File: NCBI_Entrez2.mod.dtd

package info (click to toggle)
python-biopython 1.68%2Bdfsg-3
  • links: PTS, VCS
  • area: main
  • in suites: stretch
  • size: 46,860 kB
  • ctags: 13,237
  • sloc: python: 160,306; xml: 93,216; ansic: 9,118; sql: 1,208; makefile: 155; sh: 63
file content (747 lines) | stat: -rw-r--r-- 21,922 bytes parent folder | download | duplicates (7)
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
<!-- ============================================
     ::DATATOOL:: Generated from "entrez2.asn"
     ::DATATOOL:: by application DATATOOL version 1.9.0
     ::DATATOOL:: on 04/10/2008 16:04:22
     ============================================ -->

<!-- ============================================ -->
<!-- This section is mapped from module "NCBI-Entrez2"
================================================= -->

<!--
$Revision: 1.12 $********************************************

  entrez2.asn
   Version 1

   API to Entrez Engine (1999)
   Retrieval of sequence done through ID1 module
     Also, SeqId queries
   Retrieval of PubMed records through PubMed module
   Retrieval of Structures through PubStruct module
   Retrieval of Genomes through Genomes module

***************************************************************
-->

<!--
**************************************
  Entrez2 common elements
**************************************
 a date/time stamp
-->
<!ELEMENT Entrez2-dt (%INTEGER;)>

<!-- database name -->
<!ELEMENT Entrez2-db-id (#PCDATA)>

<!-- field name -->
<!ELEMENT Entrez2-field-id (#PCDATA)>

<!-- link name -->
<!ELEMENT Entrez2-link-id (#PCDATA)>

<!-- list of record UIDs -->
<!ELEMENT Entrez2-id-list (
        Entrez2-id-list_db, 
        Entrez2-id-list_num, 
        Entrez2-id-list_uids?)>

<!-- the database -->
<!ELEMENT Entrez2-id-list_db (Entrez2-db-id)>

<!-- number of uids -->
<!ELEMENT Entrez2-id-list_num (%INTEGER;)>

<!-- coded uids -->
<!ELEMENT Entrez2-id-list_uids (%OCTETS;)>

<!--
****************************************
 The structured form of the boolean is the same in a request or
    return so that it easy to modify a query. This means some
    fields are only considered in a return value, like counts
    by term. They are ignored in a request.
 The structured boolean supports specific boolean components,
    an unparsed string in query syntax, and UID lists as
    elements of a boolean. This makes it possible to submit
    a single string, a fully structured query, or a mixture.
    The UID list feature means one can also perform refinements
    on UID lists from links, neighbors, or other operations.
    UID list query now returns a history key for subsequent use.
*****************************************
-->
<!ELEMENT Entrez2-boolean-exp (
        Entrez2-boolean-exp_db, 
        Entrez2-boolean-exp_exp, 
        Entrez2-boolean-exp_limits?)>

<!-- database for this query -->
<!ELEMENT Entrez2-boolean-exp_db (Entrez2-db-id)>

<!-- the Boolean -->
<!ELEMENT Entrez2-boolean-exp_exp (Entrez2-boolean-element*)>

<!-- date bounds -->
<!ELEMENT Entrez2-boolean-exp_limits (Entrez2-limits)>


<!ELEMENT Entrez2-boolean-element (
        Entrez2-boolean-element_str | 
        Entrez2-boolean-element_op | 
        Entrez2-boolean-element_term | 
        Entrez2-boolean-element_ids | 
        Entrez2-boolean-element_key)>

<!-- unparsed query string -->
<!ELEMENT Entrez2-boolean-element_str (#PCDATA)>

<!-- logical operator -->
<!ELEMENT Entrez2-boolean-element_op (Entrez2-operator)>

<!-- fielded term -->
<!ELEMENT Entrez2-boolean-element_term (Entrez2-boolean-term)>

<!-- list of UIDs - returns history key in reply -->
<!ELEMENT Entrez2-boolean-element_ids (Entrez2-id-list)>

<!-- history key for uploaded UID list or other query -->
<!ELEMENT Entrez2-boolean-element_key (#PCDATA)>

<!--
*****************************************
 the term is both sent and received as parts of
   queries and replies. The attributes can be filled in
   by either, but may be ignored by one or the other. Flags are
   shown if a real value is only of use in the query (Q), only
   in the reply (R), or used in both (B)
 do-not-explode and do-not-translate are only active set by
   by the query. However, they retain those settings in the
   return value so they can be resent with a new query
******************************************
-->
<!ELEMENT Entrez2-boolean-term (
        Entrez2-boolean-term_field, 
        Entrez2-boolean-term_term, 
        Entrez2-boolean-term_term-count?, 
        Entrez2-boolean-term_do-not-explode?, 
        Entrez2-boolean-term_do-not-translate?)>

<!-- B -->
<!ELEMENT Entrez2-boolean-term_field (Entrez2-field-id)>

<!-- B -->
<!ELEMENT Entrez2-boolean-term_term (#PCDATA)>

<!-- R count of records with term -->
<!ELEMENT Entrez2-boolean-term_term-count (%INTEGER;)>

<!-- Q do not explode term -->
<!ELEMENT Entrez2-boolean-term_do-not-explode EMPTY>
<!ATTLIST Entrez2-boolean-term_do-not-explode value ( true | false ) "false" >


<!-- Q do not use synonyms -->
<!ELEMENT Entrez2-boolean-term_do-not-translate EMPTY>
<!ATTLIST Entrez2-boolean-term_do-not-translate value ( true | false ) "false" >



<!ELEMENT Entrez2-operator (%INTEGER;)>
<!ATTLIST Entrez2-operator value (
        and |
        or |
        butnot |
        range |
        left-paren |
        right-paren
        ) #IMPLIED >


<!--
***************************************
  Entrez2 Request types
***************************************
****************************************
 The basic request wrapper leaves space for a version which
   allow the server to support older clients
 The tool parameter allows us to log the client types for
   debugging and tuning
 The cookie is a session ID returned by the first Entrez2-reply
****************************************
 a standard request
-->
<!ELEMENT Entrez2-request (
        Entrez2-request_request, 
        Entrez2-request_version, 
        Entrez2-request_tool?, 
        Entrez2-request_cookie?, 
        Entrez2-request_use-history?)>

<!-- the actual request -->
<!ELEMENT Entrez2-request_request (E2Request)>

<!-- ASN1 spec version -->
<!ELEMENT Entrez2-request_version (%INTEGER;)>

<!-- tool making request -->
<!ELEMENT Entrez2-request_tool (#PCDATA)>

<!-- history session cookie -->
<!ELEMENT Entrez2-request_cookie (#PCDATA)>

<!-- request should use history -->
<!ELEMENT Entrez2-request_use-history EMPTY>
<!ATTLIST Entrez2-request_use-history value ( true | false ) "false" >


<!-- request types -->
<!ELEMENT E2Request (
        E2Request_get-info | 
        E2Request_eval-boolean | 
        E2Request_get-docsum | 
        E2Request_get-term-pos | 
        E2Request_get-term-list | 
        E2Request_get-term-hierarchy | 
        E2Request_get-links | 
        E2Request_get-linked | 
        E2Request_get-link-counts)>

<!-- ask for info block -->
<!ELEMENT E2Request_get-info EMPTY>

<!-- Boolean lookup -->
<!ELEMENT E2Request_eval-boolean (Entrez2-eval-boolean)>

<!-- get the DocSums -->
<!ELEMENT E2Request_get-docsum (Entrez2-id-list)>

<!-- get position in term list -->
<!ELEMENT E2Request_get-term-pos (Entrez2-term-query)>

<!-- get Term list by position -->
<!ELEMENT E2Request_get-term-list (Entrez2-term-pos)>

<!-- get a hierarchy from a term -->
<!ELEMENT E2Request_get-term-hierarchy (Entrez2-hier-query)>

<!-- get specific links from a UID list -->
<!ELEMENT E2Request_get-links (Entrez2-get-links)>

<!-- get subset of UID list which has links -->
<!ELEMENT E2Request_get-linked (Entrez2-get-links)>

<!-- get all links from one UID -->
<!ELEMENT E2Request_get-link-counts (Entrez2-id)>

<!--
****************************************
 When evaluating a boolean query the counts of hits is always
    returned.
 In addition, you can request the UIDs of the hits or the
    the parsed query in structured form (with counts by term),
    or both.
****************************************
 evaluate Boolean query
-->
<!ELEMENT Entrez2-eval-boolean (
        Entrez2-eval-boolean_return-UIDs?, 
        Entrez2-eval-boolean_return-parse?, 
        Entrez2-eval-boolean_query)>

<!-- return UID list? -->
<!ELEMENT Entrez2-eval-boolean_return-UIDs EMPTY>
<!ATTLIST Entrez2-eval-boolean_return-UIDs value ( true | false ) "false" >


<!-- return parsed query? -->
<!ELEMENT Entrez2-eval-boolean_return-parse EMPTY>
<!ATTLIST Entrez2-eval-boolean_return-parse value ( true | false ) "false" >


<!-- the actual query -->
<!ELEMENT Entrez2-eval-boolean_query (Entrez2-boolean-exp)>


<!ELEMENT Entrez2-dt-filter (
        Entrez2-dt-filter_begin-date, 
        Entrez2-dt-filter_end-date, 
        Entrez2-dt-filter_type-date)>
<!--
**************************************
  Entrez2 common elements
**************************************
 a date/time stamp
-->
<!ELEMENT Entrez2-dt-filter_begin-date (Entrez2-dt)>
<!--
**************************************
  Entrez2 common elements
**************************************
 a date/time stamp
-->
<!ELEMENT Entrez2-dt-filter_end-date (Entrez2-dt)>
<!-- field name -->
<!ELEMENT Entrez2-dt-filter_type-date (Entrez2-field-id)>

<!-- date limits -->
<!ELEMENT Entrez2-limits (
        Entrez2-limits_filter-date?, 
        Entrez2-limits_max-UIDs?, 
        Entrez2-limits_offset-UIDs?)>

<!ELEMENT Entrez2-limits_filter-date (Entrez2-dt-filter)>

<!-- max UIDs to return in list -->
<!ELEMENT Entrez2-limits_max-UIDs (%INTEGER;)>

<!-- start partway into UID list -->
<!ELEMENT Entrez2-limits_offset-UIDs (%INTEGER;)>

<!-- a single UID -->
<!ELEMENT Entrez2-id (
        Entrez2-id_db, 
        Entrez2-id_uid)>
<!-- database name -->
<!ELEMENT Entrez2-id_db (Entrez2-db-id)>

<!ELEMENT Entrez2-id_uid (%INTEGER;)>


<!ELEMENT Entrez2-term-query (
        Entrez2-term-query_db, 
        Entrez2-term-query_field, 
        Entrez2-term-query_term)>
<!-- database name -->
<!ELEMENT Entrez2-term-query_db (Entrez2-db-id)>
<!-- field name -->
<!ELEMENT Entrez2-term-query_field (Entrez2-field-id)>

<!ELEMENT Entrez2-term-query_term (#PCDATA)>


<!ELEMENT Entrez2-hier-query (
        Entrez2-hier-query_db, 
        Entrez2-hier-query_field, 
        Entrez2-hier-query_term?, 
        Entrez2-hier-query_txid?)>
<!-- database name -->
<!ELEMENT Entrez2-hier-query_db (Entrez2-db-id)>
<!-- field name -->
<!ELEMENT Entrez2-hier-query_field (Entrez2-field-id)>

<!-- query with either term -->
<!ELEMENT Entrez2-hier-query_term (#PCDATA)>

<!-- or Taxonomy ID -->
<!ELEMENT Entrez2-hier-query_txid (%INTEGER;)>

<!-- request portions of term list -->
<!ELEMENT Entrez2-term-pos (
        Entrez2-term-pos_db, 
        Entrez2-term-pos_field, 
        Entrez2-term-pos_first-term-pos, 
        Entrez2-term-pos_number-of-terms?)>
<!-- database name -->
<!ELEMENT Entrez2-term-pos_db (Entrez2-db-id)>
<!-- field name -->
<!ELEMENT Entrez2-term-pos_field (Entrez2-field-id)>

<!ELEMENT Entrez2-term-pos_first-term-pos (%INTEGER;)>

<!-- optional for hierarchy only -->
<!ELEMENT Entrez2-term-pos_number-of-terms (%INTEGER;)>

<!-- request links of one type -->
<!ELEMENT Entrez2-get-links (
        Entrez2-get-links_uids, 
        Entrez2-get-links_linktype, 
        Entrez2-get-links_max-UIDS?, 
        Entrez2-get-links_count-only?, 
        Entrez2-get-links_parents-persist?)>

<!-- docs to link from -->
<!ELEMENT Entrez2-get-links_uids (Entrez2-id-list)>

<!-- type of link -->
<!ELEMENT Entrez2-get-links_linktype (Entrez2-link-id)>

<!-- maximum number of links to return -->
<!ELEMENT Entrez2-get-links_max-UIDS (%INTEGER;)>

<!-- return only the counts -->
<!ELEMENT Entrez2-get-links_count-only EMPTY>
<!ATTLIST Entrez2-get-links_count-only value ( true | false ) #REQUIRED >


<!-- allow original uids in list -->
<!ELEMENT Entrez2-get-links_parents-persist EMPTY>
<!ATTLIST Entrez2-get-links_parents-persist value ( true | false ) #REQUIRED >


<!--
**********************************************************
 Replies from the Entrez server
  all replies contain the date/time stamp when they were executed
  to do reqular date bounded searches use this value+1 to search
  again later instead of recording the date/time on the client machine
  the cookie allows a simple key string to represent UID lists in the history
**********************************************************
-->
<!ELEMENT Entrez2-reply (
        Entrez2-reply_reply, 
        Entrez2-reply_dt, 
        Entrez2-reply_server, 
        Entrez2-reply_msg?, 
        Entrez2-reply_key?, 
        Entrez2-reply_cookie?)>

<!-- the actual reply -->
<!ELEMENT Entrez2-reply_reply (E2Reply)>

<!-- date/time stamp from server -->
<!ELEMENT Entrez2-reply_dt (Entrez2-dt)>

<!-- server version info -->
<!ELEMENT Entrez2-reply_server (#PCDATA)>

<!-- possibly a message to the user -->
<!ELEMENT Entrez2-reply_msg (#PCDATA)>

<!-- history key for query -->
<!ELEMENT Entrez2-reply_key (#PCDATA)>

<!-- history session cookie -->
<!ELEMENT Entrez2-reply_cookie (#PCDATA)>


<!ELEMENT E2Reply (
        E2Reply_error | 
        E2Reply_get-info | 
        E2Reply_eval-boolean | 
        E2Reply_get-docsum | 
        E2Reply_get-term-pos | 
        E2Reply_get-term-list | 
        E2Reply_get-term-hierarchy | 
        E2Reply_get-links | 
        E2Reply_get-linked | 
        E2Reply_get-link-counts)>

<!-- if nothing can be returned -->
<!ELEMENT E2Reply_error (#PCDATA)>

<!-- the database info -->
<!ELEMENT E2Reply_get-info (Entrez2-info)>

<!-- result of boolean query -->
<!ELEMENT E2Reply_eval-boolean (Entrez2-boolean-reply)>

<!ELEMENT E2Reply_get-docsum (Entrez2-docsum-list)>

<!-- position of the term -->
<!ELEMENT E2Reply_get-term-pos (%INTEGER;)>

<!ELEMENT E2Reply_get-term-list (Entrez2-term-list)>
<!-- for hierarchical index -->
<!ELEMENT E2Reply_get-term-hierarchy (Entrez2-hier-node)>
<!--
*******************************************
 Links are returned in sets also using OCTET STRINGS
*******************************************
 set of links
-->
<!ELEMENT E2Reply_get-links (Entrez2-link-set)>
<!-- list of record UIDs -->
<!ELEMENT E2Reply_get-linked (Entrez2-id-list)>
<!-- all links from 1 uid -->
<!ELEMENT E2Reply_get-link-counts (Entrez2-link-count-list)>

<!-- describes all the databases -->
<!ELEMENT Entrez2-info (
        Entrez2-info_db-count, 
        Entrez2-info_build-date, 
        Entrez2-info_db-info)>

<!-- number of databases -->
<!ELEMENT Entrez2-info_db-count (%INTEGER;)>

<!-- build date of databases -->
<!ELEMENT Entrez2-info_build-date (Entrez2-dt)>

<!-- info by database -->
<!ELEMENT Entrez2-info_db-info (Entrez2-db-info*)>

<!-- info for one database -->
<!ELEMENT Entrez2-db-info (
        Entrez2-db-info_db-name, 
        Entrez2-db-info_db-menu, 
        Entrez2-db-info_db-descr, 
        Entrez2-db-info_doc-count, 
        Entrez2-db-info_field-count, 
        Entrez2-db-info_fields, 
        Entrez2-db-info_link-count, 
        Entrez2-db-info_links, 
        Entrez2-db-info_docsum-field-count, 
        Entrez2-db-info_docsum-fields)>

<!-- internal name -->
<!ELEMENT Entrez2-db-info_db-name (Entrez2-db-id)>

<!-- short name for menu -->
<!ELEMENT Entrez2-db-info_db-menu (#PCDATA)>

<!-- longer explanatory name -->
<!ELEMENT Entrez2-db-info_db-descr (#PCDATA)>

<!-- total number of records -->
<!ELEMENT Entrez2-db-info_doc-count (%INTEGER;)>

<!-- number of field types -->
<!ELEMENT Entrez2-db-info_field-count (%INTEGER;)>

<!ELEMENT Entrez2-db-info_fields (Entrez2-field-info*)>

<!-- number of link types -->
<!ELEMENT Entrez2-db-info_link-count (%INTEGER;)>

<!ELEMENT Entrez2-db-info_links (Entrez2-link-info*)>

<!ELEMENT Entrez2-db-info_docsum-field-count (%INTEGER;)>

<!ELEMENT Entrez2-db-info_docsum-fields (Entrez2-docsum-field-info*)>

<!-- info about one field -->
<!ELEMENT Entrez2-field-info (
        Entrez2-field-info_field-name, 
        Entrez2-field-info_field-menu, 
        Entrez2-field-info_field-descr, 
        Entrez2-field-info_term-count, 
        Entrez2-field-info_is-date?, 
        Entrez2-field-info_is-numerical?, 
        Entrez2-field-info_single-token?, 
        Entrez2-field-info_hierarchy-avail?, 
        Entrez2-field-info_is-rangable?, 
        Entrez2-field-info_is-truncatable?)>

<!-- the internal name -->
<!ELEMENT Entrez2-field-info_field-name (Entrez2-field-id)>

<!-- short string suitable for menu -->
<!ELEMENT Entrez2-field-info_field-menu (#PCDATA)>

<!-- longer, explanatory name -->
<!ELEMENT Entrez2-field-info_field-descr (#PCDATA)>

<!-- number of terms in field -->
<!ELEMENT Entrez2-field-info_term-count (%INTEGER;)>

<!ELEMENT Entrez2-field-info_is-date EMPTY>
<!ATTLIST Entrez2-field-info_is-date value ( true | false ) #REQUIRED >


<!ELEMENT Entrez2-field-info_is-numerical EMPTY>
<!ATTLIST Entrez2-field-info_is-numerical value ( true | false ) #REQUIRED >


<!ELEMENT Entrez2-field-info_single-token EMPTY>
<!ATTLIST Entrez2-field-info_single-token value ( true | false ) #REQUIRED >


<!ELEMENT Entrez2-field-info_hierarchy-avail EMPTY>
<!ATTLIST Entrez2-field-info_hierarchy-avail value ( true | false ) #REQUIRED >


<!ELEMENT Entrez2-field-info_is-rangable EMPTY>
<!ATTLIST Entrez2-field-info_is-rangable value ( true | false ) #REQUIRED >


<!ELEMENT Entrez2-field-info_is-truncatable EMPTY>
<!ATTLIST Entrez2-field-info_is-truncatable value ( true | false ) #REQUIRED >


<!-- info about one link -->
<!ELEMENT Entrez2-link-info (
        Entrez2-link-info_link-name, 
        Entrez2-link-info_link-menu, 
        Entrez2-link-info_link-descr, 
        Entrez2-link-info_db-to, 
        Entrez2-link-info_data-size?)>
<!-- link name -->
<!ELEMENT Entrez2-link-info_link-name (Entrez2-link-id)>

<!ELEMENT Entrez2-link-info_link-menu (#PCDATA)>

<!ELEMENT Entrez2-link-info_link-descr (#PCDATA)>

<!-- database it links to -->
<!ELEMENT Entrez2-link-info_db-to (Entrez2-db-id)>

<!-- size of link data element     -->
<!ELEMENT Entrez2-link-info_data-size (%INTEGER;)>


<!ELEMENT Entrez2-docsum-field-type (%INTEGER;)>
<!ATTLIST Entrez2-docsum-field-type value (
        string |
        int |
        float |
        date-pubmed
        ) #IMPLIED >



<!ELEMENT Entrez2-docsum-field-info (
        Entrez2-docsum-field-info_field-name, 
        Entrez2-docsum-field-info_field-description, 
        Entrez2-docsum-field-info_field-type)>

<!ELEMENT Entrez2-docsum-field-info_field-name (#PCDATA)>

<!ELEMENT Entrez2-docsum-field-info_field-description (#PCDATA)>

<!ELEMENT Entrez2-docsum-field-info_field-type (Entrez2-docsum-field-type)>


<!ELEMENT Entrez2-boolean-reply (
        Entrez2-boolean-reply_count, 
        Entrez2-boolean-reply_uids?, 
        Entrez2-boolean-reply_query?)>

<!-- records hit -->
<!ELEMENT Entrez2-boolean-reply_count (%INTEGER;)>

<!-- if uids requested -->
<!ELEMENT Entrez2-boolean-reply_uids (Entrez2-id-list)>

<!-- if parsed query requested -->
<!ELEMENT Entrez2-boolean-reply_query (Entrez2-boolean-exp)>


<!ELEMENT Entrez2-docsum-list (
        Entrez2-docsum-list_count, 
        Entrez2-docsum-list_list)>

<!-- number of docsums -->
<!ELEMENT Entrez2-docsum-list_count (%INTEGER;)>

<!ELEMENT Entrez2-docsum-list_list (Entrez2-docsum*)>


<!ELEMENT Entrez2-docsum (
        Entrez2-docsum_uid, 
        Entrez2-docsum_docsum-data)>

<!-- primary uid (gi, pubmedid) -->
<!ELEMENT Entrez2-docsum_uid (%INTEGER;)>

<!ELEMENT Entrez2-docsum_docsum-data (Entrez2-docsum-data*)>


<!ELEMENT Entrez2-docsum-data (
        Entrez2-docsum-data_field-name, 
        Entrez2-docsum-data_field-value)>

<!ELEMENT Entrez2-docsum-data_field-name (#PCDATA)>

<!ELEMENT Entrez2-docsum-data_field-value (#PCDATA)>


<!ELEMENT Entrez2-term-list (
        Entrez2-term-list_pos, 
        Entrez2-term-list_num, 
        Entrez2-term-list_list)>

<!-- position of first term in list -->
<!ELEMENT Entrez2-term-list_pos (%INTEGER;)>

<!-- number of terms in list -->
<!ELEMENT Entrez2-term-list_num (%INTEGER;)>

<!ELEMENT Entrez2-term-list_list (Entrez2-term*)>


<!ELEMENT Entrez2-term (
        Entrez2-term_term, 
        Entrez2-term_txid?, 
        Entrez2-term_count, 
        Entrez2-term_is-leaf-node?)>

<!ELEMENT Entrez2-term_term (#PCDATA)>

<!ELEMENT Entrez2-term_txid (%INTEGER;)>

<!-- count of records with this term -->
<!ELEMENT Entrez2-term_count (%INTEGER;)>

<!-- used for hierarchy only -->
<!ELEMENT Entrez2-term_is-leaf-node EMPTY>
<!ATTLIST Entrez2-term_is-leaf-node value ( true | false ) #REQUIRED >


<!-- for hierarchical index -->
<!ELEMENT Entrez2-hier-node (
        Entrez2-hier-node_cannonical-form, 
        Entrez2-hier-node_lineage-count, 
        Entrez2-hier-node_lineage?, 
        Entrez2-hier-node_child-count, 
        Entrez2-hier-node_children, 
        Entrez2-hier-node_is-ambiguous?)>

<!-- the official name -->
<!ELEMENT Entrez2-hier-node_cannonical-form (#PCDATA)>

<!-- number of strings in lineage -->
<!ELEMENT Entrez2-hier-node_lineage-count (%INTEGER;)>

<!-- strings up the lineage -->
<!ELEMENT Entrez2-hier-node_lineage (Entrez2-term*)>

<!-- number of children of this node -->
<!ELEMENT Entrez2-hier-node_child-count (%INTEGER;)>

<!-- the children -->
<!ELEMENT Entrez2-hier-node_children (Entrez2-term*)>

<!-- used for hierarchy only -->
<!ELEMENT Entrez2-hier-node_is-ambiguous EMPTY>
<!ATTLIST Entrez2-hier-node_is-ambiguous value ( true | false ) #REQUIRED >


<!--
*******************************************
 Links are returned in sets also using OCTET STRINGS
*******************************************
 set of links
-->
<!ELEMENT Entrez2-link-set (
        Entrez2-link-set_ids, 
        Entrez2-link-set_data-size?, 
        Entrez2-link-set_data?)>
<!-- list of record UIDs -->
<!ELEMENT Entrez2-link-set_ids (Entrez2-id-list)>

<!-- size of data elements -->
<!ELEMENT Entrez2-link-set_data-size (%INTEGER;)>

<!-- coded scores -->
<!ELEMENT Entrez2-link-set_data (%OCTETS;)>

<!-- all links from 1 uid -->
<!ELEMENT Entrez2-link-count-list (
        Entrez2-link-count-list_link-type-count, 
        Entrez2-link-count-list_links)>

<!-- number of types of links -->
<!ELEMENT Entrez2-link-count-list_link-type-count (%INTEGER;)>

<!ELEMENT Entrez2-link-count-list_links (Entrez2-link-count*)>

<!-- link count of one type -->
<!ELEMENT Entrez2-link-count (
        Entrez2-link-count_link-type, 
        Entrez2-link-count_link-count)>
<!-- link name -->
<!ELEMENT Entrez2-link-count_link-type (Entrez2-link-id)>

<!ELEMENT Entrez2-link-count_link-count (%INTEGER;)>