ebinocle-ng-rsclient

EBI Search Angular REST client

Documentation

The documentation can be found at: http://ebi-wp.gitdocs.ebi.ac.uk/ebinocle-ng-rsclient

Install

npm i @ebi-wp/ebinocle-ng-rsclient

Usage example

The following example, creates a SearchRequest object, sets the domain and query. Then it gets the search results using that object.

import { Component } from '@angular/core';
import { Configuration, SearchRequest, SearchService } from '@ebi-wp/ebinocle-ng-rsclient';

@Component({
  selector: 'app-search',
  templateUrl: './search.component.html'
})
export class SearchComponent {
  constructor(private readonly searchService: SearchService) {}

  public search() {
    const searchRequest = new SearchRequest(new Configuration());
    searchRequest.setDB('embl');
    searchRequest.query = 'mouse';

    return this.searchService.getSearchResults(searchRequest);
  }
}

Simple search

In the following example we use the SearchService to submit a search to the embl domain with the query "mouse".

import { Component, OnInit } from '@angular/core';
import { Configuration, SearchRequest, SearchResults, SearchService } from '@ebi-wp/ebinocle-ng-rsclient';
import { Observable } from 'rxjs';

@Component({
  selector: 'app-search',
  templateUrl: './search.component.html'
})
export class SearchComponent implements OnInit {
  public searchResults: SearchResults;

  constructor(private readonly searchService: SearchService) {}

  public ngOnInit(): void {
    this.search().subscribe((searchResults) => {
      this.searchResults = searchResults;
    });
  }

  public search(): Observable<SearchResults> {
    const searchRequest = new SearchRequest(new Configuration());
    searchRequest.setDB('embl');
    searchRequest.query = 'mouse';

    return this.searchService.getSearchResults(searchRequest);
  }
}

Then in the HTML template:

<ng-container *ngIf="searchResults && searchResults.hitCount > 0">
  <div *ngFor="let entry of searchResults.entries">
    <p>{{ entry.id }}</p>
    <p>{{ entry.fields.description[0] }}</p>
  </div>
</ng-container>

Faceted search

To get facets along with a search result, the query and facetcount parameters are needed:

// ...
public search(): Observable<SearchResults> {
  const searchRequest = new SearchRequest(new Configuration());
  searchRequest.setDB('embl');
  searchRequest.query = 'mouse';
  searchRequest.facetcount = 10;

  return this.searchService.getSearchResults(searchRequest);
}
// ...

To extract the facets use:

// ...
this.search().subscribe((searchResults) => {
  this.facets = searchResults.facets;
});
// ...

To filter out by a list of selected facet values, the facets parameter can help. The value format for the parameter is a comma separated list of facet id:facet value:

// ...
public search(): Observable<SearchResults> {
  const searchRequest = new SearchRequest(new Configuration());
  searchRequest.setDB('embl');
  searchRequest.query = 'plantae';
  searchRequest.facetcount = 10;
  searchRequest.facets = 'taxonomy:1842';

  return this.searchService.getSearchResults(searchRequest);
}
// ...

Cross reference searching

Finding domains referred by an entry

Given a source domain and an entry we want to retrieve the referenced (target) domains:

// ...
public search(): Observable<SearchResults> {
  return this.searchService.getReferencedDomains('uniprot', 'Q9BYF1');
}
// ...

To extract the results:

// ...
this.search().subscribe((searchResults) => {
  for (const domain of searchResults.domains) {
    console.log(`Referenced domain ${domain.id} with ${domain.referenceEntryCount} entries`);
  }
});
// ...

Cross reference searching

To find entries in a target domain (europepmc in this case) referred to by a source domain (uniprot) and entry (Q9BYF1) use the following:

// ...
public search(): Observable<SearchResults> {
  return this.searchService.getReferencedEntries(
    'uniprot',
    'Q9BYF1',
    'europepmc',
    1
  );
}

// ...

To extract the results:

// ...
this.search().subscribe((searchResults) => {
  const reference = this.searchResults.entries[0];

  this.referencesResult = {
    hitCount: reference?.referenceCount,
    entries: reference?.references
  };
});
// ...