotations":[{"value":"required : Recommended","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"condition : None","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"filterElement : None","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"type : String","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"size : 30","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"valueRange : None","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"value":"notes : None","annotation_term_label":"hasConstraint","annotation_term_ilx":"tmp_0139457"},{"annotation_term_ilx":"","value":"","annotation_term_label":"Synonym"}],"ontologies":[]}}]}}

Term Utilization Mappings

Services are available to denote where terms are used (e.g. in databases, datasets, etc...)

Submit term - source mapping

  • source: The source where a term has been matched to or used in
  • value: Full value of the matched entity
  • martched_value: Term variant that matched
  • is_ambiguous: Are there multiple potential matches [true, false]
  • is_whole: Did the term match the full entity value [true, false]
  • source_level_1: First level of source where match occurred
  • source_level_2: Second level of source where match occurred
  • concept_id: The CURIE ID of the matched term
  • API Key: Your API key from your SciCrunch user dashboard
curl -sv -H 'Content-type: application/json' -X POST 'https://beta.scicrunch.org/api/1/term/mappings?key=[API Key]' --data '
{
    "source": “NIDM",
    "value": "test value 1",
    "matched_value": "value 1",
    "is_ambiguous": "false",
    "is_whole": "false",
    "source_level_1": "Source Part",
    "source_level_2": "Source Subpart",
    "concept_id": "CHEBI:48282"
}
'

Retrieve mappings by CURIE

  • CURIE: CURIE to search for (e.g. CHEBI:48282)
  • API Key: Your API key from your SciCrunch user dashboard
# search by curie
curl -sv 'https://beta.scicrunch.org/api/1/ilx/mappings/curie/[CURIE]?key=[API Key]'

Retrieve mappings by matched value

  • Matched Value: Value to search for (e.g. cerebellum)
  • API Key: Your API key from your SciCrunch user dashboard
curl -sv 'https://beta.scicrunch.org/api/1/ilx/mappings/value/[Matched Value]?key=[API Key]'
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