-
Notifications
You must be signed in to change notification settings - Fork 1
/
Faq.html
831 lines (353 loc) · 24.8 KB
/
Faq.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
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
<!DOCTYPE HTML>
<html lang="" >
<head>
<title>FAQ · GitBook</title>
<meta charset="UTF-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge" />
<meta content="text/html; charset=utf-8" http-equiv="Content-Type">
<meta name="description" content="">
<meta name="generator" content="GitBook 3.1.1">
<link rel="stylesheet" href="gitbook/style.css">
<link rel="stylesheet" href="gitbook/gitbook-plugin-highlight/website.css">
<link rel="stylesheet" href="gitbook/gitbook-plugin-search/search.css">
<link rel="stylesheet" href="gitbook/gitbook-plugin-fontsettings/website.css">
<meta name="HandheldFriendly" content="true"/>
<meta name="viewport" content="width=device-width, initial-scale=1, user-scalable=no">
<meta name="apple-mobile-web-app-capable" content="yes">
<meta name="apple-mobile-web-app-status-bar-style" content="black">
<link rel="apple-touch-icon-precomposed" sizes="152x152" href="gitbook/images/apple-touch-icon-precomposed-152.png">
<link rel="shortcut icon" href="gitbook/images/favicon.ico" type="image/x-icon">
<link rel="next" href="WhoUsesPsicquic.html" />
<link rel="prev" href="DataEnricher.html" />
</head>
<body>
<div class="book">
<div class="book-summary">
<div id="book-search-input" role="search">
<input type="text" placeholder="Type to search" />
</div>
<nav role="navigation">
<ul class="summary">
<li class="chapter " data-level="1.1" data-path="./">
<a href="./">
Introduction
</a>
<ul class="articles">
<li class="chapter " data-level="1.1.1" data-path="PsicquicSpecification.html">
<a href="PsicquicSpecification.html">
Specification
</a>
<ul class="articles">
<li class="chapter " data-level="1.1.1.1" data-path="PsicquicSpec_1_4_Soap.html">
<a href="PsicquicSpec_1_4_Soap.html">
SOAP
</a>
</li>
<li class="chapter " data-level="1.1.1.2" data-path="PsicquicSpec_1_4_Rest.html">
<a href="PsicquicSpec_1_4_Rest.html">
REST
</a>
</li>
</ul>
</li>
<li class="chapter " data-level="1.1.2" data-path="Registry.html">
<a href="Registry.html">
Registry
</a>
<ul class="articles">
<li class="chapter " data-level="1.1.2.1" data-path="PsicquicServiceTags.html">
<a href="PsicquicServiceTags.html">
Registry Service Tags
</a>
</li>
<li class="chapter " data-level="1.1.2.2" data-path="RegistryJavaClient.html">
<a href="RegistryJavaClient.html">
Java client
</a>
</li>
</ul>
</li>
</ul>
</li>
<li class="chapter " data-level="1.2" data-path="MiqlDefinition.html">
<a href="MiqlDefinition.html">
Usage MIQL
</a>
<ul class="articles">
<li class="chapter " data-level="1.2.1" data-path="MiqlReference.html">
<a href="MiqlReference.html">
MIQL Reference 2.5
</a>
</li>
<li class="chapter " data-level="1.2.2" data-path="MiqlReference27.html">
<a href="MiqlReference27.html">
MIQL Extension 2.7
</a>
</li>
<li class="chapter " data-level="1.2.3" data-path="MiqlReference28.html">
<a href="MiqlReference28.html">
MIQL Extension 2.8
</a>
</li>
</ul>
</li>
<li class="chapter " data-level="1.3" data-path="Clients.html">
<a href="Clients.html">
Clients
</a>
<ul class="articles">
<li class="chapter " data-level="1.3.1" >
<a target="_blank" href="http://www.bioconductor.org/packages/release/bioc/html/PSICQUIC.html">
R Bioconductor package
</a>
</li>
<li class="chapter " data-level="1.3.2" data-path="JavaClient.html">
<a href="JavaClient.html">
Java
</a>
</li>
<li class="chapter " data-level="1.3.3" data-path="PerlCodeSamples.html">
<a href="PerlCodeSamples.html">
Perl
</a>
</li>
<li class="chapter " data-level="1.3.4" data-path="PythonCodeSamples.html">
<a href="PythonCodeSamples.html">
Python
</a>
</li>
<li class="chapter " data-level="1.3.5" data-path="CytoscapeClient.html">
<a href="CytoscapeClient.html">
Cytoscape
</a>
</li>
</ul>
</li>
<li class="chapter " data-level="1.4" data-path="formats.html">
<a href="formats.html">
Formats
</a>
<ul class="articles">
<li class="chapter " data-level="1.4.1" data-path="PSIMITAB.html">
<a href="PSIMITAB.html">
PSI-MI TAB
</a>
<ul class="articles">
<li class="chapter " data-level="1.4.1.1" data-path="MITAB25Format.html">
<a href="MITAB25Format.html">
MITAB 2.5
</a>
</li>
<li class="chapter " data-level="1.4.1.2" data-path="MITAB26Format.html">
<a href="MITAB26Format.html">
MITAB 2.6
</a>
</li>
<li class="chapter " data-level="1.4.1.3" data-path="MITAB27Format.html">
<a href="MITAB27Format.html">
MITAB 2.7
</a>
</li>
<li class="chapter " data-level="1.4.1.4" data-path="MITAB28Format.html">
<a href="MITAB28Format.html">
MITAB 2.8
</a>
</li>
</ul>
</li>
<li class="chapter " data-level="1.4.2" data-path="PSIMIXML.html">
<a href="PSIMIXML.html">
PSI-MI XML
</a>
<ul class="articles">
<li class="chapter " data-level="1.4.2.1" data-path="MIXML25Format.html">
<a href="MIXML25Format.html">
PSI-MI XML 2.5
</a>
</li>
<li class="chapter " data-level="1.4.2.2" data-path="MIXML30Format.html">
<a href="MIXML30Format.html">
PSI-MI XML 3.0
</a>
</li>
<li class="chapter " data-level="1.4.2.3" >
<a target="_blank" href="https://github.com/MICommunity/psi-jami/tree/master/jami-xml">
Java Examples
</a>
</li>
</ul>
</li>
</ul>
</li>
<li class="divider"></li>
<li class="chapter " data-level="2.1" data-path="PsicquicServiceProviders.html">
<a href="PsicquicServiceProviders.html">
Service providers
</a>
<ul class="articles">
<li class="chapter " data-level="2.1.1" data-path="HowToInstallPsicquicSolr.html">
<a href="HowToInstallPsicquicSolr.html">
How to install PSICQUIC Solr (recommened)
</a>
<ul class="articles">
<li class="chapter " data-level="2.1.1.1" data-path="HowToInstallPsicquicAndSolrJetty.html">
<a href="HowToInstallPsicquicAndSolrJetty.html">
Single jetty server
</a>
</li>
<li class="chapter " data-level="2.1.1.2" data-path="HowToInstallPsicquicSolrDifferentServers.html">
<a href="HowToInstallPsicquicSolrDifferentServers.html">
Using a solr server independent from the PSICQUIC server
</a>
</li>
</ul>
</li>
<li class="chapter " data-level="2.1.2" data-path="HowToInstallPsicquicLucene.html">
<a href="HowToInstallPsicquicLucene.html">
How to install PSICQUIC using LUCENE
</a>
<ul class="articles">
<li class="chapter " data-level="2.1.2.1" data-path="HowToInstall.html">
<a href="HowToInstall.html">
Using LUCENE
</a>
</li>
</ul>
</li>
<li class="chapter " data-level="2.1.3" data-path="DataDistributionBestPractices.html">
<a href="DataDistributionBestPractices.html">
Data Distribution Best Practices
</a>
</li>
<li class="chapter " data-level="2.1.4" data-path="DataEnricher.html">
<a href="DataEnricher.html">
Data Enricher
</a>
</li>
<li class="chapter active" data-level="2.1.5" data-path="Faq.html">
<a href="Faq.html">
FAQ
</a>
</li>
</ul>
</li>
<li class="chapter " data-level="2.2" data-path="WhoUsesPsicquic.html">
<a href="WhoUsesPsicquic.html">
Who uses PSICQUIC?
</a>
</li>
<li class="chapter " data-level="2.3" data-path="PreparingARelease.html">
<a href="PreparingARelease.html">
How to release the project
</a>
</li>
<li class="divider"></li>
<li>
<a href="https://www.gitbook.com" target="blank" class="gitbook-link">
Published with GitBook
</a>
</li>
</ul>
</nav>
</div>
<div class="book-body">
<div class="body-inner">
<div class="book-header" role="navigation">
<!-- Title -->
<h1>
<i class="fa fa-circle-o-notch fa-spin"></i>
<a href="." >FAQ</a>
</h1>
</div>
<div class="page-wrapper" tabindex="-1" role="main">
<div class="page-inner">
<div id="book-search-results">
<div class="search-noresults">
<section class="normal markdown-section">
<p><br></p>
<h2 id="are-there-guidelines-on-how-to-create-valid-psimitab-">Are there guidelines on how to create valid PSIMITAB ?</h2>
<p>The original format (version 2.5) itself was first described in <a href="http://www.ncbi.nlm.nih.gov/pubmed/17925023" target="_blank">Kerrien et al. (2007)</a> but you can also find it as part of the PSI-MI and PSICQUIC documentation. These documents only describe the various columns of the PSIMITAB format (2.5, 2.6, 2.7 and 2.8) and the syntax of the data that can be stored. In addition to the format, the PSI-MI workgroup has defined a guideline referred to as <a href="DataDistributionBestPractices.html">Data Distribution Best Practices</a> that aims at standardising the use of the format to maximize its effectiveness. It is strongly recommended to read these documents before attempting to build a dataset using the <a href="MITAB25Format.html">PSIMITAB 2.5</a>, <a href="MITAB26Format.html">PSIMITAB 2.6</a>, <a href="MITAB27Format.html">PSIMITAB 2.7</a> or <a href="MITAB28Format.html">PSIMITAB 2.8</a> format.
<br></p>
<h2 id="what-identifier-should-i-use-to-describe-my-interacting-proteins-">What identifier should I use to describe my Interacting Proteins ?</h2>
<p>Most PSICQUIC providers are using UniProtKB ACs to describe their proteins, and this allows these services to be easily combined together. For more information, look at the <a href="DataDistributionBestPractices.html">Data Distribution Best Practices</a>.
<br></p>
<h2 id="how-can-i-map-my-identifiers-to-uniprotkb-ac-">How can I map my identifiers to UniProtKB AC ?</h2>
<p>If you happen to be using another identifier space to describe your proteins, there are several tools you could be using to map to UniProtKB:</p>
<ul>
<li><a href="http://www.ebi.ac.uk/Tools/picr/" target="_blank">PICR</a></li>
<li><a href="http://www.uniprot.org/?tab=mapping" target="_blank">UniProt Mapping</a>
<br></li>
</ul>
<h2 id="why-are-my-chebi-identifiers-not-linked-properly-in-psicquic-view">Why are my ChEBI identifiers not linked properly in PSICQUIC View</h2>
<p>If you are using ChEBI, or any database identifier using reserved character such as column (':') you will have to escape them as follow: <code>CHEBI:"CHEBI:114264"</code>.</p>
<h2 id="how-can-i-easily-browse-the-various-ontology-types-of-psi-mi-">How can I easily browse the various ontology types of PSI-MI ?</h2>
<p>We recommend you use the <a href="http://www.ebi.ac.uk/ontology-lookup/" target="_blank">Ontology Lookup Service (OLS)</a>. You can browse the PSI-MI ontology as a simple tree structure here or perform the following searches from the OLS home page:
search by term name (with auto-completion),
search by term id.
<br></p>
<h2 id="can-i-cluster-multiple-interaction-evidences-into-a-single-mitab-line-">Can I cluster multiple interaction evidences into a single MITAB line ?</h2>
<p>Yes you can, but we do not recommend you doing it if you are intending to distribute the data using PSICQUIC. While PSICQUIC isn’t affected by clustered data, it doesn’t allow users to effectively query the service.</p>
<p>Let’s describe the issue using an example, say you have 2 MITAB lines:</p>
<pre><code> P12345 Q98765 - - - - two hybrid …
P12345 Q98765 - - - - coip …
</code></pre><p>Now let’s consider the clustered equivalent of these 2 lines:</p>
<pre><code> P12345 Q98765 - - - - two hybrid|coip …
</code></pre><p>So now if a user queries the non-clustered service with the following MIQL:</p>
<pre><code>NOT detmethod:coip
</code></pre><p>the response contains a single line (i.e. the two hybrid evidence).
When the user runs the same query on the clustered service, the response shows no data because the whole line has been removed as it contains a coip evidence, leading the user to miss potentially critical information.
<br></p>
<h2 id="how-do-i-define-confidence-values-">How do I define confidence values ?</h2>
<p>Column 15 of MITAB was designed to accommodate this type of data. There are numerous methods in used and in most cases, data providers tend to design their own. For this reason, we have defined a set of controlled vocabulary terms to help categorising broad classes of scoring methods. You can view the current list on the <a href="http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI%3A1064&termName=interaction%20confidence" target="_blank">Ontology Lookup Service</a>.
<br></p>
<h2 id="how-much-additional-information-ie-alternative-identifiers-aliases-should-i-add-about-my-interacting-molecules-">How much additional information (i.e. alternative identifiers, aliases) should I add about my interacting molecules ?</h2>
<p>While providing a UniProtKB AC is a great start to providing a broadly accepted referencing system for your proteins, many users are searching PSICQUIC services using gene names. For this reason, columns 5 and 6 will allow the storage of aliases for, respectively, molecule A and B. It is strongly encouraged to stored in these columns information such as:</p>
<ul>
<li><code>gene name (e.g. uniprotkb:BRCA2(gene name))</code></li>
<li><code>orf name (e.g.uniprotkb:F14J9.23(orf name))</code></li>
<li><code>locus name (e.g. uniprotkb:At1g09570(locus name))</code></li>
<li><code>gene name synonym (e.g. uniprotkb:Protein ELONGATED HYPOCOTYL 8(gene name synonym))</code>
The data type that can be used are defined in this branch of the <a href="http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI%3A0300&termName=alias%20type" target="_blank">PSI-MI ontology</a>.
<br></li>
</ul>
<h2 id="how-should-i-use-the-unique-identifieralternative-identifier-columns-">How should I use the Unique Identifier/Alternative Identifier columns ?</h2>
<p>These columns have different purposes, all of which are geared toward identifying the interacting molecule unambiguously. While the unique identifier is meant as a single cross reference to a public database, the alternative identifier column should be used to maintain a collection of alternative identifiers potentially encompassing secondary identifiers (e.g. UniProtKB), model organism databases (SGD, FlyBase...), translation to other biological concept (e.g. the molecule descibed is a protein but I could store an ensembl or entrez geneid). The <a href="DataDistributionBestPractices.html">Data Distribution Best Practices</a> does give some additional information with respect to which specific cross reference to use.</p>
</section>
</div>
<div class="search-results">
<div class="has-results">
<h1 class="search-results-title"><span class='search-results-count'></span> results matching "<span class='search-query'></span>"</h1>
<ul class="search-results-list"></ul>
</div>
<div class="no-results">
<h1 class="search-results-title">No results matching "<span class='search-query'></span>"</h1>
</div>
</div>
</div>
</div>
</div>
</div>
<a href="DataEnricher.html" class="navigation navigation-prev " aria-label="Previous page: Data Enricher">
<i class="fa fa-angle-left"></i>
</a>
<a href="WhoUsesPsicquic.html" class="navigation navigation-next " aria-label="Next page: Who uses PSICQUIC?">
<i class="fa fa-angle-right"></i>
</a>
</div>
<script>
var gitbook = gitbook || [];
gitbook.push(function() {
gitbook.page.hasChanged({"page":{"title":"FAQ","level":"2.1.5","depth":2,"next":{"title":"Who uses PSICQUIC?","level":"2.2","depth":1,"path":"WhoUsesPsicquic.md","ref":"WhoUsesPsicquic.md","articles":[]},"previous":{"title":"Data Enricher","level":"2.1.4","depth":2,"path":"DataEnricher.md","ref":"DataEnricher.md","articles":[]},"dir":"ltr"},"config":{"gitbook":"3.1.1","theme":"default","variables":{},"plugins":[],"pluginsConfig":{"highlight":{},"search":{},"lunr":{"maxIndexSize":1000000},"sharing":{"facebook":true,"twitter":true,"google":false,"weibo":false,"instapaper":false,"vk":false,"all":["facebook","google","twitter","weibo","instapaper"]},"fontsettings":{"theme":"white","family":"sans","size":2},"theme-default":{"styles":{"website":"styles/website.css","pdf":"styles/pdf.css","epub":"styles/epub.css","mobi":"styles/mobi.css","ebook":"styles/ebook.css","print":"styles/print.css"},"showLevel":false}},"structure":{"langs":"LANGS.md","readme":"README.md","glossary":"GLOSSARY.md","summary":"SUMMARY.md"},"pdf":{"pageNumbers":true,"fontSize":12,"fontFamily":"Arial","paperSize":"a4","chapterMark":"pagebreak","pageBreaksBefore":"/","margin":{"right":62,"left":62,"top":56,"bottom":56}},"styles":{"website":"styles/website.css","pdf":"styles/pdf.css","epub":"styles/epub.css","mobi":"styles/mobi.css","ebook":"styles/ebook.css","print":"styles/print.css"}},"file":{"path":"Faq.md","mtime":"2022-02-09T13:58:44.498Z","type":"markdown"},"gitbook":{"version":"3.1.1","time":"2022-02-09T15:46:01.286Z"},"basePath":".","book":{"language":""}});
});
</script>
</div>
<script src="gitbook/gitbook.js"></script>
<script src="gitbook/theme.js"></script>
<script src="gitbook/gitbook-plugin-search/search-engine.js"></script>
<script src="gitbook/gitbook-plugin-search/search.js"></script>
<script src="gitbook/gitbook-plugin-lunr/lunr.min.js"></script>
<script src="gitbook/gitbook-plugin-lunr/search-lunr.js"></script>
<script src="gitbook/gitbook-plugin-sharing/buttons.js"></script>
<script src="gitbook/gitbook-plugin-fontsettings/fontsettings.js"></script>
</body>
</html>