Exploring at the network-level: Related Interactions

package.json

@@ -90,6 +90,7 @@
     "soap": "^0.25.0",
     "socket.io": "^2.1.1",
     "socket.io-client": "^2.1.1",
+    "string-similarity": "^4.0.4",
     "swagger-jsdoc": "^4.0.0",
     "swagger-ui-express": "^4.1.4",
     "tippy.js": "^2.6.0",

src/client-env-vars.json

@@ -22,5 +22,6 @@
   "DEMO_CAN_BE_SHARED_MULTIPLE_TIMES",
   "SAMPLE_DOC_ID",
   "EMAIL_ADDRESS_INFO",
-  "MAX_WAIT_TWEET"
+  "MAX_WAIT_TWEET",
+  "MAX_DOC_RELATED_PAPERS"
 ]

src/client/components/element-info/entity-info.js

@@ -9,7 +9,7 @@ import Notification from '../notification';
 import assocDisp from './entity-assoc-display';
 import CancelablePromise from 'p-cancelable';
 import { isComplex, isGGP, ELEMENT_TYPE } from '../../../model/element/element-type';
-import RelatedPapers from '../related-papers';
+import { RelatedInteractions } from '../related-papers';
 import Organism from '../../../model/organism';
 
 import { makeClassList, focusDomElement } from '../../dom';
@@ -605,7 +605,7 @@ class EntityInfo extends DataComponent {
         if( isComplex(s.element.type()) ){
           children.push( h('div.entity-info-assoc', targetFromAssoc({ type, name, entityNames }, true )) );
           children.push( h('div.entity-info-related-papers', [
-            h(RelatedPapers, { document, source: s.element })
+            h(RelatedInteractions, { document, source: s.element })
           ]) );
         } else {
           children.push( h('div.entity-info-no-assoc', [
@@ -618,10 +618,10 @@ class EntityInfo extends DataComponent {
       } else {
         children.push( h('div.entity-info-assoc', allAssoc( assoc, true, false )) );
 
-        children.push( h('div.entity-info-reld-papers-title', `Recommended articles`) );
+        children.push( h('div.entity-info-reld-papers-title', `Related interactions`) );
 
         children.push( h('div.entity-info-related-papers', [
-          h(RelatedPapers, { document, source: s.element })
+          h(RelatedInteractions, { document, source: s.element })
         ]) );
       }
     } else {

src/client/components/element-info/interaction-info.js

@@ -10,7 +10,7 @@ import Progression from './progression';
 import EventEmitter from 'eventemitter3';
 import { INTERACTION_TYPES, INTERACTION_TYPE } from '../../../model/element/interaction-type';
 // import { Carousel, CAROUSEL_CONTENT } from '../carousel';
-import RelatedPapers from '../related-papers';
+import { RelatedInteractions } from '../related-papers';
 
 let stageCache = new WeakMap();
 
@@ -236,10 +236,10 @@ class InteractionInfo extends DataComponent {
         //   h(Carousel, { content: CAROUSEL_CONTENT.ABSTRACT })
         // ]) );
 
-        summaryChildren.push( h('div.interaction-info-reld-papers-title', 'Recommended articles') );
-        
+        summaryChildren.push( h('div.interaction-info-reld-papers-title', 'Related interactions') );
+
         summaryChildren.push( h('div.interaction-info-related-papers', [
-          h(RelatedPapers, { document, source: el })
+          h(RelatedInteractions, { document, source: el })
         ]) );
       }
 

src/client/components/related-papers.js

@@ -1,8 +1,48 @@
 import h from 'react-hyperscript';
 import { Component } from 'react';
-import { DOI_LINK_BASE_URL, PUBMED_LINK_BASE_URL } from '../../config';
+import _ from 'lodash';
+import {
+  DOI_LINK_BASE_URL,
+  PUBMED_LINK_BASE_URL,
+  MAX_DOC_RELATED_PAPERS
+} from '../../config';
 
-const MAX_PAPERS = 6;
+class RelatedPapersLoading extends Component {
+  render(){
+    return h('div.related-papers.related-papers-loading', [
+      h('div.related-papers-empty-icon', [
+        h('i.icon.icon-spinner')
+      ]),
+      h('p.related-papers-loading-msg', [
+        `Biofactoid is looking for other interesting articles.`,
+        h('br'),
+        `They'll be ready for you in a moment.`
+      ])
+    ]);
+  }
+}
+
+class RelatedPaper extends Component {
+
+  render(){
+    const { title, authors: { abbreviation: author }, reference: journal, doi, pmid, pubTypes } = this.props.citation;
+    let link = `${DOI_LINK_BASE_URL}${doi}`;
+    if( !doi ) link = `${PUBMED_LINK_BASE_URL}${pmid}`;
+    const isReview = _.find(  pubTypes, ["UI", "D016454"] ) === undefined ? false : true;
+
+    return h('div.related-paper', [
+      h('a.related-paper-title.related-paper-link', {
+        href: link,
+        target: '_blank'
+      }, title),
+      h('div.related-paper-author', author),
+      h('div.related-paper-journal', [
+        isReview ? h('span.related-paper-journal-badge.super-salient-button', 'Review'): null,
+        journal
+      ])
+    ]);
+  }
+}
 
 export class RelatedPapers extends Component {
   constructor(props){
@@ -29,37 +69,134 @@ export class RelatedPapers extends Component {
     let { papers } = this.state;
 
     if( !papers ){
-      return h('div.related-papers.related-papers-empty', [
-        h('div.related-papers-empty-icon', [
-          h('i.icon.icon-spinner')
-        ]),
-        h('p.related-papers-empty-msg', [
-          `Biofactoid is looking for other interesting articles.`,
-          h('br'),
-          `They'll be ready for you in a moment.`
-        ])
-      ]);
+      return h( RelatedPapersLoading );
+    } else {
+      papers = papers.slice(0, MAX_DOC_RELATED_PAPERS);
+      return h('div.related-papers', papers.map( paper => h( RelatedPaper, { citation: paper.pubmed } ) ) );
+    }
+  }
+}
+
+export class EvidenceComponent extends Component {
+  constructor(props){
+    super(props);
+  }
+
+  render(){
+
+    const { evidence } = this.props;
+    const { source, citation } = evidence;
+
+    // Format excerpts from the top evidence's sources
+    let excerptComponent = null;
+    const texts = _.compact( source.map( s => _.get( s, 'text' ) ) );
+    const hasExcerpts = !_.isEmpty( texts );
+    if( hasExcerpts ){
+      let excerpts = texts.map( text => h('div.related-interaction-evidence-source-excerpt', text ) );
+      excerptComponent = h('div.related-interaction-evidence-source-excerpts', excerpts );
     }
 
-    papers = papers.slice(0, MAX_PAPERS);
+    let paperComponent = h('div.related-interaction-evidence-paper', [ h( RelatedPaper, { citation } ) ]);
 
-    return h('div.related-papers', papers.map( paper => {
-      const { pubmed: { title, authors: { abbreviation: author }, reference: journal, abstract, doi, pmid } } = paper;
-      let link = `${DOI_LINK_BASE_URL}${doi}`;
-      if( !doi ) link = `${PUBMED_LINK_BASE_URL}${pmid}`;
+    // Database/source names
+    const isDatabaseType = s => s.type == 'db';
+    const getSourceName = s => s.name;
+    let sourceNames = source
+      .filter( isDatabaseType )
+      .map( getSourceName );
+    sourceNames = _.uniqBy( sourceNames, 'name' );
+    // names = _.filter( names, [ 'type', 'db' ] );
+    let namesComponent = sourceNames.length ?
+      h('div..related-interaction-evidence-sources', `Source: ${sourceNames.join( '; ' )}` ) :
+      null;
 
-      return h('a.related-paper', {
-        href: link,
-        target: '_blank'
-      }, [
-        h('div.related-paper-title', [
-          h('span.link-like.plain-link', title)
+    return h('div.related-interaction-evidence', [
+        excerptComponent,
+        paperComponent,
+        namesComponent
+    ]);
+  }
+}
+
+export class RelatedInteraction extends Component {
+  constructor(props){
+    super(props);
+  }
+
+  render(){
+
+    const { interaction } = this.props;
+    const { evidence, sentence } = interaction;
+
+    //// NB: To reduce data size, only show top evidence
+    // Link to more evidence (i.e. papers for the interaction )
+    // let additionalEvidenceLink = null;
+    // let numArticles = evidence.length;
+    // let hasMoreEvidence = numArticles > 1;
+    // if( hasMoreEvidence ){
+    //   additionalEvidenceLink = h('a.related-interaction-additional-evidence.related-paper-link', {
+    //     target: '_blank'
+    //   }, `Show more articles (${numArticles})` );
+    // }
+
+    return h('div.related-interaction', [
+      h('div.related-interaction-body', [
+        h('div.related-interaction-meta', [
+          h('div.related-interaction-sentence', sentence )
         ]),
-        h('div.related-paper-abstract', abstract),
-        h('div.related-paper-author', author),
-        h('div.related-paper-journal', journal)
-      ]);
-    }));
+        h( EvidenceComponent, { evidence: _.head( evidence ) })
+      ]),
+      // h('div.related-interaction-footer', [
+      //   additionalEvidenceLink
+      // ])
+    ]);
+
+  }
+}
+
+export class RelatedInteractions extends Component {
+  constructor(props){
+    super(props);
+
+    this.state = {
+      papers: this.props.source.relatedPapers()
+    };
+  }
+
+  componentDidMount(){
+    this.onRefresh = () => {
+      this.setState({ papers: this.props.source.relatedPapers() });
+    };
+
+    this.props.source.on('relatedpapers', this.onRefresh);
+  }
+
+  componentWillUnmount(){
+    this.props.source.removeListener('relatedpapers', this.onRefresh);
+  }
+
+  render(){
+    let { papers } = this.state;
+
+    // Haven't loaded yet
+    if( !papers ) return h( RelatedPapersLoading );
+
+    const emptyComponent = h('div.related-papers.related-papers-empty', [
+      h('p.related-papers-empty-msg', 'There were no interactions found for the selected item' )
+    ]);
+
+    // Nothing here to show
+    if( _.isEmpty( papers ) ) return emptyComponent;
+
+    // Backwards-compatibility: Check schema { type, sentence, evidence, participants }
+    let areInteractions = papers.every( paper => _.has( paper, 'evidence' ) && _.has( paper, 'sentence' ) );
+    if( !areInteractions )  return emptyComponent;
+
+    // OK - Display interactions
+    const interactions = papers;
+    return h('div.related-interactions',
+              interactions.map( interaction => h( RelatedInteraction, { interaction } ) )
+            );
   }
 }
 

src/config.js

@@ -125,7 +125,10 @@ export const SAMPLE_DOC_ID = env('SAMPLE_DOC_ID', '5df17c41-acb7-4c42-a37b-fe323
 export const NO_ABSTRACT_HANDLING = env('NO_ABSTRACT_HANDLING', 'text');
 export const MIN_SEMANTIC_SCORE = env('MIN_SEMANTIC_SCORE', 0.47);
 export const SEMANTIC_SEARCH_LIMIT = env('SEMANTIC_SEARCH_LIMIT', 30);
-export const MIN_RELATED_PAPERS = env('MIN_RELATED_PAPERS', 6);
+export const MAX_DOC_RELATED_PAPERS = env('MAX_DOC_RELATED_PAPERS', 5);
+export const MAX_STATEMENTS =  env('MAX_STATEMENTS', 10);
+export const MAX_STATEMENTS_ELEMENT = env('MAX_STATEMENTS_ELEMENT', 5);
+export const EVIDENCE_LIMIT =  env('EVIDENCE_LIMIT', 1);
 
 // google analytics
 export const GA_ID = env('GA_ID', 'UA-43341809-12');