PDBe-KB Literature Panel Component

This repository is for the codebase of a lightweight Angular v7 web component that provides information on literature, generally from PubMed/EuropePMC.

This component is used on the PDBe-KB Aggregated Views of Proteins to display publications related to all the PDB entries of a UniProt accession.

Important: This web component depends on the "csv-exporter" component which is available from https://github.com/PDBe-KB/component-csv-exporter

Example:

Quick Start

Get the code and install dependencies

git clone https://github.com/PDBe-KB/component-literature-panel.git
cd component-literature-panel
npm i

Running the app

ng serve

Running tests

ng test

Dependencies

This web component embeds another PDBe web component: https://github.com/PDBe-KB/component-csv-exporter

In order to use all the features of this web component, retrieve the csv-exporter component and replace the contents of the src/app/csv-exporter folder with those files.

The main template (i.e. index.html by default) should also have the following CSS imports:

<link rel="stylesheet" href="https://ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.3/css/ebi-global.css" type="text/css" media="all"/>
<link rel="stylesheet" href="https://ebi.emblstatic.net/web_guidelines/EBI-Icon-fonts/v1.3/fonts.css" type="text/css" media="all"/>
<link rel="stylesheet" href="https://ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.3/css/theme-pdbe-green.css" type="text/css" media="all"/>

Basic usage

The component can be added to any Angular v7 apps.

1.) Import the component:

Import the component in app.module.ts by default.

import { BrowserModule } from '@angular/platform-browser';
import { NgModule } from '@angular/core';

import { AppComponent } from './app.component';
import { LiteratureComponent } from './literature/literature.component';
import { CsvExporterComponent } from './csv-exporter/csv-exporter.component';

@NgModule({
  declarations: [
    AppComponent,
    LiteratureComponent,
    CsvExporterComponent
  ],
  imports: [
    BrowserModule
  ],
  providers: [],
  bootstrap: [AppComponent]
})
export class AppModule { }

2.) Add the component to a template:

<app-literature [data]="publicationData" [accession]="accession"></app-literature>

The data model for the input data is described in src/app/literature/literature.models.ts

Example input data

{
  category: 'category',
  show_limit: 1,
  publications: [
    {
      title: 'Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation.',
      authors: 'Hendriks I.A., Lyon D., Young C., Jensen L.J., Vertegaal A.C. et al.',
      journal: 'Nat. Struct. Mol. Biol.',
      issue: '',
      pages: '325-336',
      year: 2017,
      citation_count: 1,
      pubmed_id: '28112733',
      doi: '',
      associated_pdbs: ['']
    }
  ]
}

Versioning

We use SemVer for versioning. For the versions available, see the tags on this repository.

Authors

• Mihaly Varadi - Initial Implementation - mvaradi

See also the list of contributors who participated in this project.

License

This project is licensed under the EMBL-EBI License - see the LICENSE file for details

Acknowledgements

We would like to thank the PDBe team and the PDBe-KB partner resources for their feedback and contributions.