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comparison generate_macros_xml.pl @ 3:e267701c187b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
author iuc
date Wed, 23 Sep 2020 09:48:26 +0000
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children 67602de82f6e
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2:c6096cd97120 3:e267701c187b
1 #!/usr/bin/env perl
2
3 #Usage: perl generate_macros_xml.pl > macros.xml
4
5 #Note, this script uses einfo.py to get database info. It also uses manually compiled data stored at the bottom of this script that is based on: https://www.ncbi.nlm.nih.gov/books/NBK25499/table/chapter4.T._valid_values_of__retmode_and/?report=objectonly
6 #The data in the table on that page was manipulated to replace nulls with 'none', remove duplicates, and add missing formats based on correspondence with MLN.
7
8 ##
9 ## use einfo to retrieve all the valid databases
10 ##
11
12 print STDERR "Retrieving database list\n";
13
14 my $dbxml = `python einfo.py --user_email "planemo@galaxyproject.org" --admin_email "planemo@galaxyproject.org;test@bx.psu.edu"`;
15
16 my(@dblist);
17 my $dbs = {};
18 my $dbfroms = {};
19 my $dbnames = {};
20 foreach(split(/\n/,$dbxml))
21 {
22 if(/<DbName>(.+)<\/DbName>/)
23 {
24 my $db = $1;
25 push(@dblist,$db);
26 $dbs->{$db} = 0;
27 $dbfroms->{$db} = 0;
28 $dbnames->{$db} = $_;
29 }
30 }
31
32 ##
33 ## Use einfo to retrieve all the valid links for each database (Note: some databases are not linked)
34 ##
35
36 my $h = {};
37 foreach my $db (sort {$dbnames->{$a} cmp $dbnames->{$b}} @dblist)
38 {
39 sleep(2);
40
41 print STDERR "Retrieving info for $db\n";
42
43 my $response = `python einfo.py --db $db --user_email "planemo\@galaxyproject.org" --admin_email "planemo\@galaxyproject.org;test\@bx.psu.edu"`;
44
45 my $dolinks = 0;
46 my $link = "";
47 my $name = "";
48
49 foreach(split(/\n/,$response))
50 {
51 if(/<LinkList>/)
52 {
53 $dolinks = 1;
54 #Save whether there exist links from this database
55 $dbfroms->{$db} = 1;
56 }
57 elsif(!$dolinks)
58 {
59 if(/<MenuName>(.+)<\/MenuName>/)
60 {$dbnames->{$db} = "$1 ($db)"}
61 }
62 elsif($dolinks)
63 {
64 if(/<Name>(.+)<\/Name>/)
65 {$link=$1}
66 elsif(/<Menu>(.*)<\/Menu>/)
67 {$name=$1}
68 elsif(/<DbTo>(.+)<\/DbTo>/)
69 {
70 $dbto=$1;
71 push(@{$h->{$db}->{$dbto}},[$link,$name]);
72 $link="";
73 $name="";
74 }
75 }
76 }
77 }
78
79 my @sorted_dblist = sort {$dbnames->{$a} cmp $dbnames->{$b}} @dblist;
80
81 ##
82 ## Generate XML to govern the valid databases to use with efetch
83 ##
84
85 my $efetch_dbhash = {}; #->{efetch-compatible-db}->{rettype-retmode-galaxy_format} = format_name (galaxy_format)
86 while(<DATA>)
87 {
88 chomp;
89 my($db,$galaxy_format,$retmode,$rettype,$format_name) = split(/\t/,$_);
90 $efetch_dbhash->{$db}->{"$rettype-$retmode-$galaxy_format"} =
91 "$format_name ($galaxy_format)";
92 }
93
94 #EFetch database select list
95
96 print << 'EOXML';
97 <xml name="dbselect_efetch" token_name="db_select" token_label="NCBI Database to Query">
98 <param name="@NAME@" type="select" label="@LABEL@">
99 EOXML
100
101 foreach my $db (grep {exists($dbs->{$_})}
102 sort {$dbnames->{$a} cmp $dbnames->{$b}}
103 keys(%$efetch_dbhash))
104 {
105 my $selected = '';
106 if($db eq 'pubmed')
107 {$selected = ' selected="True"'}
108 print << " EOXML";
109 <option value="$db"$selected>$dbnames->{$db}</option>
110 EOXML
111 }
112
113 print << 'EOXML';
114 </param>
115 </xml>
116 EOXML
117
118 #EFetch output formats
119
120 print << 'EOXML';
121 <xml name="efetchdb">
122 <conditional name="db">
123 <expand macro="dbselect_efetch" />
124 EOXML
125
126 foreach my $db (grep {exists($dbs->{$_})}
127 sort {$dbnames->{$a} cmp $dbnames->{$b}}
128 keys(%$efetch_dbhash))
129 {
130 print << " EOXML";
131 <when value="$db">
132 <param name="output_format" type="select" label="Output Format">
133 EOXML
134
135 foreach my $eutils_format (sort {$efetch_dbhash->{$db}->{$a} cmp
136 $efetch_dbhash->{$db}->{$b}}
137 keys(%{$efetch_dbhash->{$db}}))
138 {
139 print << " EOXML";
140 <option value="$eutils_format">$efetch_dbhash->{$db}->{$eutils_format}</option>
141 EOXML
142 }
143
144 print << " EOXML";
145 </param>
146 </when>
147 EOXML
148 }
149
150 print << 'EOXML';
151 </conditional>
152 </xml>
153 EOXML
154
155 ##
156 ## Create a select list for the databases linked *from*
157 ##
158
159 print << 'EOXML';
160 <xml name="dbselect" token_name="db_select" token_label="NCBI Database to Query">
161 <param name="@NAME@" type="select" label="@LABEL@">
162 EOXML
163
164 foreach my $from (@sorted_dblist)
165 {
166 print << " EOXML";
167 <option value="$from">$dbnames->{$from}</option>
168 EOXML
169 }
170
171 print << 'EOXML';
172 </param>
173 </xml>
174 EOXML
175
176 ##
177 ## Create a select list for the databases linked *to*
178 ##
179
180 print << 'EOXML';
181 <xml name="dbselect_linked" token_name="db_select_linked" token_label="NCBI Database to Use">
182 <param name="@NAME@" type="select" label="@LABEL@">
183 EOXML
184
185 foreach my $from (grep {$dbfroms->{$_}} @sorted_dblist)
186 {
187 print << " EOXML";
188 <option value="$from">$dbnames->{$from}</option>
189 EOXML
190 }
191
192 print << 'EOXML';
193 </param>
194 </xml>
195 EOXML
196
197 ##
198 ## Create empty entries for commands that take no *to* database or link
199 ##
200
201 print << 'EOXML';
202 <xml name="none_link_macro">
203 <conditional name="db_to">
204 <param name="db_select_to" type="select" label="To NCBI Database (n/a)">
205 <option value="n/a">Not applicable</option>
206 </param>
207 <when value="n/a">
208 <param name="linkname" type="select" label="Link Name (n/a)">
209 <option value="n/a">Not applicable</option>
210 </param>
211 </when>
212 </conditional>
213 </xml>
214 <xml name="db_link_macro">
215 <conditional name="db_from_link">
216 <expand macro="dbselect_linked" name="db_select_from_link" label="From NCBI Database" />
217 EOXML
218
219 foreach(grep {$dbfroms->{$_}} @sorted_dblist)
220 {
221 print << " EOXML";
222 <when value="$_">
223 <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" />
224 </when>
225 EOXML
226 }
227
228 print << 'EOXML';
229 </conditional>
230 </xml>
231 EOXML
232
233 ##
234 ## This is the master macro for the command selection
235 ##
236
237 print << 'EOXML';
238 <xml name="linkmacro">
239 <conditional name="cmd">
240 <param name="cmd_select" type="select" label="Link Method" help="Fetch UIDs from the 'To' Database that are linked to supplied UIDs in the 'From' database">
241 <option value="neighbor" selected="true">Neighbor (neighbor)</option>
242 <option value="neighbor_history">Neighbor, save result in history server (neighbor_history)</option>
243 <option value="neighbor_score">Neighbor Score (neighbor_score)</option>
244 <option value="acheck">Show available links to any database (acheck)</option>
245 <option value="ncheck">Show available links within the same database (ncheck)</option>
246 <option value="lcheck">Show available links to external sources (LinkOuts) (lcheck)</option>
247 <option value="llinks">Show available URLs and attributes for non-library LinkOut providers (llinks)</option>
248 <option value="llinkslib">Show available URLs and attributes for all LinkOut Providers (llinkslib)</option>
249 <option value="prlinks">Show available primary LinkOut Provider Links (prlinks)</option>
250 </param>
251 <when value="neighbor">
252 <expand macro="db_db_link_macro" name="link_select" label="Link name" />
253 <param name="output_format" type="select" label="Output Format">
254 <option value="xml">ID File (xml)</option>
255 <option value="json">ID File (json)</option>
256 <option value="text" selected="true">ID File (tabular)</option>
257 </param>
258 </when>
259 <when value="neighbor_history">
260 <expand macro="db_db_link_macro" name="link_select" label="Link name" />
261 <param name="output_format" type="select" label="Output Format">
262 <option value="json">History File (json)</option>
263 <option value="xml" selected="true">History File (xml)</option>
264 </param>
265 </when>
266 <when value="neighbor_score">
267 <expand macro="db_db_link_macro" name="link_select" label="Link name" />
268 <param name="output_format" type="select" label="Output Format">
269 <option value="xml">ID File (xml)</option>
270 <option value="json">ID File (json)</option>
271 <option value="text" selected="true">ID File (tabular)</option>
272 </param>
273 </when>
274 <when value="acheck">
275 <expand macro="db_link_macro" name="db_select_from_link" label="From NCBI Database" />
276 <param name="output_format" type="select" label="Output Format">
277 <option value="xml" selected="True">Link Description File (xml)</option>
278 <option value="json">Link Description File (json)</option>
279 </param>
280 </when>
281 <when value="ncheck">
282 <expand macro="db_link_macro" name="db_select_from_link" label="From NCBI Database" />
283 <param name="output_format" type="select" label="Output Format">
284 <option value="xml" selected="True">Link Description File (xml)</option>
285 <option value="json">Link Description File (json)</option>
286 </param>
287 </when>
288 <when value="lcheck">
289 <expand macro="db_link_macro" name="db_select_from_link" label="From NCBI Database" />
290 <param name="output_format" type="select" label="Output Format">
291 <option value="xml" selected="True">Link Description File (xml)</option>
292 <option value="json">Link Description File (json)</option>
293 </param>
294 </when>
295 <when value="llinks">
296 <expand macro="db_link_macro" name="db_select_from_link" label="From NCBI Database" />
297 <param name="output_format" type="select" label="Output Format">
298 <option value="xml" selected="True">Link Description File (xml)</option>
299 <option value="json">Link Description File (json)</option>
300 </param>
301 </when>
302 <when value="llinkslib">
303 <expand macro="db_link_macro" name="db_select_from_link" label="From NCBI Database" />
304 <param name="output_format" type="select" label="Output Format">
305 <option value="xml" selected="true">Link Description File (xml)</option>
306 <option value="json">Link Description File (json)</option>
307 </param>
308 </when>
309 <when value="prlinks">
310 <expand macro="db_link_macro" name="db_select_from_link" label="From NCBI Database" />
311 <param name="output_format" type="select" label="Output Format">
312 <option value="xml" selected="true">Link Description File (xml)</option>
313 <option value="json">Link Description File (json)</option>
314 </param>
315 </when>
316 </conditional>
317 </xml>
318 EOXML
319
320 ##
321 ## Create selections for valid links for command types neighbor, neighbor_history, and neighbor_score
322 ##
323
324 print << 'EOXML';
325 <xml name="db_db_link_macro">
326 <conditional name="db_from_link">
327 <expand macro="dbselect_linked" name="db_select_from_link" label="From NCBI Database" />
328 EOXML
329
330 foreach my $from (grep {$dbfroms->{$_}} @sorted_dblist)
331 {
332 print STDERR ("Creating Links From: $from\n");
333
334 print << " EOXML";
335 <when value="$from">
336 <conditional name="db_to">
337 <param name="db_select_to" type="select" label="To NCBI Database">
338 EOXML
339
340 my @dbtos = (grep {exists($h->{$from}) && exists($h->{$from}->{$_})}
341 @sorted_dblist);
342 foreach(@dbtos)
343 {
344 print << " EOXML";
345 <option value="$_">$dbnames->{$_}</option>
346 EOXML
347 }
348 if(scalar(@dbtos) == 0)
349 {
350 #Provide an option for a self-link: from->from
351 print << " EOXML";
352 <option value="$from">$dbnames->{$from}</option>
353 EOXML
354 }
355
356 print << ' EOXML';
357 </param>
358 EOXML
359
360 if(exists($h->{$from}))
361 {
362 #There do exist links to invalid(/outdated/non-existant) databases that
363 #would result in an error if they are selected, so we use the original
364 #@dblist instead of the keys present in the sub hash of $h->{$from}, and
365 #then check for existence in the sub-hash
366 foreach my $to (grep {exists($h->{$from}->{$_})} @sorted_dblist)
367 {
368 print STDERR ("\tTo: $to Links: ",
369 join(',',map {$_->[0]} @{$h->{$from}->{$to}}),
370 "\n");
371
372 print << " EOXML";
373 <when value="$to">
374 <param name="linkname" type="select" label="Link Name">
375 <option value="None">All Links</option>
376 EOXML
377
378 foreach(sort {"$a->[1] ($a->[0])" cmp "$b->[1] ($b->[0])"}
379 @{$h->{$from}->{$to}})
380 {
381 print << " EOXML";
382 <option value="$_->[0]">$_->[1] ($_->[0])</option>
383 EOXML
384 }
385
386 print << " EOXML";
387 </param>
388 </when>
389 EOXML
390
391 }
392 }
393 else
394 {
395 ##
396 ## Add-on selections for self-links for command types neighbor,
397 ## neighbor_history, and neighbor_score
398 ## Note, I'm not sure this would yield a valid result from elink
399 ##
400
401 #This shows $from, but this is the 'when' for db_to conditional
402 print << " EOXML";
403 <when value="$from">
404 <param name="linkname" type="select" label="Link Name">
405 <option value="none">All Links</option>
406 </param>
407 </when>
408 EOXML
409 }
410
411 print << ' EOXML';
412 </conditional>
413 </when>
414 EOXML
415 }
416
417 ##
418 ## Add-on selections for self-links for command types neighbor,
419 ## neighbor_history, and neighbor_score
420 ## Note, I'm not sure this would yield a valid result from elink
421 ##
422
423 foreach my $from (grep {!exists($h->{$_})} @sorted_dblist)
424 {
425 print << "EOXML";
426 <when value=\"$from\">
427 <conditional name=\"db_to\">
428 <param name=\"db_select_to\" type=\"select\" label=\"To NCBI Database\">
429 <option value=\"none\">Not applicable</option>
430 </param>
431 <when value=\"none\">
432 <param name=\"linkname\" type=\"select\" label=\"Link Name\">
433 <option value=\"none\">Not applicable</option>
434 </param>
435 </when>
436 </conditional>
437 </when>
438 EOXML
439 }
440
441 ##
442 ## This is the corresponding code for using the selections to add the respective command line options
443 ##
444
445 print << 'EOXML';
446 </conditional>
447 </xml>
448 EOXML
449
450 print << 'EOXML';
451 <token name="@LINK_TOKEN@">
452 <![CDATA[
453 #if $cmd.db_from_link.db_to.db_select_to == 'n/a':
454 none
455 #else:
456 $cmd.db_from_link.db_to.db_select_to
457 #end if
458
459 $cmd.db_from_link.db_select_from_link
460
461 $cmd.cmd_select
462
463 #if $cmd.output_format == 'json':
464 --retmode json
465 #elif $cmd.output_format == 'text':
466 --retmode uilist
467 #else:
468 --retmode xml
469 #end if
470
471 #if $cmd.db_from_link.db_to.linkname != 'None' and $cmd.cmd_select in ('neighbor', 'neighbor_history', 'neighbor_score'):
472 --linkname $cmd.db_from_link.db_to.linkname
473 #end if
474 ]]>
475 </token>
476 EOXML
477
478 sub startXML
479 {
480 print << ' EOXML';
481 <?xml version="1.0"?>
482 <macros>
483 <token name="@PROFILE@">18.01</token>
484 <token name="@WRAPPER_VERSION@">1.70</token>
485 <token name="@EMAIL_ARGUMENTS@">
486 --user_email "$__user_email__"
487 #set admin_emails = ';'.join(str($__admin_users__).split(','))
488 --admin_email "$admin_emails"
489 </token>
490 <!-- TODO: citation -->
491 <token name="@REFERENCES@"><![CDATA[
492 ]]></token>
493 <token name="@DISCLAIMER@"><![CDATA[
494 Usage Guidelines and Requirements
495 =================================
496
497 Frequency, Timing, and Registration of E-utility URL Requests
498 -------------------------------------------------------------
499
500 In order not to overload the E-utility servers, NCBI recommends that users
501 limit large jobs to either weekends or between 9:00 PM and 5:00 AM Eastern time
502 during weekdays. Failure to comply with this policy may result in an IP address
503 being blocked from accessing NCBI.
504
505 Minimizing the Number of Requests
506 ---------------------------------
507
508 If a task requires searching for and/or downloading a large number of
509 records, it is much more efficient to use the Entrez History to upload
510 and/or retrieve these records in batches rather than using separate
511 requests for each record. Please refer to Application 3 in Chapter 3
512 for an example. Many thousands of IDs can be uploaded using a single
513 EPost request, and several hundred records can be downloaded using one
514 EFetch request.
515
516
517 Disclaimer and Copyright Issues
518 -------------------------------
519
520 In accordance with requirements of NCBI's E-Utilities, we must provide
521 the following disclaimer:
522
523 Please note that abstracts in PubMed may incorporate material that may
524 be protected by U.S. and foreign copyright laws. All persons
525 reproducing, redistributing, or making commercial use of this
526 information are expected to adhere to the terms and conditions asserted
527 by the copyright holder. Transmission or reproduction of protected
528 items beyond that allowed by fair use (PDF) as defined in the copyright
529 laws requires the written permission of the copyright owners. NLM
530 provides no legal advice concerning distribution of copyrighted
531 materials. Please consult your legal counsel. If you wish to do a large
532 data mining project on PubMed data, you can enter into a licensing
533 agreement and lease the data for free from NLM. For more information on
534 this please see `https://www.nlm.nih.gov/databases/download/data_distrib_main.html <https://www.nlm.nih.gov/databases/download/data_distrib_main.html>`__
535
536 The `full disclaimer <https://www.ncbi.nlm.nih.gov/home/about/policies/>`__ is available on
537 their website
538
539 Liability
540 ~~~~~~~~~
541
542 For documents and software available from this server, the
543 U.S. Government does not warrant or assume any legal liability or
544 responsibility for the accuracy, completeness, or usefulness of any
545 information, apparatus, product, or process disclosed.
546
547 Endorsement
548 ~~~~~~~~~~~
549
550 NCBI does not endorse or recommend any commercial
551 products, processes, or services. The views and opinions of authors
552 expressed on NCBI's Web sites do not necessarily state or reflect those
553 of the U.S. Government, and they may not be used for advertising or
554 product endorsement purposes.
555
556 External Links
557 ~~~~~~~~~~~~~~
558
559 Some NCBI Web pages may provide links to other Internet
560 sites for the convenience of users. NCBI is not responsible for the
561 availability or content of these external sites, nor does NCBI endorse,
562 warrant, or guarantee the products, services, or information described
563 or offered at these other Internet sites. Users cannot assume that the
564 external sites will abide by the same Privacy Policy to which NCBI
565 adheres. It is the responsibility of the user to examine the copyright
566 and licensing restrictions of linked pages and to secure all necessary
567 permissions.
568 ]]></token>
569 <token name="@LIST_OR_HIST@">
570 #if $query_source.qss == "history_json":
571 --history_file $query_source.history_file
572 #else if $query_source.qss == "history_xml":
573 --history_xml $query_source.history_xml
574 #else if $query_source.qss == "id_file":
575 --id_list $query_source.id_file
576 #else if $query_source.qss == "id_list":
577 --id $query_source.id_list
578 #else if $query_source.qss == "id_xml":
579 --id_xml $query_source.id_xml
580 #else if $query_source.qss == "id_json":
581 --id_json $query_source.id_json
582 #end if
583 </token>
584 <xml name="list_or_hist">
585 <conditional name="query_source">
586 <param name="qss" type="select" label="Enter Query IDs by..." help="Files output by ELink or ESearch are acceptable. Query IDs in an ELink result are ignored.">
587 <option value="history_json">History File (JSON)</option>
588 <option value="history_xml">History File (XML)</option>
589 <option value="id_file" selected="True">ID file (Tabular)</option>
590 <option value="id_xml">ID File (XML)</option>
591 <option value="id_json">ID File (JSON)</option>
592 <option value="id_list">Paste IDs</option>
593 </param>
594 <when value="history_json">
595 <param label="History File (JSON)" name="history_file" type="data" format="json" help="A JSON file containing the WebEnv ID and Query Key referencing the search on the NCBI history server"/>
596 </when>
597 <when value="history_xml">
598 <param label="History File (XML)" name="history_xml" type="data" format="xml" help="An XML file containing the WebEnv ID and Query Key referencing the search on the NCBI history server"/>
599 </when>
600 <when value="id_file">
601 <param label="ID File (Text)" name="id_file" type="data" format="text,tabular" help="A Text file containing one ID per line"/>
602 </when>
603 <when value="id_xml">
604 <param label="ID File (XML)" name="id_xml" type="data" format="xml" help="ESearch or ELink Result XML file"/>
605 </when>
606 <when value="id_json">
607 <param label="ID File (JSON)" name="id_json" type="data" format="json" help="ESearch or ELink Result JSON file"/>
608 </when>
609 <when value="id_list">
610 <param label="Paste ID List" name="id_list" type="text" area="true" help="Newline/Comma separated list of IDs"/>
611 </when>
612 </conditional>
613 </xml>
614 <xml name="citations">
615 <citations>
616 <citation type="bibtex">@Book{ncbiEutils,
617 author = {Eric Sayers},
618 title = {Entrez Programming Utilities Help},
619 year = {2010},
620 publisher = {National Center for Biotechnology Information, Bethesda, Maryland},
621 note = {https://www.ncbi.nlm.nih.gov/books/NBK25500/}
622 }</citation>
623 </citations>
624 </xml>
625 <xml name="requirements">
626 <requirements>
627 <requirement type="package" version="1.70">biopython</requirement>
628 </requirements>
629 </xml>
630 <token name="@EFETCH_FORMAT_TOKEN@">
631 <![CDATA[
632
633 ## This token must go at the end of the efetch command
634
635 #set rettype, retmode, format = str($db.output_format).split('-')
636
637 #if retmode != "none":
638 --retmode $retmode
639 #end if
640 ## Otherwise, defaults to a None/empty which implies 'default' to NCBI
641
642 #if rettype != "none":
643 --rettype $rettype
644 #end if
645
646 --galaxy_format $format
647
648 ]]>
649 </token>
650 EOXML
651 }
652
653 sub endXML
654 {
655 print << ' EOXML';
656 </macros>
657 EOXML
658 }
659
660 BEGIN {startXML()}
661 END {endXML()}
662
663
664 ##
665 ## Output formats for efetch mapped to galaxy formats
666 ##
667
668 #Based on:
669 #https://www.ncbi.nlm.nih.gov/books/NBK25499/table/chapter4.T._valid_values_of__retmode_and/?report=objectonly
670
671 #Note: While json works for esearch and elink, the only database that supports
672 #json (according to an NLM support ticket I have about this) is snp
673
674 #The output_format param value for these will be "rettype-retmode-format"
675
676 #db galaxy retmode rettype format_name
677 __DATA__
678 bioproject tabular text uilist List of UIDs
679 bioproject xml xml docsum Document summary
680 bioproject xml xml uilist List of UIDs
681 bioproject xml xml xml Full record
682 biosample tabular text uilist List of UIDs
683 biosample txt text full Full record
684 biosample xml xml docsum Document summary
685 biosample xml xml full Full record
686 biosample xml xml uilist List of UIDs
687 biosystems tabular text uilist List of UIDs
688 biosystems xml xml docsum Document summary
689 biosystems xml xml uilist List of UIDs
690 biosystems xml xml xml Full record
691 clinvar tabular text uilist List of UIDs
692 clinvar xml xml clinvarset ClinVar Set
693 clinvar xml xml docsum Document summary
694 clinvar xml xml uilist List of UIDs
695 clinvar xml none none Full
696 gds tabular text uilist List of UIDs
697 gds txt text summary Summary
698 gds xml xml docsum Document summary
699 gds xml xml uilist List of UIDs
700 gds xml none none Full
701 gene txt text gene_table Gene table
702 gene tabular text uilist List of UIDs
703 gene txt asn.1 none text ASN.1
704 gene xml xml docsum Document summary
705 gene xml xml none Full
706 gene xml xml uilist List of UIDs
707 gtr tabular text uilist List of UIDs
708 gtr xml xml docsum Document summary
709 gtr xml xml gtracc GTR Test Report
710 gtr xml xml uilist List of UIDs
711 gtr xml none none Full
712 homologene fasta text fasta FASTA
713 homologene tabular text alignmentscores Alignment scores
714 homologene tabular text uilist List of UIDs
715 homologene txt asn.1 none text ASN.1
716 homologene txt text homologene HomoloGene
717 homologene xml xml docsum Document summary
718 homologene xml xml none Full
719 homologene xml xml uilist List of UIDs
720 mesh tabular text uilist List of UIDs
721 mesh txt text full Full record
722 mesh xml xml docsum Document summary
723 mesh xml xml uilist List of UIDs
724 nlmcatalog tabular text uilist List of UIDs
725 nlmcatalog txt text none Full record
726 nlmcatalog xml xml docsum Document summary
727 nlmcatalog xml xml none Full
728 nlmcatalog xml xml uilist List of UIDs
729 nuccore binary asn.1 none binary ASN.1
730 nuccore fasta text fasta FASTA
731 nuccore fasta text fasta_cds_aa CDS protein FASTA
732 nuccore fasta text fasta_cds_na CDS nucleotide FASTA
733 nuccore genbank text gb GenBank flat file
734 nuccore genbank text gbwithparts GenBank flat file with full sequence (contigs)
735 nuccore tabular text acc Accession number(s)
736 nuccore txt text ft Feature table
737 nuccore tabular text seqid SeqID string
738 nuccore tabular text uilist List of UIDs
739 nuccore txt text none text ASN.1
740 nuccore xml xml docsum Document summary
741 nuccore xml xml fasta TinySeq
742 nuccore xml xml gb GBSeq
743 nuccore xml xml gbc INSDSeq
744 nuccore xml xml native Full record
745 nuccore xml xml uilist List of UIDs
746 nucest binary asn.1 none binary ASN.1
747 nucest fasta text fasta FASTA
748 nucest genbank text gb GenBank flat file
749 nucest tabular text acc Accession number(s)
750 nucest tabular text seqid SeqID string
751 nucest tabular text uilist List of UIDs
752 nucest txt text est EST report
753 nucest txt text none text ASN.1
754 nucest xml xml docsum Document summary
755 nucest xml xml fasta TinySeq
756 nucest xml xml gb GBSeq
757 nucest xml xml gbc INSDSeq
758 nucest xml xml native Full record
759 nucest xml xml uilist List of UIDs
760 nucgss binary asn.1 none binary ASN.1
761 nucgss fasta text fasta FASTA
762 nucgss genbank text gb GenBank flat file
763 nucgss tabular text acc Accession number(s)
764 nucgss tabular text seqid SeqID string
765 nucgss tabular text uilist List of UIDs
766 nucgss txt text gss GSS report
767 nucgss txt text none text ASN.1
768 nucgss xml xml docsum Document summary
769 nucgss xml xml fasta TinySeq
770 nucgss xml xml gb GBSeq
771 nucgss xml xml gbc INSDSeq
772 nucgss xml xml native Full record
773 nucgss xml xml uilist List of UIDs
774 pmc tabular text uilist List of UIDs
775 pmc txt text medline MEDLINE
776 pmc xml xml docsum Document summary
777 pmc xml xml none FULL
778 pmc xml xml uilist List of UIDs
779 popset binary asn.1 none binary ASN.1
780 popset fasta text fasta FASTA
781 popset genbank text gb GenBank flat file
782 popset tabular text acc Accession number(s)
783 popset tabular text seqid SeqID string
784 popset tabular text uilist List of UIDs
785 popset txt text none text ASN.1
786 popset xml xml docsum Document summary
787 popset xml xml fasta TinySeq
788 popset xml xml gb GBSeq
789 popset xml xml gbc INSDSeq
790 popset xml xml native Full record
791 popset xml xml uilist List of UIDs
792 protein binary asn.1 none binary ASN.1
793 protein fasta text fasta FASTA
794 protein tabular text acc Accession number(s)
795 protein txt text ft Feature table
796 protein tabular text seqid SeqID string
797 protein tabular text uilist List of UIDs
798 protein txt text gp GenPept flat file
799 protein txt text none text ASN.1
800 protein xml xml docsum Document summary
801 protein xml xml fasta TinySeq
802 protein xml xml gp GBSeq
803 protein xml xml gpc INSDSeq
804 protein xml xml ipg Identical Protein
805 protein xml xml native Full record
806 protein xml xml uilist List of UIDs
807 pubmed tabular text uilist List of UIDs
808 pubmed txt asn.1 none text ASN.1
809 pubmed txt text abstract Abstract
810 pubmed txt text medline MEDLINE
811 pubmed xml xml docsum Document summary
812 pubmed xml xml none Full
813 pubmed xml xml uilist List of UIDs
814 sequences fasta text fasta FASTA
815 sequences tabular text acc Accession number(s)
816 sequences tabular text seqid SeqID string
817 sequences tabular text uilist List of UIDs
818 sequences txt text none text ASN.1
819 sequences xml xml docsum Document summary
820 sequences xml xml uilist List of UIDs
821 sequences xml none none Full
822 snp fasta text fasta FASTA
823 snp json json docsum Document summary
824 snp json json uilist List of UIDs
825 snp tabular text ssexemplar SS Exemplar list
826 snp tabular text uilist List of UIDs
827 snp txt asn.1 none text ASN.1
828 snp txt text chr Chromosome report
829 snp txt text docset Summary
830 snp txt text flt Flat file
831 snp txt text rsr RS Cluster report
832 snp xml xml docsum Document summary
833 snp xml xml none XML
834 snp xml xml uilist List of UIDs
835 sra tabular text uilist List of UIDs
836 sra xml xml docsum Document summary
837 sra xml xml full Full
838 taxonomy tabular text uilist List of UIDs
839 taxonomy xml xml none Full
840 taxonomy xml xml docsum Document summary
841 taxonomy xml xml uilist List of UIDs