-
Notifications
You must be signed in to change notification settings - Fork 1
/
index.html
255 lines (248 loc) · 14 KB
/
index.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<link rel="icon" type="image/png" href="assets/favicon.png">
<link href="https://cdn.jsdelivr.net/npm/bootstrap@5.0.1/dist/css/bootstrap.min.css" rel="stylesheet"
integrity="sha384-+0n0xVW2eSR5OomGNYDnhzAbDsOXxcvSN1TPprVMTNDbiYZCxYbOOl7+AMvyTG2x" crossorigin="anonymous">
<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap-icons@1.8.3/font/bootstrap-icons.css">
<title>BioDWH2</title>
<style>
.links a:link,
.links a:visited,
.links a:hover,
.links a:active {
color: #000000 !important;
text-decoration: none;
}
</style>
</head>
<body style="padding-top: 55px;">
<nav class="navbar navbar-expand-md navbar-light fixed-top bg-light">
<div class="container-fluid">
<img src="assets/BioDWH2-logo.svg" style="height: 42px">
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarText"
aria-controls="navbarText" aria-expanded="false" aria-label="Toggle navigation">
<span class="navbar-toggler-icon"></span>
</button>
<div class="collapse navbar-collapse" id="navbarText">
<ul class="navbar-nav ms-auto mb-2 mb-lg-0">
<li class="nav-item active">
<a class="nav-link btn btn-outline-secondary" type="button" href="https://github.com/BioDWH2"
target="_blank">GitHub</a>
</li>
<li class="nav-item active ms-1">
<a class="nav-link btn btn-outline-secondary" type="button"
href="https://github.com/BioDWH2/BioDWH2/blob/master/README.md" target="_blank">Documentation</a>
</li>
<li class="nav-item active ms-1">
<a class="nav-link btn btn-outline-secondary" type="button" href="https://github.com/BioDWH2/BioDWH2/issues"
target="_blank">Issues</a>
</li>
</ul>
</div>
</div>
</nav>
<main role="main">
<div class="mb-4" style="background-color: #EAECEF !important;">
<div class="container-fluid py-4" style="max-width: 1150px;">
<h1 class="display-4">BioDWH2: An Automated Graph-Based Data Warehouse and Mapping Tool</h1>
<object id="jumbotron-svg" type="image/svg+xml" data="assets/graph.svg"
style="width: 120px; height: 120px; float: left; margin-right: 16px;"></object>
<p>
BioDWH2 is an easy-to-use, automated, graph-based data warehouse and mapping tool for bioinformatics and
medical informatics. It is developed to be usable out of the box without any prerequisites except a suitable
Java Runtime.
</p>
<p>
<a class="btn btn-primary" href="https://github.com/BioDWH2/BioDWH2/releases/latest" role="button"
target="_blank">Download latest release</a>
<a class="btn btn-outline-primary" href="https://github.com/BioDWH2/BioDWH2/blob/master/README.md"
role="button" target="_blank">Getting started
<svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="currentColor" viewBox="0 0 16 16">
<path fill-rule="evenodd"
d="M1 8a.5.5 0 0 1 .5-.5h11.793l-3.147-3.146a.5.5 0 0 1 .708-.708l4 4a.5.5 0 0 1 0 .708l-4 4a.5.5 0 0 1-.708-.708L13.293 8.5H1.5A.5.5 0 0 1 1 8z" />
</svg>
</a>
</p>
<p>
<img src="https://img.shields.io/github/license/BioDWH2/BioDWH2">
<img src="https://img.shields.io/github/v/release/BioDWH2/BioDWH2?label=BioDWH2">
</p>
<span style="clear: both;"></span>
</div>
</div>
<div class="container-fluid" style="max-width: 1150px;">
<div class="row">
<div class="col">
<div id="workspace-icon" style="width: 64px; height: 64px; float: left; margin-right: 8px;"></div>
<h2 style="line-height: 64px;">Workspace</h2>
<p style="clear: both;">The simple and clean workspace structure helps you keep all data in one place. Easily
configure which data sources you need and BioDWH2 will take care of the rest.</p>
</div>
<div class="col">
<div id="uptodate-icon" style="width: 64px; height: 64px; float: left; margin-right: 8px;"></div>
<h2 style="line-height: 64px;">Up-To-Date</h2>
<p style="clear: both;">Make use of the latest information with automated data source updates. BioDWH2 checks
for new data source versions and can update them if necessary. Wish to keep the workspace as it is at the
end of a research project? No problem, updates can easily be disabled.</p>
</div>
</div>
<div class="row mt-4">
<div class="col">
<div id="mapped-icon" style="width: 64px; height: 64px; float: left; margin-right: 8px;"></div>
<h2 style="line-height: 64px;">Mapped</h2>
<p style="clear: both;">The data source modules of BioDWH2 provide mapping descriptions for the most common
entities and relationships. A mapping layer is generated automatically, connecting heterogeneous data sources
and helping to uncover new and meaningful information.</p>
</div>
<div class="col">
<div id="readyforanalysis-icon" style="width: 64px; height: 64px; float: left; margin-right: 8px;"></div>
<h2 style="line-height: 64px;">Ready for Analysis</h2>
<p style="clear: both;">The resulting graph database is ready to be analyzed with your favorite tools.
Starting from the mapping layer, or diving deep into the data sources, all in one graph.</p>
</div>
</div>
<hr>
<div class="row">
<div class="col">
<h2>Citing BioDWH2</h2>
<p>
If you make use of BioDWH2 or it's companion tools as part or your research cite the BioDWH2 manuscript in any resulting publications.
</p>
<ul class="list-group">
<li class="list-group-item">
Friedrichs M. BioDWH2: an automated graph-based data warehouse and mapping tool. <em>Journal of Integrative Bioinformatics</em>. 2021;18(2):167-176.
DOI: <em><a href="https://doi.org/10.1515/jib-2020-0033" target="_blank">10.1515/jib-2020-0033</a></em>
</li>
<li class="list-group-item">
Friedrichs M. Automation in graph-based data integration and mapping. In: Chen M, Hofestädt R, eds. Integrative Bioinformatics. Springer Singapore; 2022:97-110.
DOI: <em><a href="https://doi.org/10.1007/978-981-16-6795-4_5" target="_blank">10.1007/978-981-16-6795-4_5</a></em>
</li>
</ul>
</div>
</div>
<hr>
<div class="row">
<div class="col">
<h2>Worflow Overview</h2>
<img src="assets/BioDWH-complete-overview.png" class="img-fluid mt-1" />
</div>
</div>
<hr>
<div class="row">
<div class="col">
<h2>Analysis & Tools</h2>
<table class="table table-striped table-sm text-center">
<thead>
<tr>
<th scope="col" style="border-right: 1px solid black"></th>
<th scope="col"><a style="text-decoration: none" href="https://github.com/BioDWH2/BioDWH2-Neo4j-Server" target="_blank">BioDWH2-Neo4j-Server</a></th>
<th scope="col"><a style="text-decoration: none" href="https://github.com/BioDWH2/BioDWH2-OrientDB-Server" target="_blank">BioDWH2-OrientDB-Server</a></th>
<th scope="col"><a style="text-decoration: none" href="https://github.com/BioDWH2/BioDWH2-ArcadeDB-Server" target="_blank">BioDWH2-ArcadeDB-Server</a></th>
<th scope="col"><a style="text-decoration: none" href="https://github.com/BioDWH2/BioDWH2-GraphQL-Server" target="_blank">BioDWH2-GraphQL-Server</a></th>
<th scope="col"><a style="text-decoration: none" href="https://github.com/BioDWH2/BioDWH2-SQL-Exporter" target="_blank">BioDWH2-SQL-Exporter</a></th>
<th scope="col" class="fst-italic">Direct GraphML Access</th>
</tr>
</thead>
<tbody>
<tr>
<th scope="row" style="border-right: 1px solid black">Version</th>
<td><a href="https://github.com/BioDWH2/BioDWH2-Neo4j-Server/releases/latest" target="_blank"><img src="https://img.shields.io/github/v/release/BioDWH2/BioDWH2-Neo4j-Server"></a></td>
<td><a href="https://github.com/BioDWH2/BioDWH2-OrientDB-Server/releases/latest" target="_blank"><img src="https://img.shields.io/github/v/release/BioDWH2/BioDWH2-OrientDB-Server"></a></td>
<td><a href="https://github.com/BioDWH2/BioDWH2-ArcadeDB-Server/releases/latest" target="_blank"><img src="https://img.shields.io/github/v/release/BioDWH2/BioDWH2-ArcadeDB-Server"></a></td>
<td><a href="https://github.com/BioDWH2/BioDWH2-GraphQL-Server/releases/latest" target="_blank"><img src="https://img.shields.io/github/v/release/BioDWH2/BioDWH2-GraphQL-Server"></a></td>
<td><a href="https://github.com/BioDWH2/BioDWH2-SQL-Exporter/releases/latest" target="_blank"><img src="https://img.shields.io/github/v/release/BioDWH2/BioDWH2-SQL-Exporter"></a></td>
<td>-</td>
</tr>
<tr>
<th scope="row" style="border-right: 1px solid black">Database</th>
<td><a href="https://neo4j.com" target="_blank" rel="noopener norefferer">Neo4j</a> Community Embedded</td>
<td><a href="https://orientdb.com" target="_blank" rel="noopener norefferer">OrientDB</a> Community Embedded</td>
<td><a href="https://arcadedb.com" target="_blank" rel="noopener norefferer">ArcadeDB</a> Embedded</td>
<td>BioDWH2 Graph + <a href="https://www.graphql-java.com" target="_blank" rel="noopener norefferer">GraphQL Java</a></td>
<td>(Depending on used SQL server)</td>
<td>-</td>
</tr>
<tr>
<th scope="row" style="border-right: 1px solid black">Interface</th>
<td>Neo4j Browser</td>
<td>OrientDB Studio</td>
<td>ArcadeDB Studio</td>
<td>
<a href="https://github.com/graphql/graphql-playground" target="_blank" rel="noopener noreferrer">GraphQL Playground</a>,<br/>
<a href="https://github.com/graphql/graphiql" target="_blank" rel="noopener noreferrer">Graph<i>i</i>QL</a>
</td>
<td>(Depending on used SQL server)</td>
<td>-</td>
</tr>
<tr>
<th scope="row" style="border-right: 1px solid black">Commercial Use</th>
<td>
<i class="bi bi-exclamation-triangle-fill text-warning"></i><br/>
Depending on<br/>
use-case<sup><a href="https://neo4j.com/licensing/" target="_blank" rel="noopener norefferer">[1]</a></sup>
</td>
<td>
<i class="bi bi-check-circle-fill text-success"></i><br/>
Apache 2 License<sup><a href="https://orientdb.org/download" target="_blank" rel="noopener norefferer">[2]</a></sup>
</td>
<td>
<i class="bi bi-check-circle-fill text-success"></i><br/>
Apache 2 License<sup><a href="https://github.com/ArcadeData/arcadedb/blob/main/LICENSE" target="_blank" rel="noopener norefferer">[3]</a></sup>
</td>
<td>
<i class="bi bi-check-circle-fill text-success"></i><br/>
MIT License<sup><a href="https://github.com/graphql-java/graphql-java/blob/master/LICENSE.md" target="_blank" rel="noopener norefferer">[4]</a></sup>
</td>
<td>
<i class="bi bi-check-circle-fill text-success"></i><br/>
(Depending on used SQL server)
</td>
<td><i class="bi bi-check-circle-fill text-success"></i></td>
</tr>
<tr>
<th scope="row" style="border-right: 1px solid black">Limitations</th>
<td>-</td>
<td>-</td>
<td>No array property indices</td>
<td>-</td>
<td>Name length limits</td>
<td>No DBMS</td>
</tr>
</tbody>
</table>
</div>
</div>
<hr>
</div>
</main>
<footer class="container-fluid" style="max-width: 1150px;">
<a href="https://agbi.techfak.uni-bielefeld.de" target="_blank">
<img src="assets/ag_bioinformatics_logo.png" style="float: right;">
</a>
<p class="links">
© 2022 -
<a href="https://agbi.techfak.uni-bielefeld.de" target="_blank">Bioinformatics/Medical Informatics department</a>,
<a href="http://techfak.de" target="_blank">Faculty of Technology</a>,
<a href="https://www.uni-bielefeld.de" target="_blank">Bielefeld University</a>
</p>
<span style="clear: both;"></span>
</footer>
<script src="https://cdn.jsdelivr.net/npm/bootstrap@5.0.1/dist/js/bootstrap.bundle.min.js"
integrity="sha384-gtEjrD/SeCtmISkJkNUaaKMoLD0//ElJ19smozuHV6z3Iehds+3Ulb9Bn9Plx0x4"
crossorigin="anonymous"></script>
<script src="//cdn.jsdelivr.net/npm/vivus@latest/dist/vivus.min.js"></script>
<script>
window.addEventListener('load', function() {
new Vivus('jumbotron-svg', { duration: 75, type: 'delayed' }, function() {
new Vivus('workspace-icon', { duration: 100, type: 'delayed', file: 'assets/workspace.svg' }, function() { });
new Vivus('uptodate-icon', { duration: 100, type: 'delayed', file: 'assets/uptodate.svg' }, function() { });
new Vivus('mapped-icon', { duration: 100, type: 'delayed', file: 'assets/mapped.svg' }, function() { });
new Vivus('readyforanalysis-icon', { duration: 100, type: 'delayed', file: 'assets/readyforanalysis.svg' }, function() { });
});
}, false);
</script>
</body>
</html>