This repository has been archived by the owner on Jul 10, 2020. It is now read-only.
-
Notifications
You must be signed in to change notification settings - Fork 2
/
Copy pathqa.html
214 lines (154 loc) · 7.21 KB
/
qa.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
<!DOCTYPE html>
<html><head>
<title>QA For The BioGRID Viewer</title>
<meta charset="UTF-8">
<link rel="stylesheet" href="html.css"></style>
</head><body>
<h1>Quality Assurance</h1>
<p>Well, not really, but it's something.</p>
<p>This is not a place to store issues, but a list of things to test
before updating main site.</p>
<h2>Repository</h2>
<p>The BioGRID Viewer's repository is at:
<a href="https://github.com/svenmh/BioGRID-Viewer"><code>https://github.com/svenmh/BioGRID-Viewer</code></a>.
There is a <abbr>FAQ</abbr> at:
<a href="https://github.com/svenmh/BioGRID-Viewer/wiki/FAQ"><code>https://github.com/svenmh/BioGRID-Viewer/wiki/FAQ</code></a>.</p>
<p>Bugs should be reported to the
<a href="https://github.com/svenmh/BioGRID-Viewer/issues">Issues
Page</a> at <a href="https://github.com/">GitHub</a>. Modifications
to this page should be pushed via git. Of course you can contact Sven
with any issues or changes.</p>
<h2>Queries</h2>
<p>Any <a href="http://wiki.thebiogrid.org/doku.php/biogridrest">REST</a>
options that returns
a <a href="http://wiki.thebiogrid.org/doku.php/biogrid_tab_version_2.0">TAB2</a>
files <em>should</em> do, report them on
the <a href="https://github.com/svenmh/BioGRID-Viewer/issues">Issues
Page</a> if they don't.</p>
<h3>Default Query</h3>
<blockquote><samp>http://biogrid-dev.princeton.edu/BioGRID-Viewer/ring.html?searchBiogridIds=TRUE&geneList=<var>id</var></samp></blockquote>
<p>Where <var>id</var> is the biogrid id of the desired gene you wish to view.</p>
<h3>Query By Gene Name</h3>
<p>This query should be done with the following
format:</p>
<blockquote><samp>http://biogrid-dev.princeton.edu/BioGRID-Viewer/ring.html?searchNames=true&geneList=<var>name</var>&taxId=<var>taxid</var></samp></blockquote>
<p>Where <var>name</var> is the gene you are looking for
and <var>taxid</var> is the species you are looking for. A list of
species <var>taxid</var>s supported can be received from
the <a href="BGV/taxa.json"><code>BGV/taxa.json</code> file</a>.</p>
<h3>Test Queries</h3>
<p>If there are problems fist check the <a href="config.json"><code>config.json</code></a> file.</a>
<h2>Yeast CCC2</h2>
<dl>
<dt><a href="ring.html?searchNames=true&geneList=ccc2&taxId=559292">Name Search</a></dt>
<dd>Not the default search, but make sure it looks the same of the default search.</dd>
<dt><a href="ring.html?searchBiogridIds=TRUE&geneList=32325">Default Search</a></dt>
<dd>Human PRKACA should be present.</dd>
<dt><a href="ring.html?searchBiogridIds=TRUE&geneList=32325&interSpeciesExcluded=TRUE">&interSpeciesExcluded=TRUE</a></dt>
<dd>Make sure Human PRKACA is missing and "Include Interspecies Interactions" is deselected.</dd>
<dt><a href="ring.html?searchBiogridIds=TRUE&geneList=32325&throughputTag=low">&throughputTag=low</a></dt>
<dd>Make sure the only "Throughput" checkbox that is checked is "Low", also fewer edges (15 as of BioGRID v3.1.88). Human PRKACA should be present.</dd>
<dt><a href="ring.html?searchBiogridIds=TRUE&geneList=32325&interSpeciesExcluded=TRUE&throughputTag=low">&interSpeciesExcluded=TRUE&throughputTag=low</a></dt>
<dd>Now Human PRKACA should be gone too.</dd>
<dt><a href="ring.html?searchBiogridIds=TRUE&geneList=32325&evidenceList=Biochemical%20Activity%7CFRET">Evidence List</a></dt>
<dd>Only Human PRKACA should be connected, check that "Biochemical Activity" and "FRET" are the only highlighted evidence check boxes.</dd>
</dl>
<h2>Human PRKACA</h2>
<dl>
<dt><a href="ring.html?searchBiogridIds=TRUE&geneList=111553">Default Query</a></dt>
<dd>Yeast CCC2 should be the only nonhuman gene present.</dd>
</dl>
<h2>HIV tat</h2>
<dl>
<dt><a href="ring.html?searchBiogridIds=TRUE&geneList=1205541">Default Query</a></dt>
<dd>Only connects to human genes.</dd>
<dt><a href="ring.html?searchBiogridIds=TRUE&geneList=1205541&interSpeciesExcluded=TRUE">&interSpeciesExcluded=TRUE</a></dt>
<dd>Contains only one edge, to itself.</dd>
</dl>
<h2>Large Queries</h2>
<p>Queries with over an amount, defaults to 10000, <code>Throughput</code> will change to <code>Low</code>.</p>
<dl>
<dt><a href="ring.html?searchBiogridIds=TRUE&geneList=31107">Yeast ACT1</a></dt>
<dd>Use the <code>[search]</code> button to find TUB1 and then click the <code>[follow]</code> butten.</dd>
<dt><a href="ring.html?searchBiogridIds=TRUE&geneList=113164">Human UBC</a></dt>
<dd>Search for RSP5 & follow it.</dd>
</dl>
<h2>Pubmed Queries</h2>
<p><strong>Don't try</strong> the links in this section unless you know it uses the Poor Persons REST server. Currently that will only be if you are on the <a href="http://biogridrest.princeton.edu/BioGRID-Viewer/"><code>biogridrest.princeton.edu</code></a> server. Viewing data from <a href="http://www.ncbi.nlm.nih.gov/pubmed?term=20093466"><cite>The genetic landscape of a cell.</cite> by Costanzo M, et al</a>.</p>
<dl>
<dt><a href="ring.html?pubmedList=20093466">&pubmedList=20093466</a>
<dd>This should click in the <code>Throughput</code> to <code>Low</code>, follow SGT2 and chenge the <code>Throughput</code> to </code> Any. It should look like the following:
<dt><a href="ring.html?pubmedList=20093466&searchBiogridIds=TRUE&geneList=34410">SGT2</a>
</dl>
<h2>Other Queries</h2>
<p>All are the default query.</p>
<dl>
<dt><a href="ring.html?searchBiogridIds=TRUE&geneList=125073">Human FOXP2</a></dt>
<dt><a href="ring.html?searchBiogridIds=TRUE&geneList=36131">Yeast DIG1</a></dt>
<dt><a href="ring.html?searchBiogridIds=TRUE&geneList=36669">Yeast PRB1</a></dt>
</dl>
<h2>Browsers</h2>
<p>Primary development is done on Google Chrome on GNU/Linux. Entries
with no border are not tested; entries containing <samp>n/a</samp>
indicate that the browser is not available on the given platform.</p>
<table>
<tr>
<td class="blank"></td>
<th>Google Chrome</th>
<th>Firefox</th>
<th>Safari</th>
<th>IE9</th>
</tr>
<tr>
<th>GNU/Linux</th>
<td></td>
<td><ol>
<li>Firefox only browser to support SVG alternative stylesheets.</li>
<li><code>Unknown property 'alignment-baseline'. Declaration dropped.</code></li>
<li><code><svg onresize="…</code> doesn't work.</li>
</ol></td>
<td class="blank">n/a</td>
<td class="blank">n/a</td>
</tr>
<tr>
<th>Mac OS X 10</th>
<td class="blank"></td>
<td><ol>
<li>ibid.</li>
<li>wait curser doesn't stop until one moves the mouse.</li>
</ol></td>
<td></td>
<td class="blank">n/a</td>
</tr>
<tr>
<th>Windows 7</th>
<td class="blank"></td>
<td class="blank"></td>
<td class="blank"></td>
<td><ol>
<li><a href="http://d3js.org/">D3.js</a> <a href="https://github.com/mbostock/d3/wiki/Transitions">transitions</a> Skipped (Works in IE10).</li>
</ol></td>
</tr>
<tr>
<th>iOS 4.3 (Simulator)</th>
<td class="blank">n/a</td>
<td class="blank">n/a</td>
<td><ol>
<li>Use drag to surf genes.</li>
<li>Checkbox alignment issue fixed in later versions of iOS. Please ignore.</li>
<li>Sometimes times out with large queries (i.e. Human UBC)</li>
</ol></td>
<td class="blank">n/a</td>
</tr>
<tr>
<th>Android 4.0.3 (Virtual Device)</th>
<td><ol>
<li>Use drag to surf genes.</li>
<li>No ballot box font support, uses '＋' and '－' instead.</li>
</ol></td>
<td class="blank"></td>
<td class="blank">n/a</td>
<td class="blank">n/a</td>
</tr>
</table>
</body></head>