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Merge pull request #60 from ncats/development
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iwwwish authored Jun 22, 2022
2 parents 8f69b08 + 9b8502e commit 331d994
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Showing 36 changed files with 666 additions and 209 deletions.
5 changes: 4 additions & 1 deletion Dockerfile-ncats
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@@ -1,4 +1,4 @@
FROM node:12 AS build
FROM node:16 AS build

WORKDIR /opt/adme

Expand All @@ -11,6 +11,9 @@ RUN ng build --configuration production --deploy-url=/models/client/ --base-href

FROM continuumio/miniconda:4.7.12

# Install NCATS required packages
RUN apt-get install -y net-tools

WORKDIR /opt/adme

COPY server ./
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5 changes: 4 additions & 1 deletion Dockerfile-opendata
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@@ -1,4 +1,4 @@
FROM node:12 AS build
FROM node:16 AS build

WORKDIR /opt/adme

Expand All @@ -11,6 +11,9 @@ RUN ng build --configuration production --deploy-url=/adme/client/ --base-href=/

FROM continuumio/miniconda:4.7.12

# Install NCATS required packages
RUN apt-get install -y net-tools

WORKDIR /opt/adme

COPY server ./
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8 changes: 8 additions & 0 deletions client/src/app/app-routing.module.ts
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Expand Up @@ -4,6 +4,7 @@ import { HomeComponent } from './home/home.component';
import { PredictionsComponent } from './predictions/predictions.component';
import { MethodComponent } from './method/method.component';
import { ContactComponent } from './contact/contact.component';
import { DataComponent } from './data/data.component';

const routes: Routes = [
{
Expand All @@ -27,6 +28,13 @@ const routes: Routes = [
pageTitle: 'model'
}
},
{
path: 'data',
component: DataComponent,
data: {
pageTitle: 'data'
}
},
{
path: 'contact',
component: ContactComponent,
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5 changes: 3 additions & 2 deletions client/src/app/app.component.html
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@@ -1,7 +1,8 @@
<adme-loading></adme-loading>
<mat-toolbar color="primary">
<a class="title" routerLink="/home">ADME @ NCATS</a>
<a class="title" routerLink="/home">ADME@NCATS</a>
<div class="navigation">
<a class="nav-item" routerLink="/predictions">Predict</a>
<a class="nav-item" [matMenuTriggerFor]="navMenu" >Models</a>
<mat-menu #navMenu="matMenu">
<button mat-menu-item routerLink="/models/rlm">RLM Stability</button>
Expand All @@ -11,7 +12,7 @@
<button mat-menu-item routerLink="/models/hlc">HLC Stability</button>
<button mat-menu-item routerLink="/models/cyp450">CYP450</button>
</mat-menu>
<a class="nav-item" routerLink="/predictions">Predict</a>
<a class="nav-item" routerLink="/data/">Data</a>
<a class="nav-item" routerLink="/contact">Contact</a>
</div>
<span class="fill-middle"></span>
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4 changes: 2 additions & 2 deletions client/src/app/app.component.scss
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Expand Up @@ -52,10 +52,10 @@

.footer {
position: relative;
bottom: 0;
bottom: 0 !important;
height: 80px;
width: 100%;
color:#fff;
color: #fff;
padding-bottom: 0px;
padding-top: 10px;
font-size: 13px;
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2 changes: 1 addition & 1 deletion client/src/app/contact/contact.component.scss
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Expand Up @@ -76,4 +76,4 @@ h1 {
.profile-info-container {
padding-left: 10px;
}
}
}
20 changes: 10 additions & 10 deletions client/src/app/contact/contact.component.ts
Original file line number Diff line number Diff line change
Expand Up @@ -19,19 +19,19 @@ export class ContactComponent implements OnInit {
epamImgSrc: SafeResourceUrl;

constructor(
private domSanatizer: DomSanitizer,
private domSanitizer: DomSanitizer,
@Inject(DEPLOY_URL) public deployUrl: string
) {
this.jordanImgSrc = domSanatizer.bypassSecurityTrustResourceUrl(`${this.deployUrl}assets/profile_images/williamsjos.jpg`);
this.vishalImgSrc = domSanatizer.bypassSecurityTrustResourceUrl(`${this.deployUrl}assets/profile_images/siramshettyv2.jpg`);
this.pranavImgSrc = domSanatizer.bypassSecurityTrustResourceUrl(`${this.deployUrl}assets/profile_images/shahpa2.png`);
this.ewyImgSrc = domSanatizer.bypassSecurityTrustResourceUrl(`${this.deployUrl}assets/profile_images/mathee.jpg`);
this.xinImgSrc = domSanatizer.bypassSecurityTrustResourceUrl(`${this.deployUrl}assets/profile_images/xux7.jpg`);
this.jordanImgSrc = domSanitizer.bypassSecurityTrustResourceUrl(`${this.deployUrl}assets/profile_images/williamsjos.jpg`);
this.vishalImgSrc = domSanitizer.bypassSecurityTrustResourceUrl(`${this.deployUrl}assets/profile_images/siramshettyv2.jpg`);
this.pranavImgSrc = domSanitizer.bypassSecurityTrustResourceUrl(`${this.deployUrl}assets/profile_images/shahpa2.png`);
this.ewyImgSrc = domSanitizer.bypassSecurityTrustResourceUrl(`${this.deployUrl}assets/profile_images/mathee.jpg`);
this.xinImgSrc = domSanitizer.bypassSecurityTrustResourceUrl(`${this.deployUrl}assets/profile_images/xux7.jpg`);

this.rdkitImgSrc = domSanatizer.bypassSecurityTrustResourceUrl(`${this.deployUrl}assets/images/rdkit.png`);
this.pythonImgSrc = domSanatizer.bypassSecurityTrustResourceUrl(`${this.deployUrl}assets/images/python.png`);
this.angularImgSrc = domSanatizer.bypassSecurityTrustResourceUrl(`${this.deployUrl}assets/images/angular.png`);
this.epamImgSrc = domSanatizer.bypassSecurityTrustResourceUrl(`${this.deployUrl}assets/images/epam_ketcher.png`);
this.rdkitImgSrc = domSanitizer.bypassSecurityTrustResourceUrl(`${this.deployUrl}assets/images/rdkit.png`);
this.pythonImgSrc = domSanitizer.bypassSecurityTrustResourceUrl(`${this.deployUrl}assets/images/python.png`);
this.angularImgSrc = domSanitizer.bypassSecurityTrustResourceUrl(`${this.deployUrl}assets/images/angular.png`);
this.epamImgSrc = domSanitizer.bypassSecurityTrustResourceUrl(`${this.deployUrl}assets/images/epam_ketcher.png`);
}

ngOnInit(): void {
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197 changes: 197 additions & 0 deletions client/src/app/data/data.component.html
Original file line number Diff line number Diff line change
@@ -0,0 +1,197 @@
<div class="container">
<div class="inner-container">
<h1>
Data Availability
</h1>

<p style="text-align: justify;">
Along with the predictions, we provide open access to the data underlying the prediction models. The experimental data associated with
all compounds that could be made public have been deposited into the PubChem database as bioassay records that are open for public access.
Links to the bioassay records and downloadable data files are provided below. Further details on the datasets are provided
in individual model pages.
</p>

<div class="table-container">
<div class="table-responsive-container">
<table class="mat-table more-padding">
<thead>
<tr class="mat-header-row">
<th class="mat-header-cell center">
ADME Endpoint
</th>
<th class="mat-header-cell center">
Training Data<sup>a</sup>
</th>
<th class="mat-header-cell center">
Public Data<sup>b</sup>
</th>
<th class="mat-header-cell center">
PubChem Bioassay
</th>
<th class="mat-header-cell center">
Data File
</th>
</tr>
</thead>
<tbody>
<tr class="mat-row">
<td class="mat-cell center">
RLM Stability
</td>
<td class="mat-cell center">
22,016
</td>
<td class="mat-cell center">
2,525
</td>
<td class="mat-cell center">
<a
href="https://pubchem.ncbi.nlm.nih.gov/bioassay/1508591" target="_blank" admeTrackLinkEvent evLabel="rlm pubchem">AID
1508591</a>
</td>
<td class="mat-cell center">
<a [href]="rlm_DownloadHref" target="_blank"><img class="img-icon" [src]="downloadIcon"></a>
</td>
</tr>
<tr class="mat-row">
<td class="mat-cell center">
PAMPA pH 5
</td>
<td class="mat-cell center">
5,227
</td>
<td class="mat-cell center">
486
</td>
<td class="mat-cell center">
<a
href="https://pubchem.ncbi.nlm.nih.gov/bioassay/1645871" target="_blank" admeTrackLinkEvent evLabel="pampa 50 pubchem">AID
1645871</a>
</td>
<td class="mat-cell center">
<a [href]="pampa50_DownloadHref" target="_blank"><img class="img-icon" [src]="downloadIcon"></a>
</td>
</tr>
<tr class="mat-row">
<td class="mat-cell center">
PAMPA pH 7.4
</td>
<td class="mat-cell center">
16,624
</td>
<td class="mat-cell center">
2,528
</td>
<td class="mat-cell center">
<a
href="https://pubchem.ncbi.nlm.nih.gov/bioassay/1508612" target="_blank" admeTrackLinkEvent evLabel="pampa 74 pubchem">AID
1508612</a>
</td>
<td class="mat-cell center">
<a [href]="pampa74_DownloadHref" target="_blank"><img class="img-icon" [src]="downloadIcon"></a>
</td>
</tr>
<tr class="mat-row">
<td class="mat-cell center">
Solubility
</td>
<td class="mat-cell center">
22,209
</td>
<td class="mat-cell center">
2,529
</td>
<td class="mat-cell center">
<a
href="https://pubchem.ncbi.nlm.nih.gov/bioassay/1645848" target="_blank" admeTrackLinkEvent evLabel="sol pubchem">AID
1645848</a>
</td>
<td class="mat-cell center">
<a [href]="sol_DownloadHref" target="_blank"><img class="img-icon" [src]="downloadIcon"></a>
</td>
</tr>
<tr class="mat-row">
<td class="mat-cell center">
HLC Stability
</td>
<td class="mat-cell center">
1,214
</td>
<td class="mat-cell center">
189
</td>
<td class="mat-cell center">
<a
href="https://pubchem.ncbi.nlm.nih.gov/bioassay/1508603" target="_blank" admeTrackLinkEvent evLabel="hlc pubchem">AID
1508603</a>
</td>
<td class="mat-cell center">
<a [href]="hlc_DownloadHref" target="_blank"><img class="img-icon" [src]="downloadIcon"></a>
</td>
</tr>
<tr class="mat-row">
<td class="mat-cell center">
CYP2D6
</td>
<td class="mat-cell center">
5,094
</td>
<td class="mat-cell center">
5,094
</td>
<td class="mat-cell center">
<a
href="https://pubchem.ncbi.nlm.nih.gov/bioassay/1645840" target="_blank" admeTrackLinkEvent evLabel="cyp2d6 pubchem">AID
1645840</a>
</td>
<td class="mat-cell center">
<a [href]="cyp2d6_DownloadHref" target="_blank"><img class="img-icon" [src]="downloadIcon"></a>
</td>
</tr>
<tr class="mat-row">
<td class="mat-cell center">
CYP3A4
</td>
<td class="mat-cell center">
5,094
</td>
<td class="mat-cell center">
5,094
</td>
<td class="mat-cell center">
<a
href="https://pubchem.ncbi.nlm.nih.gov/bioassay/1645841" target="_blank" admeTrackLinkEvent evLabel="cyp3a4 pubchem">AID
1645841</a>
</td>
<td class="mat-cell center">
<a [href]="cyp3a4_DownloadHref" target="_blank"><img class="img-icon" [src]="downloadIcon"></a><br>
</td>
</tr>
<tr class="mat-row">
<td class="mat-cell center">
CYP2C9
</td>
<td class="mat-cell center">
5,094
</td>
<td class="mat-cell center">
5,094
</td>
<td class="mat-cell center">
<a
href="https://pubchem.ncbi.nlm.nih.gov/bioassay/1645842" target="_blank" admeTrackLinkEvent evLabel="cyp2c9 pubchem">AID
1645842</a>
</td>
<td class="mat-cell center">
<a [href]="cyp2c9_DownloadHref" target="_blank"><img class="img-icon" [src]="downloadIcon"></a>
</td>
</tr>
</tbody>
</table>
<p class="footer-line"><sup>a</sup> <i>Total number of compounds present in the training dataset.</i><br>
<sup>b</sup> <i>Total number of compounds present in the publicly available dataset.</i>
</p>
</div>
</div>
</div>
</div>
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