corefmentions.json

{
  "documents":{
    "350376968":{
      "id":"",
      "text":"Phosphorylated MEK activates K-RAS.",
      "sentences":[{
        "words":["Phosphorylated","MEK","activates","K-RAS","."],
        "startOffsets":[0,15,19,29,34],
        "endOffsets":[14,18,28,34,35],
        "tags":["VBN","NN","VBZ","NN","."],
        "lemmas":["phosphorylate","mek","activate","k-ra","."],
        "entities":["O","B-Family","O","B-Gene_or_gene_product","O"],
        "chunks":["B-NP","I-NP","B-VP","B-NP","O"],
        "graphs":{
          "stanford-basic":{
            "edges":[{
              "source":0,
              "destination":1,
              "relation":"dobj"
            },{
              "source":2,
              "destination":0,
              "relation":"csubj"
            },{
              "source":2,
              "destination":3,
              "relation":"dobj"
            }],
            "roots":[2]
          },
          "stanford-collapsed":{
            "edges":[{
              "source":0,
              "destination":1,
              "relation":"dobj"
            },{
              "source":2,
              "destination":0,
              "relation":"csubj"
            },{
              "source":2,
              "destination":3,
              "relation":"dobj"
            }],
            "roots":[2]
          }
        }
      }]
    }
  },
  "mentions":[{
    "type":"CorefTextBoundMention",
    "id":"T:-1519180061",
    "text":"MEK",
    "labels":["Family","Equivalable","BioChemicalEntity","BioEntity","Entity","PossibleController"],
    "tokenInterval":{
      "start":1,
      "end":2
    },
    "characterStartOffset":15,
    "characterEndOffset":18,
    "sentence":0,
    "document":"350376968",
    "keep":true,
    "foundBy":"ner-family-entities",
    "modifications":[{
      "modification-type":"PTM",
      "label":"Phosphorylation",
      "evidence":{
        "type":"CorefTextBoundMention",
        "id":"T:396586846",
        "text":"Phosphorylated",
        "labels":["ModificationTrigger"],
        "tokenInterval":{
          "start":0,
          "end":1
        },
        "characterStartOffset":0,
        "characterEndOffset":14,
        "sentence":0,
        "document":"350376968",
        "keep":true,
        "foundBy":"modification_trigger_1",
        "grounding":{
          "text":"Phosphorylated",
          "key":"phosphorylated",
          "namespace":"uaz",
          "id":"UAZ00001",
          "species":""
        },
        "displayLabel":"ModificationTrigger"
      },
      "negated":false
    }],
    "grounding":{
      "text":"MEK",
      "key":"mek",
      "namespace":"uaz",
      "id":"UAZ-PF-132",
      "species":"human"
    },
    "displayLabel":"Family"
  },{
    "type":"CorefTextBoundMention",
    "id":"T:-2037729273",
    "text":"K-RAS",
    "labels":["Gene_or_gene_product","MacroMolecule","Equivalable","BioChemicalEntity","BioEntity","Entity","PossibleController"],
    "tokenInterval":{
      "start":3,
      "end":4
    },
    "characterStartOffset":29,
    "characterEndOffset":34,
    "sentence":0,
    "document":"350376968",
    "keep":true,
    "foundBy":"ner-gene_or_gene_product-entities",
    "grounding":{
      "text":"KRAS",
      "key":"kras",
      "namespace":"uniprot",
      "id":"P01116",
      "species":"human"
    },
    "displayLabel":"Protein"
  },{
    "type":"CorefEventMention",
    "id":"E:38453071",
    "text":"MEK activates K-RAS",
    "labels":["Positive_activation","ActivationEvent","ComplexEvent","Event","PossibleController"],
    "trigger":{
      "type":"CorefTextBoundMention",
      "id":"T:786232869",
      "text":"activates",
      "labels":["Positive_activation","ActivationEvent","ComplexEvent","Event","PossibleController"],
      "tokenInterval":{
        "start":2,
        "end":3
      },
      "characterStartOffset":19,
      "characterEndOffset":28,
      "sentence":0,
      "document":"350376968",
      "keep":true,
      "foundBy":"Positive_activation_token_1_verb",
      "displayLabel":"Positive_activation"
    },
    "arguments":{
      "controller":[{
        "type":"CorefTextBoundMention",
        "id":"T:-1519180061",
        "text":"MEK",
        "labels":["Family","Equivalable","BioChemicalEntity","BioEntity","Entity","PossibleController"],
        "tokenInterval":{
          "start":1,
          "end":2
        },
        "characterStartOffset":15,
        "characterEndOffset":18,
        "sentence":0,
        "document":"350376968",
        "keep":true,
        "foundBy":"ner-family-entities",
        "modifications":[{
          "modification-type":"PTM",
          "label":"Phosphorylation",
          "evidence":{
            "type":"CorefTextBoundMention",
            "id":"T:396586846",
            "text":"Phosphorylated",
            "labels":["ModificationTrigger"],
            "tokenInterval":{
              "start":0,
              "end":1
            },
            "characterStartOffset":0,
            "characterEndOffset":14,
            "sentence":0,
            "document":"350376968",
            "keep":true,
            "foundBy":"modification_trigger_1",
            "grounding":{
              "text":"Phosphorylated",
              "key":"phosphorylated",
              "namespace":"uaz",
              "id":"UAZ00001",
              "species":""
            },
            "displayLabel":"ModificationTrigger"
          },
          "negated":false
        }],
        "grounding":{
          "text":"MEK",
          "key":"mek",
          "namespace":"uaz",
          "id":"UAZ-PF-132",
          "species":"human"
        },
        "displayLabel":"Family"
      }],
      "controlled":[{
        "type":"CorefTextBoundMention",
        "id":"T:-2037729273",
        "text":"K-RAS",
        "labels":["Gene_or_gene_product","MacroMolecule","Equivalable","BioChemicalEntity","BioEntity","Entity","PossibleController"],
        "tokenInterval":{
          "start":3,
          "end":4
        },
        "characterStartOffset":29,
        "characterEndOffset":34,
        "sentence":0,
        "document":"350376968",
        "keep":true,
        "foundBy":"ner-gene_or_gene_product-entities",
        "grounding":{
          "text":"KRAS",
          "key":"kras",
          "namespace":"uniprot",
          "id":"P01116",
          "species":"human"
        },
        "displayLabel":"Protein"
      }]
    },
    "tokenInterval":{
      "start":1,
      "end":4
    },
    "characterStartOffset":15,
    "characterEndOffset":34,
    "sentence":0,
    "document":"350376968",
    "keep":true,
    "foundBy":"Positive_activation_token_1_verb",
    "displayLabel":"Positive_activation",
    "isDirect":false
  }]
}

ReachJSONExample.scala

import org.clulab.reach.PaperReader
import org.clulab.reach.mentions._
import org.clulab.reach.serialization.json._ 
import java.io.File


/** Example demonstrating how to serialize/deserialize 
 * [[org.clulab.reach.mentions.CorefMention]] to/from json 
 */
object ReachJSONExample extends App {
  
  val text = "Phosphorylated MEK activates K-RAS."
  // extract mentions and covert each to CorefMention
  val corefmentions: Seq[CorefMention] = PaperReader.getMentionsFromText(text).map(_.toCorefMention)

  // print the json string for the extracted mentions
  println(corefmentions.json(pretty=true))

  // save the json to a file  
  corefmentions.saveJSON("corefmentions.json", pretty = true)

  // deserialize the mentions json that was written in the last step
  val corefmentions2 = JSONSerializer.toCorefMentions(new File("corefmentions.json"))

  // demonstrate that the json of the deserialized mentions is equivalent to the original Seq[CorefMention]
  corefmentions.json(pretty = true) == corefmentions2.json(pretty = true)
}