schema.gql

define

# common attributes
confidence sub attribute, datatype double;

pubmed-article sub entity,
  has pmid,
  has title,
  has annotated-abstract,
  plays mined-text;

pmid sub attribute, datatype string;
title sub attribute, datatype string;
annotated-abstract sub attribute, datatype string,
  plays abstract-container,
  plays owner;

sentence sub entity,
  has sentiment,
  has text,
  plays contained-sentence,
  plays sentence-container,
  plays mentioning-sentence;

sentiment sub attribute, datatype string;
text sub attribute, datatype string;

token sub entity,
  has start-position,
  has end-position,
  has tag,
  has ner,
  has lemma,
  plays contained-token,
  plays object,
  plays subject;

start-position sub attribute, datatype double;
end-position sub attribute, datatype double;
tag sub attribute, datatype string;
ner sub attribute, datatype string,
    has confidence;
lemma sub attribute, datatype string;

mined-relation sub relation,
    has relation-type,
    has confidence,
    relates object,
    relates subject,
    relates mentioning-sentence,
    plays extracted-relation;

relation-type sub attribute, datatype string;

entity-mention sub entity,
    has value,
    has entity-type,
    plays mentioned-entity,
    plays containing-entity;

entity-type sub attribute, datatype string;
value sub attribute, datatype string;

mention sub relation,
    relates mentioned-entity,
    relates mentioning-sentence,
    plays owned,
    plays representative;

coref-chain sub relation,
    has chain-id,
    relates owner,
    relates owned,
    relates representative;

chain-id sub attribute, datatype double;

abstract-containing-sentence sub relation,
    relates abstract-container,
    relates contained-sentence;

sentence-containing-token sub relation,
    relates sentence-container,
    relates contained-token;

entity-containing-token sub relation,
    relates containing-entity,
    relates contained-token;

knowledge-extraction sub relation,
   relates extracted-knowledge,
   relates mined-text;

entity-extraction sub knowledge-extraction,
    relates extracted-entity as extracted-knowledge,
    relates mined-text;

relation-extraction sub knowledge-extraction,
    relates extracted-relation as extracted-knowledge,
    relates mined-text;


entity-extraction-rule sub rule,
when {
   $p isa pubmed-article, has annotated-abstract $a;
   ($a, $s) isa abstract-containing-sentence;
   ($s, $e) isa mention;
},
then {
  (extracted-entity: $e, mined-text: $p) isa entity-extraction;
};

relation-extraction-rule sub rule,
when {
   $p isa pubmed-article, has annotated-abstract $a;
   ($a, $s) isa abstract-containing-sentence;
   $mr ($s, $o, $su) isa mined-relation;
},
then {
  (extracted-relation: $mr, mined-text: $p) isa relation-extraction;
};