source: branches/uk_ac_ebi_Tab2MageImporter/html/experiment.html @ 511

Last change on this file since 511 was 511, checked in by mbayer, 14 years ago
  • have tidied up the interface to the point where it is usable as it is
  • have provided defaults for every field in every form for testing
File size: 16.2 KB
Line 
1<html>
2
3<head>
4<title>Tab2MAGE Importer -- Experiment</title>
5<link rel="stylesheet" type="text/css" href="styles.css" />
6
7<script type="text/javascript">
8
9    //function to display or hide a given element
10    function showHideItems(myItem, myButton)
11    {
12       //this is the ID of the hidden item
13      var myItem = document.getElementById(myItem);
14
15      //this is the ID of the plus/minus button image
16      var myButton = document.getElementById(myButton);
17
18        if (myItem.style.display != "none") 
19        {
20            //items are currently displayed, so hide them
21            myItem.style.display = "none";
22            swapImage(myButton,"plus");
23        }
24        else 
25        {
26            //items are currently hidden, so display them
27            myItem.style.display = "block";
28            swapImage(myButton,"minus");
29        }
30    }
31
32    //function to swap an image based on its current state
33    function swapImage(myImage, state) 
34    {
35        if (state == "minus") 
36        {
37            myImage.src = "hide.gif";
38        }
39
40        else 
41        {
42            myImage.src = "show.gif";
43      }
44    }
45
46</script>
47
48</head>
49
50<body>
51
52<h2>Tab2MAGE Importer -- Your Experiment</h2>
53Page 1 of 3
54<p>
55
56Please configure your experiment for upload by answering the questions on this and the following two pages.
57<br>
58The answers you provide will be used to automatically create a new experiment in BASE and your raw data will be imported
59into this.
60<p>
61
62<form action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/protocols.jsp" method="post">
63<input type="hidden" name="ID" value="<%=ID%>"> 
64
65<table cellpadding="10">
66
67  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
68  <tr>
69    <td class="boldText">Domain:</td>
70    <td class="input"><input type="text" size="45" name="domain" value="" /></td>
71    <td >The domain tag provides information on the originator of the output MAGE-ML document. This field can contain
72    any suitable string, such as the originating internet domain name (e.g., "ebi.ac.uk").</td>
73  </tr>
74  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
75  <tr>
76    <td class="boldText">Accession:</td>
77    <td class="input"><input type="text" size="45" name="accession" value="" /></td>
78    <td >The experiment accession number is a unique identifier assigned to each experiment. Accession numbers for
79    experiments submitted to ArrayExpress have the format E-XXXX-n.</td>
80  </tr>
81  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
82  <tr>
83    <td  class="boldText">Quality Control:</td>
84    <td class="input">
85
86    <table class="noBorder" cellpadding="1">
87
88      <tr class="noBorder">
89        <td>biological replicate</td>
90        <td><input type="checkbox" name="biological replicate" value="biological replicate" /></td>
91      </tr>
92
93      <tr class="noBorder">
94        <td>dye swap quality control</td>
95        <td><input type="checkbox" name="dye swap quality control" value="dye swap quality control" /></td>
96      </tr>
97
98      <tr class="noBorder">
99        <td>peer review quality control</td>
100        <td><input type="checkbox" name="peer review quality control" value="peer review quality control" /></td>
101      </tr>
102
103      <tr class="noBorder">
104        <td>real time PCR quality control</td>
105        <td><input type="checkbox" name="real time PCR quality control" value="real time PCR quality control" /></td>
106      </tr>
107
108      <tr class="noBorder">
109        <td>reverse transcription PCR quality control</td>
110        <td><input type="checkbox" name="reverse transcription PCR quality control"
111          value="reverse transcription PCR quality control" /></td>
112      </tr>
113
114      <tr class="noBorder">
115        <td>spike quality control</td>
116        <td><input type="checkbox" name="spike quality control" value="spike quality control" /></td>
117      </tr>
118
119      <tr class="noBorder">
120        <td>technical replicate</td>
121        <td><input type="checkbox" name="technical replicate" value="technical replicate" /></td>
122      </tr>
123
124    </table>
125
126  </td>
127  <td>A list of terms taken from the MGED ontology. Multiple values can be selected.</td>
128  </tr>
129  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
130  <tr>
131    <td class="boldText">Experiment Design Type:</td>
132    <td class="input">
133
134    <table class="noBorder" cellpadding="3>
135
136      <tr class="noBorder">
137        <td valign="top">Biological Property<br/>
138        </td>
139        <td colspan="2"><a onclick="showHideItems('BiologicalProperty', 'buttonBiologicalProperty');"
140          title="Show/hide items"> <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonBiologicalProperty"
141          name="buttonBiologicalProperty" /></a> <!-- begin div containing hidden items -->
142        <div id="BiologicalProperty" style="display:none"><select multiple="multiple">
143          <option>cell_component_comparison_design</option>
144          <option>cell_cycle_design</option>
145          <option>cell_type_comparison_design</option>
146          <option>cellular_process_design</option>
147          <option>development_or_differentiation_design</option>
148          <option>imprinting_design</option>
149          <option>individual_genetic_characteristics_design</option>
150          <option>innate_behavior_design</option>
151          <option>is_expressed_design</option>
152          <option>organism_part_comparison_design</option>
153          <option>organism_status_design</option>
154          <option>physiological_process_design</option>
155          <option>sex_design</option>
156          <option>species_design</option>
157          <option>strain_or_line_design</option>
158          <option>unknown_experiment_design_type</option>
159        </select></div>
160        </td>
161      </tr>
162
163      <tr class="noBorder">
164        <td>BioMolecular Annotation</td>
165        <td><a onclick="showHideItems('BioMolecularAnnotation', 'buttonBioMolecularAnnotation');"
166          title="Show/hide items"> <img src="show.gif" border="0" id="buttonBioMolecularAnnotation"
167          name="buttonBioMolecularAnnotation" /></a> <!-- begin div containing hidden items -->
168        <div id="BioMolecularAnnotation" style="display:none"><select multiple="multiple">
169          <option>RNA_stability_design</option>
170          <option>binding_site_identification_design</option>
171          <option>co-expression_design</option>
172          <option>comparative_genome_hybridization_design</option>
173          <option>genotyping_design</option>
174          <option>operon_identification_design</option>
175          <option>secreted_protein_identification_design</option>
176          <option>tiling_path_design</option>
177          <option>transcript_identification_design</option>
178          <option>translational_bias_design</option>
179          <option>unknown_experiment_design_type</option>
180        </select></div>
181        </td>
182      </tr>
183
184      <tr class="noBorder">
185        <td>Epidemiological Design</td>
186        <td><a onclick="showHideItems('EpidemiologicalDesign', 'buttonEpidemiologicalDesign');" title="Show/hide items">
187        <img src="show.gif" border="0" id="buttonEpidemiologicalDesign" name="buttonEpidemiologicalDesign" /></a> <!-- begin div containing hidden items -->
188        <div id="EpidemiologicalDesign" style="display:none"><select multiple="multiple">
189          <option>clinical_history_design</option>
190          <option>disease_state_design</option>
191          <option>family_history_design</option>
192          <option>unknown_experiment_design_type</option>
193          </option>
194        </select></div>
195        </td>
196      </tr>
197
198      <tr class="noBorder">
199        <td>Methodological Design</td>
200        <td><a onclick="showHideItems('MethodologicalDesign', 'buttonMethodologicalDesign');" title="Show/hide items">
201        <img src="show.gif" border="0" id="buttonMethodologicalDesign" name="buttonMethodologicalDesign" /></a> <!-- begin div containing hidden items -->
202        <div id="MethodologicalDesign" style="display:none"><select multiple="multiple">
203          <option>all_pairs</option>
204          <option>array_platform_variation_design</option>
205          <option>dye_swap_design</option>
206          <option>ex_vivo_design</option>
207          <option>hardware_variation_design</option>
208          <option>in_vitro_design</option>
209          <option>in_vivo_design</option>
210          <option>loop_design</option>
211          <option>normalization_testing_design</option>
212          <option>operator_variation_design</option>
213          <option>optimization_design</option>
214          <option>quality_control_testing_design</option>
215          <option>reference_design</option>
216          <option>replicate_design</option>
217          <option>self_vs_self_design</option>
218          <option>software_variation_design</option>
219          <option>time_series_design</option>
220          <option>unknown_experiment_design_type</option>
221          </option>
222        </select></div>
223        </td>
224      </tr>
225
226      <tr class="noBorder">
227        <td>Perturbational Design</td>
228        <td><a onclick="showHideItems('PerturbationalDesign', 'buttonPerturbationalDesign');" title="Show/hide items">
229        <img src="show.gif" border="0" id="buttonPerturbationalDesign" name="buttonPerturbationalDesign" /></a> <!-- begin div containing hidden items -->
230        <div id="PerturbationalDesign" style="display:none"><select multiple="multiple">
231          <option>cellular_modification_design</option>
232          <option>compound_treatment_design</option>
233          <option>disease_state_design</option>
234          <option>dose_response_design</option>
235          <option>genetic_modification_design</option>
236          <option>growth_condition_design</option>
237          <option>injury_design</option>
238          <option>non-targeted_transgenic_variation_design</option>
239          <option>pathogenicity_design</option>
240          <option>stimulated_design_type</option>
241          <option>stimulus_or_stress_design</option>
242          <option>unknown_experiment_design_type</option>
243        </select></div>
244        </td>
245      </tr>
246
247      <tr class="noBorder">
248        <td>Technological Design</td>
249        <td><a onclick="showHideItems('TechnologicalDesign', 'buttonTechnologicalDesign');" title="Show/hide items">
250        <img src="show.gif" border="0" id="buttonTechnologicalDesign" name="TechnologicalDesign" /></a> <!-- begin div containing hidden items -->
251        <div id="TechnologicalDesign" style="display:none"><select multiple="multiple">
252          <option>binding_site_identification_design</option>
253          <option>cellular_modification_design</option>
254          <option>comparative_genome_hybridization_design</option>
255          <option>transcript_identification_design</option>
256          </option>
257        </select></div>
258        </td>
259      </tr>
260
261    </table>
262
263
264    </td>
265    <td>A list of terms taken from the MGED ontology. Multiple values can be selected.
266    <p>Click "expand" for an item to see list boxes with specific choices.<br>
267    Hold down the 'Ctrl' key and click to select multiple options.
268    </td>
269  </tr>
270  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
271  <tr>
272    <td class="boldText">Experiment Name:</td>
273    <td class="input"> 
274    <textarea rows="2" cols="30" name="experimentName">my first experiment</textarea>
275    </td>
276    <td>The name you have chosen for the Experiment.</td>
277  </tr>
278  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
279  <tr>
280    <td class="boldText">Experiment Description:</td>
281    <td class="input">
282    <textarea rows="2" cols="30" name="description">description</textarea>
283    </td>
284    <td>A short paragraph describing the purpose of the experiment.</td>
285  </tr>
286  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
287  <tr>
288    <td class="boldText">Release Date:</td>
289    <td class="input"><input type="text" size="10" name="" value="2007-12-03" /></td>
290    <td>Date for public release, in the format YYYY-MM-DD.</td>
291  </tr>
292  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
293  <tr>
294    <td class="boldText">Submission Date:</td>
295    <td class="input"><input type="text" size="10" name="submissionDate" value="2007-12-03" /></td>
296    <td>Date of submission, in the format YYYY-MM-DD.</td>
297  </tr>
298  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
299  <tr>
300    <td class="boldText">Submitter:</td>
301    <td class="input"><input type="text" size="45" name="submitter" value="Micha Bayer" /></td>
302    <td>The name of the person responsible for submitting the experiment to the database.</td>
303  </tr>
304  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
305  <tr>
306    <td class="boldText">Organization:</td>
307    <td class="input"><input type="text" size="45" name="organization" value="SCRI" /></td>
308    <td>The organization to which the submitter is affiliated.</td>
309  </tr>
310  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
311
312  <tr class="noBorder">
313    <td class="boldText">Publication Details:</td>
314    <td  class="input"></td>
315    <td></td>
316  </tr>
317
318  <tr class="noBorder">
319    <td>Title:</td>
320    <td class="input"><textarea rows="2" cols="30" name="publicationTitle">publicationTitle</textarea></td>
321
322    <td rowspan="4">Publication details for any manuscript associated with the experiment. The journal field should
323    contain a standard Pubmed journal abbreviated name. The authors list is a semicolon-delimited list of names.</td>
324  </tr>
325  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
326      <tr class="noBorder">
327        <td>Authors:</td>
328        <td class="input"><textarea rows="2" cols="30" name="authors">authors</textarea></td>
329        <td></td>
330      </tr>
331      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
332      <tr class="noBorder">
333        <td>Journal:</td>
334        <td class="input"><textarea rows="2" cols="30" name="journal">journal</textarea></td>
335        <td></td>
336      </tr>
337      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
338      <tr class="noBorder">
339        <td>Volume:</td>
340        <td class="input"><input type="text" size="10" name="volume" value="" /></td>
341        <td></td>
342      </tr>
343      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
344      <tr class="noBorder">
345        <td>Issue:</td>
346        <td class="input"><input type="text" size="10" name="issue" value="" /></td>
347        <td></td>
348      </tr>
349      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
350      <tr class="noBorder">
351        <td>Pages:</td>
352        <td class="input"><input type="text" size="10" name="pages" value="" /></td>
353        <td></td>
354      </tr>
355      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
356      <tr class="noBorder">
357        <td>Year:</td>
358        <td class="input"><input type="text" size="10" name="year" value="" /></td>
359        <td></td>
360      </tr>
361      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
362      <tr class="noBorder">
363        <td>Pubmed ID:</td>
364        <td class="input"><input type="text" size="30" name="pubmedId" value="" /></td>
365        <td></td>
366
367  </tr>
368
369  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
370</table>
371
372<p>
373
374<table class="noBorder" width="100%">
375<tr class="noBorder" ><td class="centered">
376<input type="submit"  value="Continue"/>
377</td>
378</tr>
379</table>
380
381</form>
382
383</body>
384</html>
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