source: branches/uk_ac_ebi_Tab2MageImporter/html/experiment.html @ 524

Last change on this file since 524 was 524, checked in by mbayer, 14 years ago

have made more changes to the UI to satisfy IE requirements
also fixed a couple of minor bugs relating to the UI

File size: 18.2 KB
Line 
1<html>
2
3<head>
4<title>Tab2MAGE Importer -- Experiment</title>
5<link rel="stylesheet" type="text/css" href="../jsp/uk/ac/ebi/nugo/plugins/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="0" cellspacing="0">
66
67  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
68  <tr >
69    <td class="boldText">Domain:</td>
70    <td class="input"><input type="text" size="45" name="domain" value="scri.ac.uk" /></td>
71    <td class="helpText">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  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
76  <tr >
77    <td class="boldText">Array Acession:</td>
78
79    <td class="input">
80
81    <div id="accession" class="selectionlist required">
82    <table class="noBorder"  cellspacing="0" cellpadding="5">
83      <tr>
84        <td style="border-style: none;"><select name="accession" onchange="arrayDesignOnChange()"></select></td>
85        <td style="border-style: none;">
86        <div class="buttonclass"
87          onmouseover="this.className='buttonclass_hover';"
88          onmouseout="this.className='buttonclass';"
89          onclick="selectArrayDesignOnClick()">
90        <div class="buttonclass_inner">Select&hellip;</div>
91        </div>
92        </td>
93      </tr>
94    </table>
95    </div>
96    </td>
97
98    <td class="helpText">Please select an existing array design from BASE or create a
99    new one. For ArrayExpress submissions, the array design name becomes
100    the array accession identifier. Accession numbers for experiments
101    submitted to ArrayExpress should have the format E-XXXX-n.</td>
102
103  </tr>
104
105
106
107      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
108    <tr >
109      <td class="boldText">Quality Control:</td>
110      <td class="input"><select multiple name="qualityControl">
111        <option selected="selected">biological replicate</option>
112        <option>dye swap quality control</option>
113        <option>peer review quality control</option>
114        <option>real time PCR quality control</option>
115        <option>reverse transcription PCR quality control</option>
116        <option selected="selected">spike quality control</option>
117        <option>technical replicate</option>
118      </select></td>
119      <td class="helpText">A list of terms taken from the <a
120        href="http://mged.sourceforge.net/ontologies/MGEDontology.php"
121        target="_blank">MGED ontology</a>. Multiple values can be selected
122      by holding down the Ctrl key and clicking on items.</td>
123    </tr>
124
125    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
126    <tr>
127      <td class="boldText">Experiment Design Type:</td>
128      <td class="input">
129
130      <table class="noBorder" cellpadding="3">
131
132        <tr>
133          <td valign="top" style="border-style: none;">Biological Property<br />
134          </td>
135          <td colspan="2" style="border-style: none;"><a
136            onclick="showHideItems('BiologicalProperty', 'buttonBiologicalProperty');"
137            title="Show/hide items"> <img
138            src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif"
139            border="0" id="buttonBiologicalProperty"
140            name="buttonBiologicalProperty" /></a> <!-- begin div containing hidden items -->
141          <div id="BiologicalProperty" style="display:none"><select
142            multiple="multiple" name="biologicalProperty">
143            <option selected="selected">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>
164          <td style="border-style: none;">BioMolecular Annotation</td>
165          <td style="border-style: none;"><a
166            onclick="showHideItems('BioMolecularAnnotation', 'buttonBioMolecularAnnotation');"
167            title="Show/hide items"> <img
168            src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif"
169            border="0" id="buttonBioMolecularAnnotation"
170            name="buttonBioMolecularAnnotation" /></a> <!-- begin div containing hidden items -->
171          <div id="BioMolecularAnnotation" style="display:none"><select
172            multiple="multiple" name="bioMolecularAnnotation">
173            <option selected="selected">RNA_stability_design</option>
174            <option>binding_site_identification_design</option>
175            <option>co-expression_design</option>
176            <option>comparative_genome_hybridization_design</option>
177            <option>genotyping_design</option>
178            <option>operon_identification_design</option>
179            <option>secreted_protein_identification_design</option>
180            <option>tiling_path_design</option>
181            <option>transcript_identification_design</option>
182            <option>translational_bias_design</option>
183            <option>unknown_experiment_design_type</option>
184          </select></div>
185          </td>
186        </tr>
187
188        <tr>
189          <td style="border-style: none;">Epidemiological Design</td>
190          <td style="border-style: none;"><a
191            onclick="showHideItems('EpidemiologicalDesign', 'buttonEpidemiologicalDesign');"
192            title="Show/hide items"> <img
193            src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif"
194            border="0" id="buttonEpidemiologicalDesign"
195            name="buttonEpidemiologicalDesign" /></a> <!-- begin div containing hidden items -->
196          <div id="EpidemiologicalDesign" style="display:none"><select
197            multiple="multiple" name="epidemiologicalDesign">
198            <option>clinical_history_design</option>
199            <option>disease_state_design</option>
200            <option selected="selected">family_history_design</option>
201            <option>unknown_experiment_design_type</option>
202          </select></div>
203          </td>
204        </tr>
205
206        <tr>
207          <td style="border-style: none;">Methodological Design</td>
208          <td style="border-style: none;"><a
209            onclick="showHideItems('MethodologicalDesign', 'buttonMethodologicalDesign');"
210            title="Show/hide items"> <img
211            src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif"
212            border="0" id="buttonMethodologicalDesign"
213            name="buttonMethodologicalDesign" /></a> <!-- begin div containing hidden items -->
214          <div id="MethodologicalDesign" style="display:none"><select
215            multiple="multiple" name="methodologicalDesign">
216            <option>all_pairs</option>
217            <option>array_platform_variation_design</option>
218            <option>dye_swap_design</option>
219            <option>ex_vivo_design</option>
220            <option>hardware_variation_design</option>
221            <option>in_vitro_design</option>
222            <option>in_vivo_design</option>
223            <option>loop_design</option>
224            <option>normalization_testing_design</option>
225            <option>operator_variation_design</option>
226            <option>optimization_design</option>
227            <option>quality_control_testing_design</option>
228            <option>reference_design</option>
229            <option>replicate_design</option>
230            <option>self_vs_self_design</option>
231            <option>software_variation_design</option>
232            <option>time_series_design</option>
233            <option>unknown_experiment_design_type</option>
234          </select></div>
235          </td>
236        </tr>
237
238        <tr>
239          <td style="border-style: none;">Perturbational Design</td>
240          <td style="border-style: none;"><a
241            onclick="showHideItems('PerturbationalDesign', 'buttonPerturbationalDesign');"
242            title="Show/hide items"> <img
243            src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif"
244            border="0" id="buttonPerturbationalDesign"
245            name="buttonPerturbationalDesign" /></a> <!-- begin div containing hidden items -->
246          <div id="PerturbationalDesign" style="display:none"><select
247            multiple="multiple" name="perturbationalDesign">
248            <option>cellular_modification_design</option>
249            <option>compound_treatment_design</option>
250            <option>disease_state_design</option>
251            <option>dose_response_design</option>
252            <option>genetic_modification_design</option>
253            <option>growth_condition_design</option>
254            <option>injury_design</option>
255            <option>non-targeted_transgenic_variation_design</option>
256            <option>pathogenicity_design</option>
257            <option>stimulated_design_type</option>
258            <option>stimulus_or_stress_design</option>
259            <option>unknown_experiment_design_type</option>
260          </select></div>
261          </td>
262        </tr>
263
264        <tr>
265          <td style="border-style: none;">Technological Design</td>
266          <td style="border-style: none;"><a
267            onclick="showHideItems('TechnologicalDesign', 'buttonTechnologicalDesign');"
268            title="Show/hide items"> <img
269            src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif"
270            border="0" id="buttonTechnologicalDesign"
271            name="TechnologicalDesign" /></a> <!-- begin div containing hidden items -->
272          <div id="TechnologicalDesign" style="display:none"><select
273            multiple="multiple" name="technologicalDesign">
274            <option>binding_site_identification_design</option>
275            <option>cellular_modification_design</option>
276            <option>comparative_genome_hybridization_design</option>
277            <option>transcript_identification_design</option>
278          </select></div>
279          </td>
280        </tr>
281
282      </table>
283
284
285      </td>
286      <td class="helpText">A list of terms taken from the <a
287        href="http://mged.sourceforge.net/ontologies/MGEDontology.php"
288        target="_blank">MGED ontology</a>.
289      <p>Click "expand" for an item to see list boxes with specific
290      choices.<br />
291      <br />
292      Multiple values can be selected by holding down the Ctrl key and
293      clicking on items.
294      </td>
295    </tr>
296
297    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
298    <tr>
299      <td class="boldText">Experiment Name:</td>
300      <td class="input"><textarea rows="2" cols="30"
301        name="experimentName"><%=expName %></textarea></td>
302      <td class="helpText">The name you have chosen for the Experiment.</td>
303    </tr>
304
305    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
306    <tr>
307      <td class="boldText">Experiment Description:</td>
308      <td class="input"><textarea rows="2" cols="30"
309        name="description">description goes here</textarea></td>
310      <td class="helpText">A short paragraph describing the purpose of the experiment.</td>
311    </tr>
312
313    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
314    <tr>
315      <td class="boldText">Release Date:</td>
316      <td class="input"><input type="text" size="10"
317        name="releaseDate" value="2007-12-03" /></td>
318      <td class="helpText">Date for public release, in the format YYYY-MM-DD.</td>
319    </tr>
320    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
321    <tr>
322      <td class="boldText">Submission Date:</td>
323      <td class="input"><input type="text" size="10"
324        name="submissionDate" value="2007-12-03" /></td>
325      <td class="helpText">Date of submission, in the format YYYY-MM-DD.</td>
326    </tr>
327    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
328    <tr>
329      <td class="boldText">Submitter:</td>
330      <td class="input"><input type="text" size="45" name="submitter"
331        value="Joe Bloggs" /></td>
332      <td class="helpText">The name of the person responsible for submitting the
333      experiment to the database.</td>
334    </tr>
335    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
336    <tr>
337      <td class="boldText">Organization:</td>
338      <td class="input"><input type="text" size="45"
339        name="organization" value="SCRI" /></td>
340      <td class="helpText">The organization to which the submitter is affiliated.</td>
341    </tr>
342    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
343
344    <tr>
345      <td class="boldText">Publication Details:</td>
346      <td class="input"></td>
347      <td class="helpText">Publication details for any manuscript
348      associated with the experiment.</td>
349    </tr>
350
351    <tr>
352      <td class="plainLabel" style="border-style: none;">Title:</td>
353      <td class="input" style="border-style: none;"><textarea rows="2" cols="30"
354        name="publicationTitle" >My Ropey Paper</textarea></td>
355      <td style="border-style: none;"></td>
356    </tr>
357    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
358    <tr>
359      <td class="plainLabel" style="border-style: none;">Authors:</td>
360      <td class="input" style="border-style: none;"><textarea rows="2" cols="30" name="authors">Bloggs, Joe</textarea></td>
361      <td  class="helpText" style="border-style: none;">The authors list is a semicolon-delimited list of names.</td>
362    </tr>
363    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
364    <tr>
365      <td class="plainLabel" style="border-style: none;">Journal:</td>
366      <td class="input" style="border-style: none;"><textarea rows="2" cols="30" name="journal">The Journal of Irreproducible Results</textarea></td>
367      <td  class="helpText" style="border-style: none;">The journal field should contain a standard Pubmed journal
368      abbreviated name. </td>
369    </tr>
370    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
371    <tr>
372      <td class="plainLabel" style="border-style: none;">Volume:</td>
373      <td class="input" style="border-style: none;"><input type="text" size="10" name="volume"
374        value="5" /></td>
375      <td style="border-style: none;"></td>
376    </tr>
377    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
378    <tr>
379      <td class="plainLabel" style="border-style: none;">Issue:</td>
380      <td class="input" style="border-style: none;"><input type="text" size="10" name="issue"
381        value="2" /></td>
382      <td style="border-style: none;"></td>
383    </tr>
384    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
385    <tr>
386      <td class="plainLabel" style="border-style: none;">Pages:</td>
387      <td class="input" style="border-style: none;"><input type="text" size="10" name="pages"
388        value="1234-1235" /></td>
389      <td style="border-style: none;"></td>
390    </tr>
391    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
392    <tr>
393      <td class="plainLabel" style="border-style: none;">Year:</td>
394      <td class="input" style="border-style: none;"><input type="text" size="10" name="year"
395        value="2007" /></td>
396      <td style="border-style: none;"></td>
397    </tr>
398    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
399    <tr>
400      <td class="plainLabel" style="border-style: none;">Pubmed ID:</td>
401      <td class="input" style="border-style: none;"><input type="text" size="30" name="pubmedId"
402        value="11009762" /></td>
403      <td style="border-style: none;"></td>
404
405    </tr>
406
407    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
408  </table>
409<p>
410
411<table class="noBorder" width="100%">
412<tr class="noBorder" ><td class="centered">
413<input type="submit"  value="Continue"/>
414</td>
415</tr>
416</table>
417
418</form>
419
420</body>
421</html>
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