Queries: TREC_QA_Sample_metamap.txt

File TREC_QA_Sample_metamap.txt, 34.1 KB (added by yy, 7 years ago)

A parsed result of TREC Questions using MetaMap.

Line 
1/MetaMap/public_mm/bin/SKRrun -L 2008 -w /MetaMap/public_mm/lexicon /MetaMap/public_mm/bin/metamap08.BINARY -I -Z 08
2
3MetaMap (2008)
4
5
6Control options:
7  mm_data_year=08
8  show_cuis
9Berkeley DB databases (normal strict 08 model) are open.
10Static variants will come from table varsan.
11Variants: Adj/noun ONLY.
12Accessing lexicon /MetaMap/public_mm/lexicon/data/lexiconStatic2008.
13Variant generation mode: static.
14
15Established connection to Tagger Server on localhost.
16Processing 00000000.tx.1: What antibodies have been used to detect protein TLR4 ?
17
18Phrase: "What antibodies"
19Meta Candidates (2):
20  1000 C0003241:Antibodies [Amino Acid, Peptide, or Protein,Immunologic Factor,Indicator, Reagent, or Diagnostic Aid]
21   966 C1621287:antibody (antibody activity) [Molecular Function]
22Meta Mapping (1000):
23  1000 C0003241:Antibodies [Amino Acid, Peptide, or Protein,Immunologic Factor,Indicator, Reagent, or Diagnostic Aid]
24
25Phrase: "have"
26
27Phrase: "been"
28
29Phrase: "used"
30Meta Candidates (4):
31   966 C0042153:use (utilization qualifier) [Functional Concept]
32   966 C0457083:Use (Usage) [Functional Concept]
33   966 C1524063:Using (Use of) [Functional Concept]
34   966 C1947944:Use (Use - dosing instruction imperative) [Intellectual Product]
35Meta Mapping (966):
36   966 C0457083:Use (Usage) [Functional Concept]
37Meta Mapping (966):
38   966 C1947944:Use (Use - dosing instruction imperative) [Intellectual Product]
39Meta Mapping (966):
40   966 C1524063:Using (Use of) [Functional Concept]
41Meta Mapping (966):
42   966 C0042153:use (utilization qualifier) [Functional Concept]
43
44Phrase: "to"
45
46Phrase: "detect"
47Meta Candidates (2):
48   966 C0442726:Detected [Finding]
49   966 C1511790:Detected (Detection) [Therapeutic or Preventive Procedure]
50Meta Mapping (966):
51   966 C0442726:Detected [Finding]
52Meta Mapping (966):
53   966 C1511790:Detected (Detection) [Therapeutic or Preventive Procedure]
54
55Phrase: "protein TLR4 ?"
56Meta Candidates (2):
57   694 C0033684:Protein (Proteins) [Amino Acid, Peptide, or Protein,Biologically Active Substance]
58   694 C0202202:Protein NOS (Protein measurement) [Laboratory Procedure]
59Meta Mapping (694):
60   694 C0202202:Protein NOS (Protein measurement) [Laboratory Procedure]
61Meta Mapping (694):
62   694 C0033684:Protein (Proteins) [Amino Acid, Peptide, or Protein,Biologically Active Substance]
63/MetaMap/public_mm/bin/SKRrun -L 2008 -w /MetaMap/public_mm/lexicon /MetaMap/public_mm/bin/metamap08.BINARY -I -Z 08
64
65MetaMap (2008)
66
67
68Control options:
69  mm_data_year=08
70  show_cuis
71Berkeley DB databases (normal strict 08 model) are open.
72Static variants will come from table varsan.
73Variants: Adj/noun ONLY.
74Accessing lexicon /MetaMap/public_mm/lexicon/data/lexiconStatic2008.
75Variant generation mode: static.
76
77Established connection to Tagger Server on localhost.
78Processing 00000000.tx.1: What biological substances have been used to measure toxicity in response to cytarabine ?
79
80Phrase: "What biological substances"
81Meta Candidates (4):
82   983 C0005522:Biological substance (Biological Products) [Biologically Active Substance,Pharmacologic Substance]
83   861 C0439861:Substances (Substance) [Substance]
84   694 C0005532:Biological (Biologic) [Biomedical Occupation or Discipline]
85   694 C0205460:biological [Functional Concept]
86Meta Mapping (983):
87   983 C0005522:Biological substance (Biological Products) [Biologically Active Substance,Pharmacologic Substance]
88
89Phrase: "have"
90
91Phrase: "been"
92
93Phrase: "used"
94Meta Candidates (4):
95   966 C0042153:use (utilization qualifier) [Functional Concept]
96   966 C0457083:Use (Usage) [Functional Concept]
97   966 C1524063:Using (Use of) [Functional Concept]
98   966 C1947944:Use (Use - dosing instruction imperative) [Intellectual Product]
99Meta Mapping (966):
100   966 C0457083:Use (Usage) [Functional Concept]
101Meta Mapping (966):
102   966 C1947944:Use (Use - dosing instruction imperative) [Intellectual Product]
103Meta Mapping (966):
104   966 C1524063:Using (Use of) [Functional Concept]
105Meta Mapping (966):
106   966 C0042153:use (utilization qualifier) [Functional Concept]
107
108Phrase: "to"
109
110Phrase: "measure"
111Meta Candidates (3):
112  1000 C0079809:Measure (Measures) [Functional Concept,Quantitative Concept]
113  1000 C0242485:Measure (Measurement) [Functional Concept]
114   966 C0444706:Measured [Qualitative Concept]
115Meta Mapping (1000):
116  1000 C0242485:Measure (Measurement) [Functional Concept]
117Meta Mapping (1000):
118  1000 C0079809:Measure (Measures) [Functional Concept,Quantitative Concept]
119
120Phrase: "toxicity"
121Meta Candidates (7):
122  1000 C0040539:toxicity (Toxicity aspects) [Quantitative Concept]
123  1000 C0600688:Toxicity (Toxic effect) [Injury or Poisoning]
124   928 C1407029:Toxic [Qualitative Concept]
125   907 C0032346:Poison (Poisons) [Hazardous or Poisonous Substance]
126   907 C1548769:Poison (Poison Risk Codes) [Intellectual Product]
127   907 C1550590:poison (Poison RIsk) [Idea or Concept]
128   900 C0040549:Toxin [Biologically Active Substance,Hazardous or Poisonous Substance]
129Meta Mapping (1000):
130  1000 C0600688:Toxicity (Toxic effect) [Injury or Poisoning]
131Meta Mapping (1000):
132  1000 C0040539:toxicity (Toxicity aspects) [Quantitative Concept]
133
134Phrase: "in response to"
135Meta Candidates (2):
136   861 C0871261:response [Clinical Attribute]
137   861 C1704632:Response (Disease Response) [Finding]
138Meta Mapping (861):
139   861 C1704632:Response (Disease Response) [Finding]
140Meta Mapping (861):
141   861 C0871261:response [Clinical Attribute]
142
143Phrase: "cytarabine ?"
144Meta Candidates (2):
145  1000 C0010711:Cytarabine [Nucleic Acid, Nucleoside, or Nucleotide,Pharmacologic Substance]
146   944 C0591320:Cytosar [Hazardous or Poisonous Substance,Nucleic Acid, Nucleoside, or Nucleotide,Pharmacologic Substance]
147Meta Mapping (1000):
148  1000 C0010711:Cytarabine [Nucleic Acid, Nucleoside, or Nucleotide,Pharmacologic Substance]
149/MetaMap/public_mm/bin/SKRrun -L 2008 -w /MetaMap/public_mm/lexicon /MetaMap/public_mm/bin/metamap08.BINARY -I -Z 08
150
151MetaMap (2008)
152
153
154Control options:
155  mm_data_year=08
156  show_cuis
157Berkeley DB databases (normal strict 08 model) are open.
158Static variants will come from table varsan.
159Variants: Adj/noun ONLY.
160Accessing lexicon /MetaMap/public_mm/lexicon/data/lexiconStatic2008.
161Variant generation mode: static.
162
163Established connection to Tagger Server on localhost.
164Processing 00000000.tx.1: What cell or tissue types express members of the mammalian TIM gene family ?
165
166Phrase: "What cell"
167Meta Candidates (6):
168  1000 C0007634:Cell (Cells) [Cell]
169  1000 C1269647:Cell (Entire cell) [Cell]
170  1000 C1704653:Cell (Cell Device Component) [Medical Device]
171  1000 C1948049:Cell [Spatial Concept]
172   928 C0178539:Cellular [Functional Concept]
173   900 C1516377:Cellularity [Qualitative Concept]
174Meta Mapping (1000):
175  1000 C1948049:Cell [Spatial Concept]
176Meta Mapping (1000):
177  1000 C1704653:Cell (Cell Device Component) [Medical Device]
178Meta Mapping (1000):
179  1000 C0007634:Cell (Cells) [Cell]
180Meta Mapping (1000):
181  1000 C1269647:Cell (Entire cell) [Cell]
182
183Phrase: "or"
184
185Phrase: "tissue types"
186Meta Candidates (10):
187  1000 C0040300:Tissue Types (Body tissue) [Tissue]
188          tissue
189   983 C0019633:Tissue Typing (Histocompatibility Testing) [Laboratory Procedure]
190   861 C0332307:Types (Type - attribute) [Qualitative Concept]
191   861 C1547928:Tissue (Tissue Specimen Code) [Intellectual Product]
192   827 C0441704:Typing (Typing Classification) [Health Care Activity]
193   827 C0872404:Typing (Keyboard Typing) [Occupational Activity]
194   827 C1547052:*Type [Quantitative Concept]
195   827 C1552651:Type (Type - ParameterizedDataType) [Intellectual Product]
196   827 C1849011:TYPE (SPONDYLOMETAEPIPHYSEAL DYSPLASIA, SHORT LIMB-HAND TYPE) [Disease or Syndrome]
197Meta Mapping (1000):
198  1000 C0040300:Tissue Types (Body tissue) [Tissue]
199
200Phrase: "express"
201Meta Candidates (3):
202   966 C0017262:Expressed (Gene Expression) [Genetic Function]
203   966 C1171362:Expressed (protein expression) [Genetic Function]
204   966 C1515670:Expressed (mRNA Expression) [Genetic Function]
205Meta Mapping (966):
206   966 C0017262:Expressed (Gene Expression) [Genetic Function]
207Meta Mapping (966):
208   966 C1515670:Expressed (mRNA Expression) [Genetic Function]
209Meta Mapping (966):
210   966 C1171362:Expressed (protein expression) [Genetic Function]
211
212Phrase: "members"
213Meta Candidates (2):
214   966 C0680022:member [Population Group]
215   966 C1551024:member (Role Class - member) [Group]
216Meta Mapping (966):
217   966 C1551024:member (Role Class - member) [Group]
218Meta Mapping (966):
219   966 C0680022:member [Population Group]
220
221Phrase: "of the mammalian TIM gene family ?"
222Meta Candidates (6):
223   861 C1517488:Gene Family [Gene or Genome]
224   812 C0015576:Family [Conceptual Entity,Family Group]
225   741 C0241888:Familial [Functional Concept]
226   687 C0600269:Familiarity [Mental Process]
227   645 C0017337:Gene (Genes) [Gene or Genome]
228   645 C0024660:Mammalian (Mammals) [Mammal]
229Meta Mapping (824):
230   645 C0024660:Mammalian (Mammals) [Mammal]
231   861 C1517488:Gene Family [Gene or Genome]
232/MetaMap/public_mm/bin/SKRrun -L 2008 -w /MetaMap/public_mm/lexicon /MetaMap/public_mm/bin/metamap08.BINARY -I -Z 08
233
234MetaMap (2008)
235
236
237Control options:
238  mm_data_year=08
239  show_cuis
240Berkeley DB databases (normal strict 08 model) are open.
241Static variants will come from table varsan.
242Variants: Adj/noun ONLY.
243Accessing lexicon /MetaMap/public_mm/lexicon/data/lexiconStatic2008.
244Variant generation mode: static.
245
246Established connection to Tagger Server on localhost.
247Processing 00000000.tx.1: What diseases are associated with lysosomal abnormalities in the nervous system ?
248
249Phrase: "What diseases"
250Meta Candidates (4):
251  1000 C0012634:Diseases (Disease) [Disease or Syndrome]
252   928 C1422572:MAL (MKL1 gene) [Gene or Genome]
253   928 C1424810:Mal (TIRAP gene) [Gene or Genome]
254   928 C1836721:MALS [Finding]
255Meta Mapping (1000):
256  1000 C0012634:Diseases (Disease) [Disease or Syndrome]
257
258Phrase: "are"
259
260Phrase: "associated"
261Meta Candidates (3):
262  1000 C0332281:Associated (Associated with) [Qualitative Concept]
263   966 C0750490:Associate (Associate - relationship) [Idea or Concept]
264   966 C1706221:Associate (Associate - assistant) [Professional or Occupational Group]
265Meta Mapping (1000):
266  1000 C0332281:Associated (Associated with) [Qualitative Concept]
267
268Phrase: "with lysosomal abnormalities"
269Meta Candidates (7):
270   861 C0000768:Abnormalities (Congenital Abnormality) [Congenital Abnormality]
271   861 C0000769:abnormalities (teratologic) [Functional Concept]
272   827 C1704258:Abnormality [Finding]
273   777 C0205161:Abnormal [Functional Concept]
274   777 C1550458:Abnormal (Observation Interpretation - Abnormal) [Idea or Concept]
275   694 C0521450:Lysosomal [Body Location or Region]
276   623 C0024369:Lysosome (Lysosomes) [Cell Component]
277Meta Mapping (888):
278   694 C0521450:Lysosomal [Body Location or Region]
279   861 C0000768:Abnormalities (Congenital Abnormality) [Congenital Abnormality]
280Meta Mapping (888):
281   694 C0521450:Lysosomal [Body Location or Region]
282   861 C0000769:abnormalities (teratologic) [Functional Concept]
283
284Phrase: "in the nervous system ?"
285Meta Candidates (12):
286  1000 C0027763:Nervous System (Nervous system structure) [Body System]
287  1000 C1269560:Nervous system (Entire nervous system) [Body System]
288   944 C0205494:Neurologic [Functional Concept]
289   907 C0027855:Neurology (Neurology speciality) [Biomedical Occupation or Discipline]
290   907 C1555868:Neurology (Psychiatry & Neurology Physicians) [Professional or Occupational Group]
291   861 C0027769:Nervous (Nervousness) [Finding]
292   861 C0449913:System [Functional Concept]
293   861 C0599851:Nervous (relating to nervous system) [Functional Concept]
294   861 C1553451:System (Entity Code - System) [Manufactured Object]
295   861 C1704459:System (Device Component System) [Medical Device]
296   789 C0205373:Systemic [Functional Concept]
297   789 C0220922:systematic [Functional Concept]
298Meta Mapping (1000):
299  1000 C1269560:Nervous system (Entire nervous system) [Body System]
300Meta Mapping (1000):
301  1000 C0027763:Nervous System (Nervous system structure) [Body System]
302/MetaMap/public_mm/bin/SKRrun -L 2008 -w /MetaMap/public_mm/lexicon /MetaMap/public_mm/bin/metamap08.BINARY -I -Z 08
303
304MetaMap (2008)
305
306
307Control options:
308  mm_data_year=08
309  show_cuis
310Berkeley DB databases (normal strict 08 model) are open.
311Static variants will come from table varsan.
312Variants: Adj/noun ONLY.
313Accessing lexicon /MetaMap/public_mm/lexicon/data/lexiconStatic2008.
314Variant generation mode: static.
315
316Established connection to Tagger Server on localhost.
317Processing 00000000.tx.1: What drugs have been tested in mouse models of Alzheimer's disease ?
318
319Phrase: "What drugs"
320Meta Candidates (5):
321  1000 C0013227:Drugs (Pharmaceutical Preparations) [Pharmacologic Substance]
322   966 C1254351:Drug (Pharmacologic Substance) [Pharmacologic Substance]
323   928 C0031336:Pharmaceutical (Pharmacy) [Biomedical Occupation or Discipline]
324   928 C1553890:Pharmaceutical (Pharmaceutical - ActMedicalServiceCode) [Intellectual Product]
325   900 C0456386:Medicament [Pharmacologic Substance]
326Meta Mapping (1000):
327  1000 C0013227:Drugs (Pharmaceutical Preparations) [Pharmacologic Substance]
328
329Phrase: "have"
330
331Phrase: "been"
332
333Phrase: "tested"
334Meta Candidates (5):
335   966 C0022885:Test (Laboratory Procedures) [Laboratory Procedure]
336   966 C0039593:Test (Testing) [Functional Concept]
337   966 C0392366:Tests [Intellectual Product]
338   966 C0456984:test (Test Result) [Finding]
339   966 C1378537:TEST [Medical Device]
340Meta Mapping (966):
341   966 C0022885:Test (Laboratory Procedures) [Laboratory Procedure]
342Meta Mapping (966):
343   966 C1378537:TEST [Medical Device]
344Meta Mapping (966):
345   966 C0456984:test (Test Result) [Finding]
346Meta Mapping (966):
347   966 C0039593:Test (Testing) [Functional Concept]
348Meta Mapping (966):
349   966 C0392366:Tests [Intellectual Product]
350
351Phrase: "in mouse"
352Meta Candidates (4):
353  1000 C0025914:Mouse (House mice) [Mammal]
354  1000 C0025929:mouse (Laboratory mice) [Mammal]
355  1000 C0026809:Mouse (Mus) [Mammal]
356  1000 C1455722:Mouse (Mouse antigen) [Immunologic Factor]
357Meta Mapping (1000):
358  1000 C0025914:Mouse (House mice) [Mammal]
359Meta Mapping (1000):
360  1000 C0025929:mouse (Laboratory mice) [Mammal]
361Meta Mapping (1000):
362  1000 C1455722:Mouse (Mouse antigen) [Immunologic Factor]
363Meta Mapping (1000):
364  1000 C0026809:Mouse (Mus) [Mammal]
365
366Phrase: "models"
367Meta Candidates (3):
368  1000 C0026336:Models (Study models) [Intellectual Product,Research Device]
369  1000 C0026339:Models (Biological Models) [Intellectual Product,Research Device]
370   966 C0870071:Modeling [Intellectual Product,Research Activity]
371Meta Mapping (1000):
372  1000 C0026339:Models (Biological Models) [Intellectual Product,Research Device]
373Meta Mapping (1000):
374  1000 C0026336:Models (Study models) [Intellectual Product,Research Device]
375
376Phrase: "of Alzheimer's disease ?"
377Meta Candidates (6):
378  1000 C0002395:Alzheimer's Disease [Disease or Syndrome]
379          Alzheimer
380   861 C0012634:Disease [Disease or Syndrome]
381   805 C1422572:MAL (MKL1 gene) [Gene or Genome]
382   805 C1424810:Mal (TIRAP gene) [Gene or Genome]
383   805 C1836721:MALS [Finding]
384Meta Mapping (1000):
385  1000 C0002395:Alzheimer's Disease [Disease or Syndrome]
386/MetaMap/public_mm/bin/SKRrun -L 2008 -w /MetaMap/public_mm/lexicon /MetaMap/public_mm/bin/metamap08.BINARY -I -Z 08
387
388MetaMap (2008)
389
390
391Control options:
392  mm_data_year=08
393  show_cuis
394Berkeley DB databases (normal strict 08 model) are open.
395Static variants will come from table varsan.
396Variants: Adj/noun ONLY.
397Accessing lexicon /MetaMap/public_mm/lexicon/data/lexiconStatic2008.
398Variant generation mode: static.
399
400Established connection to Tagger Server on localhost.
401Processing 00000000.tx.1: What centrosomal genes are implicated in diseases of brain development ?
402
403Phrase: "What centrosomal genes"
404Meta Candidates (2):
405   861 C0017337:Genes [Gene or Genome]
406   623 C0242608:Centrosome [Cell Component]
407Meta Mapping (853):
408   623 C0242608:Centrosome [Cell Component]
409   861 C0017337:Genes [Gene or Genome]
410
411Phrase: "are"
412
413Phrase: "implicated"
414
415Phrase: "in diseases"
416Meta Candidates (4):
417  1000 C0012634:Diseases (Disease) [Disease or Syndrome]
418   928 C1422572:MAL (MKL1 gene) [Gene or Genome]
419   928 C1424810:Mal (TIRAP gene) [Gene or Genome]
420   928 C1836721:MALS [Finding]
421Meta Mapping (1000):
422  1000 C0012634:Diseases (Disease) [Disease or Syndrome]
423
424Phrase: "of brain development ?"
425Meta Candidates (8):
426  1000 C1160340:brain development [Organ or Tissue Function]
427   861 C0020119:Development (Human Development) [Physiologic Function]
428   861 C0243107:development (development aspects) [Physiologic Function]
429   861 C0678723:Development (Biologic Development) [Organism Function]
430   861 C1527148:Development [Functional Concept]
431   789 C0458003:Developmental [Qualitative Concept]
432   694 C0006104:Brain [Body Part, Organ, or Organ Component]
433   694 C1269537:Brain (Entire brain) [Body Part, Organ, or Organ Component]
434Meta Mapping (1000):
435  1000 C1160340:brain development [Organ or Tissue Function]
436/MetaMap/public_mm/bin/SKRrun -L 2008 -w /MetaMap/public_mm/lexicon /MetaMap/public_mm/bin/metamap08.BINARY -I -Z 08
437
438MetaMap (2008)
439
440
441Control options:
442  mm_data_year=08
443  show_cuis
444Berkeley DB databases (normal strict 08 model) are open.
445Static variants will come from table varsan.
446Variants: Adj/noun ONLY.
447Accessing lexicon /MetaMap/public_mm/lexicon/data/lexiconStatic2008.
448Variant generation mode: static.
449
450Established connection to Tagger Server on localhost.
451Processing 00000000.tx.1: What molecular functions does helicase protein NS3 play in HCV (Hepatitis C virus) ?
452
453Phrase: "What molecular functions"
454Meta Candidates (8):
455   983 C1148560:molecular_function [Molecular Function]
456   861 C0542341:Functions (Function) [Functional Concept]
457   827 C0031843:function (physiological aspects) [Physiologic Function]
458   827 C0700205:FUNCTION (Function Axis) [Classification]
459   827 C1705273:Function (Mathematical Operator) [Intellectual Product]
460   777 C0205245:Functional [Functional Concept]
461   694 C1521991:Molecular [Qualitative Concept]
462   623 C0567416:Molecule [Substance]
463Meta Mapping (983):
464   983 C1148560:molecular_function [Molecular Function]
465
466Phrase: "does"
467
468Phrase: "helicase protein NS3"
469Meta Candidates (4):
470   827 C1860991:NS3 (NOONAN SYNDROME 3) [Disease or Syndrome]
471   660 C0033684:Protein (Proteins) [Amino Acid, Peptide, or Protein,Biologically Active Substance]
472   660 C0202202:Protein NOS (Protein measurement) [Laboratory Procedure]
473   660 C0920283:helicase [Amino Acid, Peptide, or Protein,Enzyme]
474Meta Mapping (851):
475   660 C0920283:helicase [Amino Acid, Peptide, or Protein,Enzyme]
476   660 C0202202:Protein NOS (Protein measurement) [Laboratory Procedure]
477   827 C1860991:NS3 (NOONAN SYNDROME 3) [Disease or Syndrome]
478Meta Mapping (851):
479   660 C0920283:helicase [Amino Acid, Peptide, or Protein,Enzyme]
480   660 C0033684:Protein (Proteins) [Amino Acid, Peptide, or Protein,Biologically Active Substance]
481   827 C1860991:NS3 (NOONAN SYNDROME 3) [Disease or Syndrome]
482
483Phrase: "play"
484Meta Candidates (2):
485  1000 C0032214:Play [Daily or Recreational Activity]
486   966 C0600138:Plays (Does play) [Finding]
487Meta Mapping (1000):
488  1000 C0032214:Play [Daily or Recreational Activity]
489
490Phrase: "in HCV"
491Meta Candidates (1):
492  1000 C0220847:HCV (Hepatitis C virus) [Virus]
493Meta Mapping (1000):
494  1000 C0220847:HCV (Hepatitis C virus) [Virus]
495
496Phrase: "(Hepatitis C virus"
497Meta Candidates (9):
498  1000 C0220847:Hepatitis C virus [Virus]
499          Hepatitis C
500   983 C0079500:Hepatitis C viruses (Hepatitis C-Like Viruses) [Virus]
501   913 C0019186:Hepatitis virus (Hepatitis Viruses) [Virus]
502   901 C0019196:Hepatitis C [Disease or Syndrome]
503   827 C0019158:Hepatitis [Disease or Syndrome]
504   827 C0042769:virus (Virus Diseases) [Disease or Syndrome]
505   827 C0042776:Virus [Virus]
506   793 C0521026:viruses (Viral) [Functional Concept]
507Meta Mapping (1000):
508  1000 C0220847:Hepatitis C virus [Virus]
509
510Phrase: ") ?"
511/MetaMap/public_mm/bin/SKRrun -L 2008 -w /MetaMap/public_mm/lexicon /MetaMap/public_mm/bin/metamap08.BINARY -I -Z 08
512
513MetaMap (2008)
514
515
516Control options:
517  mm_data_year=08
518  show_cuis
519Berkeley DB databases (normal strict 08 model) are open.
520Static variants will come from table varsan.
521Variants: Adj/noun ONLY.
522Accessing lexicon /MetaMap/public_mm/lexicon/data/lexiconStatic2008.
523Variant generation mode: static.
524
525Established connection to Tagger Server on localhost.
526Processing 00000000.tx.1: What mutations in apolipoprotein genes are associated with disease ?
527
528Phrase: "What mutations"
529Meta Candidates (3):
530  1000 C0026882:Mutations (Mutation) [Genetic Function]
531   966 C1705285:Mutation (Mutation Abnormality) [Cell or Molecular Dysfunction]
532   916 C0596988:Mutant [Cell or Molecular Dysfunction]
533Meta Mapping (1000):
534  1000 C0026882:Mutations (Mutation) [Genetic Function]
535
536Phrase: "in apolipoprotein genes"
537Meta Candidates (4):
538   983 C1445865:Apolipoprotein gene [Gene or Genome]
539   861 C0017337:Genes [Gene or Genome]
540   694 C0003591:Apolipoprotein (Apolipoproteins) [Amino Acid, Peptide, or Protein,Biologically Active Substance]
541   694 C1325281:apolipoprotein (apolipoprotein activity) [Molecular Function]
542Meta Mapping (983):
543   983 C1445865:Apolipoprotein gene [Gene or Genome]
544
545Phrase: "are"
546
547Phrase: "associated"
548Meta Candidates (3):
549  1000 C0332281:Associated (Associated with) [Qualitative Concept]
550   966 C0750490:Associate (Associate - relationship) [Idea or Concept]
551   966 C1706221:Associate (Associate - assistant) [Professional or Occupational Group]
552Meta Mapping (1000):
553  1000 C0332281:Associated (Associated with) [Qualitative Concept]
554
555Phrase: "with disease ?"
556Meta Candidates (4):
557  1000 C0012634:Disease [Disease or Syndrome]
558   944 C1422572:MAL (MKL1 gene) [Gene or Genome]
559   944 C1424810:Mal (TIRAP gene) [Gene or Genome]
560   944 C1836721:MALS [Finding]
561Meta Mapping (1000):
562  1000 C0012634:Disease [Disease or Syndrome]
563/MetaMap/public_mm/bin/SKRrun -L 2008 -w /MetaMap/public_mm/lexicon /MetaMap/public_mm/bin/metamap08.BINARY -I -Z 08
564
565MetaMap (2008)
566
567
568Control options:
569  mm_data_year=08
570  show_cuis
571Berkeley DB databases (normal strict 08 model) are open.
572Static variants will come from table varsan.
573Variants: Adj/noun ONLY.
574Accessing lexicon /MetaMap/public_mm/lexicon/data/lexiconStatic2008.
575Variant generation mode: static.
576
577Established connection to Tagger Server on localhost.
578Processing 00000000.tx.1: Which pathways are possibly involved in the disease ADPKD ?
579
580Phrase: "Which pathways"
581Meta Candidates (2):
582  1000 C1704259:Pathways (Biochemical Pathway) [Molecular Function]
583  1000 C1705987:Pathways (Pathway) [Conceptual Entity]
584Meta Mapping (1000):
585  1000 C1704259:Pathways (Biochemical Pathway) [Molecular Function]
586Meta Mapping (1000):
587  1000 C1705987:Pathways (Pathway) [Conceptual Entity]
588
589Phrase: "are"
590
591Phrase: "possibly"
592Meta Candidates (1):
593  1000 C0332149:Possibly (Possible) [Qualitative Concept]
594Meta Mapping (1000):
595  1000 C0332149:Possibly (Possible) [Qualitative Concept]
596
597Phrase: "involved"
598Meta Candidates (1):
599  1000 C1314939:Involved (Involvement with) [Functional Concept]
600Meta Mapping (1000):
601  1000 C1314939:Involved (Involvement with) [Functional Concept]
602
603Phrase: "in the disease ADPKD ?"
604Meta Candidates (5):
605   861 C0085413:ADPKD (Polycystic Kidney, Autosomal Dominant) [Congenital Abnormality,Disease or Syndrome]
606   694 C0012634:Disease [Disease or Syndrome]
607   638 C1422572:MAL (MKL1 gene) [Gene or Genome]
608   638 C1424810:Mal (TIRAP gene) [Gene or Genome]
609   638 C1836721:MALS [Finding]
610Meta Mapping (888):
611   694 C0012634:Disease [Disease or Syndrome]
612   861 C0085413:ADPKD (Polycystic Kidney, Autosomal Dominant) [Congenital Abnormality,Disease or Syndrome]
613/MetaMap/public_mm/bin/SKRrun -L 2008 -w /MetaMap/public_mm/lexicon /MetaMap/public_mm/bin/metamap08.BINARY -I -Z 08
614
615MetaMap (2008)
616
617
618Control options:
619  mm_data_year=08
620  show_cuis
621Berkeley DB databases (normal strict 08 model) are open.
622Static variants will come from table varsan.
623Variants: Adj/noun ONLY.
624Accessing lexicon /MetaMap/public_mm/lexicon/data/lexiconStatic2008.
625Variant generation mode: static.
626
627Established connection to Tagger Server on localhost.
628Processing 00000000.tx.1: What proteins does epsin1 interact with during endocytosis ?
629
630Phrase: "What proteins"
631Meta Candidates (2):
632  1000 C0033684:Proteins [Amino Acid, Peptide, or Protein,Biologically Active Substance]
633   966 C0202202:Protein NOS (Protein measurement) [Laboratory Procedure]
634Meta Mapping (1000):
635  1000 C0033684:Proteins [Amino Acid, Peptide, or Protein,Biologically Active Substance]
636
637Phrase: "does"
638
639Phrase: "epsin1"
640
641Phrase: "interact"
642
643Phrase: "with"
644
645Phrase: "during endocytosis ?"
646Meta Candidates (1):
647  1000 C0014139:Endocytosis [Cell Function]
648Meta Mapping (1000):
649  1000 C0014139:Endocytosis [Cell Function]
650/MetaMap/public_mm/bin/SKRrun -L 2008 -w /MetaMap/public_mm/lexicon /MetaMap/public_mm/bin/metamap08.BINARY -I -Z 08
651
652MetaMap (2008)
653
654
655Control options:
656  mm_data_year=08
657  show_cuis
658Berkeley DB databases (normal strict 08 model) are open.
659Static variants will come from table varsan.
660Variants: Adj/noun ONLY.
661Accessing lexicon /MetaMap/public_mm/lexicon/data/lexiconStatic2008.
662Variant generation mode: static.
663
664Established connection to Tagger Server on localhost.
665Processing 00000000.tx.1: What Streptococcus pneumoniae strains are resistent to penicillin and erythromycin ?
666
667Phrase: "What Streptococcus pneumoniae strains"
668Meta Candidates (10):
669   827 C0080194:Strains (Muscle strain) [Injury or Poisoning]
670   827 C0456178:Strains (Microbiology subtype strains) [Intellectual Product]
671   793 C1510453:strain (strain symptom) [Sign or Symptom]
672   793 C1518614:Strain (Organism Strain) [Mammal]
673   734 C0038410:Streptococcus pneumoniae [Bacterium]
674   734 C0370030:Streptococcus pneumoniae (Streptococcus pneumoniae antigen) [Immunologic Factor]
675   660 C0032285:Pneumoniae (Pneumonia) [Disease or Syndrome]
676   660 C0038402:Streptococcus [Bacterium]
677   560 C0024109:Lung [Body Part, Organ, or Organ Component]
678   560 C1278908:Lung (Entire lung) [Body Part, Organ, or Organ Component]
679Meta Mapping (901):
680   734 C0038410:Streptococcus pneumoniae [Bacterium]
681   827 C0456178:Strains (Microbiology subtype strains) [Intellectual Product]
682Meta Mapping (901):
683   734 C0038410:Streptococcus pneumoniae [Bacterium]
684   827 C0080194:Strains (Muscle strain) [Injury or Poisoning]
685Meta Mapping (901):
686   734 C0370030:Streptococcus pneumoniae (Streptococcus pneumoniae antigen) [Immunologic Factor]
687   827 C0456178:Strains (Microbiology subtype strains) [Intellectual Product]
688Meta Mapping (901):
689   734 C0370030:Streptococcus pneumoniae (Streptococcus pneumoniae antigen) [Immunologic Factor]
690   827 C0080194:Strains (Muscle strain) [Injury or Poisoning]
691
692Phrase: "are"
693
694Phrase: "resistent"
695Meta Candidates (5):
696  1000 C0332325:Resistant [Functional Concept]
697  1000 C1550464:resistent [Idea or Concept]
698   916 C0237834:Resistance (Psychotherapeutic Resistance) [Mental Process]
699   916 C0683598:resistance (social resistance) [Social Behavior]
700   916 C1522618:Resistance (resistance mechanism) [Clinical Attribute]
701Meta Mapping (1000):
702  1000 C0332325:Resistant [Functional Concept]
703Meta Mapping (1000):
704  1000 C1550464:resistent [Idea or Concept]
705
706Phrase: "to penicillin"
707Meta Candidates (2):
708  1000 C0030842:Penicillin (Penicillins) [Antibiotic,Organic Chemical]
709  1000 C0220892:Penicillin [Antibiotic,Organic Chemical]
710Meta Mapping (1000):
711  1000 C0220892:Penicillin [Antibiotic,Organic Chemical]
712Meta Mapping (1000):
713  1000 C0030842:Penicillin (Penicillins) [Antibiotic,Organic Chemical]
714
715Phrase: "and"
716
717Phrase: "erythromycin ?"
718Meta Candidates (4):
719  1000 C0014806:Erythromycin [Antibiotic,Organic Chemical]
720   944 C0014824:Erythrosin (Erythrosine) [Indicator, Reagent, or Diagnostic Aid,Organic Chemical]
721   944 C0699338:Erythrocin [Antibiotic,Carbohydrate]
722   944 C0699339:Ilotycin [Antibiotic,Organic Chemical]
723Meta Mapping (1000):
724  1000 C0014806:Erythromycin [Antibiotic,Organic Chemical]
725/MetaMap/public_mm/bin/SKRrun -L 2008 -w /MetaMap/public_mm/lexicon /MetaMap/public_mm/bin/metamap08.BINARY -I -Z 08
726
727MetaMap (2008)
728
729
730Control options:
731  mm_data_year=08
732  show_cuis
733Berkeley DB databases (normal strict 08 model) are open.
734Static variants will come from table varsan.
735Variants: Adj/noun ONLY.
736Accessing lexicon /MetaMap/public_mm/lexicon/data/lexiconStatic2008.
737Variant generation mode: static.
738
739Established connection to Tagger Server on localhost.
740Processing 00000000.tx.1: What signs or symptoms of anxiety disorder are related to lipid levels ?
741
742Phrase: "What signs"
743Meta Candidates (5):
744  1000 C0220912:signs (Aspects of signs) [Functional Concept]
745  1000 C0220913:Signs (Manufactured sign) [Manufactured Object]
746  1000 C0311392:SIGNS (Physical findings) [Sign or Symptom]
747   966 C1547188:Sign (Language Ability - Sign) [Idea or Concept]
748   916 C1710082:Signal [Conceptual Entity]
749Meta Mapping (1000):
750  1000 C0220912:signs (Aspects of signs) [Functional Concept]
751Meta Mapping (1000):
752  1000 C0220913:Signs (Manufactured sign) [Manufactured Object]
753Meta Mapping (1000):
754  1000 C0311392:SIGNS (Physical findings) [Sign or Symptom]
755
756Phrase: "or"
757
758Phrase: "symptoms"
759Meta Candidates (3):
760  1000 C0683368:symptoms (Symptoms aspect) [Functional Concept]
761  1000 C1457887:Symptoms [Sign or Symptom]
762   916 C0231220:Symptomatic [Functional Concept]
763Meta Mapping (1000):
764  1000 C1457887:Symptoms [Sign or Symptom]
765Meta Mapping (1000):
766  1000 C0683368:symptoms (Symptoms aspect) [Functional Concept]
767
768Phrase: "of anxiety disorder"
769Meta Candidates (4):
770  1000 C0003469:Anxiety disorder NOS (Anxiety Disorders) [Mental or Behavioral Dysfunction]
771   861 C0003467:Anxiety [Mental Process]
772   861 C0012634:Disorder (Disease) [Disease or Syndrome]
773   861 C1963064:Anxiety (Anxiety Adverse Event) [Finding]
774Meta Mapping (1000):
775  1000 C0003469:Anxiety disorder NOS (Anxiety Disorders) [Mental or Behavioral Dysfunction]
776
777Phrase: "are"
778
779Phrase: "related"
780Meta Candidates (4):
781  1000 C0439849:Related (Relationships) [Qualitative Concept]
782  1000 C0445223:Related (Related personal status) [Finding]
783   966 C0163712:Relate [Organic Chemical]
784   966 C2003855:Relating [Functional Concept]
785Meta Mapping (1000):
786  1000 C0445223:Related (Related personal status) [Finding]
787Meta Mapping (1000):
788  1000 C0439849:Related (Relationships) [Qualitative Concept]
789
790Phrase: "to lipid levels ?"
791Meta Candidates (5):
792   983 C0428460:Lipid level (Lipid level - finding) [Laboratory or Test Result]
793   861 C0441889:Levels (Degree) [Qualitative Concept]
794   827 C0456079:Level (Disease classification level) [Classification]
795   694 C0023779:Lipid (Lipids) [Lipid]
796   661 C0523744:Lipids NOS (Lipids measurement) [Laboratory Procedure]
797Meta Mapping (983):
798   983 C0428460:Lipid level (Lipid level - finding) [Laboratory or Test Result]
799/MetaMap/public_mm/bin/SKRrun -L 2008 -w /MetaMap/public_mm/lexicon /MetaMap/public_mm/bin/metamap08.BINARY -I -Z 08
800
801MetaMap (2008)
802
803
804Control options:
805  mm_data_year=08
806  show_cuis
807Berkeley DB databases (normal strict 08 model) are open.
808Static variants will come from table varsan.
809Variants: Adj/noun ONLY.
810Accessing lexicon /MetaMap/public_mm/lexicon/data/lexiconStatic2008.
811Variant generation mode: static.
812
813Established connection to Tagger Server on localhost.
814Processing 00000000.tx.1: What toxicities are associated with cytarabine ?
815
816Phrase: "What toxicities"
817Meta Candidates (7):
818   966 C0040539:toxicity (Toxicity aspects) [Quantitative Concept]
819   966 C0600688:Toxicity (Toxic effect) [Injury or Poisoning]
820   916 C1407029:Toxic [Qualitative Concept]
821   900 C0032346:Poison (Poisons) [Hazardous or Poisonous Substance]
822   900 C1548769:Poison (Poison Risk Codes) [Intellectual Product]
823   900 C1550590:poison (Poison RIsk) [Idea or Concept]
824   893 C0040549:Toxin [Biologically Active Substance,Hazardous or Poisonous Substance]
825Meta Mapping (966):
826   966 C0600688:Toxicity (Toxic effect) [Injury or Poisoning]
827Meta Mapping (966):
828   966 C0040539:toxicity (Toxicity aspects) [Quantitative Concept]
829
830Phrase: "are"
831
832Phrase: "associated"
833Meta Candidates (3):
834  1000 C0332281:Associated (Associated with) [Qualitative Concept]
835   966 C0750490:Associate (Associate - relationship) [Idea or Concept]
836   966 C1706221:Associate (Associate - assistant) [Professional or Occupational Group]
837Meta Mapping (1000):
838  1000 C0332281:Associated (Associated with) [Qualitative Concept]
839
840Phrase: "with cytarabine ?"
841Meta Candidates (2):
842  1000 C0010711:Cytarabine [Nucleic Acid, Nucleoside, or Nucleotide,Pharmacologic Substance]
843   944 C0591320:Cytosar [Hazardous or Poisonous Substance,Nucleic Acid, Nucleoside, or Nucleotide,Pharmacologic Substance]
844Meta Mapping (1000):
845  1000 C0010711:Cytarabine [Nucleic Acid, Nucleoside, or Nucleotide,Pharmacologic Substance]
846/MetaMap/public_mm/bin/SKRrun -L 2008 -w /MetaMap/public_mm/lexicon /MetaMap/public_mm/bin/metamap08.BINARY -I -Z 08
847
848MetaMap (2008)
849
850
851Control options:
852  mm_data_year=08
853  show_cuis
854Berkeley DB databases (normal strict 08 model) are open.
855Static variants will come from table varsan.
856Variants: Adj/noun ONLY.
857Accessing lexicon /MetaMap/public_mm/lexicon/data/lexiconStatic2008.
858Variant generation mode: static.
859
860Established connection to Tagger Server on localhost.
861Processing 00000000.tx.1: What tumor types are associated with Rb1 mutations ?
862
863Phrase: "What tumor types"
864Meta Candidates (6):
865   861 C0332307:Types (Type - attribute) [Qualitative Concept]
866   827 C1547052:*Type [Quantitative Concept]
867   827 C1552651:Type (Type - ParameterizedDataType) [Intellectual Product]
868   827 C1849011:TYPE (SPONDYLOMETAEPIPHYSEAL DYSPLASIA, SHORT LIMB-HAND TYPE) [Disease or Syndrome]
869   694 C0027651:Tumor (Neoplasm) [Neoplastic Process]
870   694 C1578706:Tumor (Specimen Source Codes - tumor) [Intellectual Product]
871Meta Mapping (888):
872   694 C0027651:Tumor (Neoplasm) [Neoplastic Process]
873   861 C0332307:Types (Type - attribute) [Qualitative Concept]
874Meta Mapping (888):
875   694 C1578706:Tumor (Specimen Source Codes - tumor) [Intellectual Product]
876   861 C0332307:Types (Type - attribute) [Qualitative Concept]
877
878Phrase: "are"
879
880Phrase: "associated"
881Meta Candidates (3):
882  1000 C0332281:Associated (Associated with) [Qualitative Concept]
883   966 C0750490:Associate (Associate - relationship) [Idea or Concept]
884   966 C1706221:Associate (Associate - assistant) [Professional or Occupational Group]
885Meta Mapping (1000):
886  1000 C0332281:Associated (Associated with) [Qualitative Concept]
887
888Phrase: "with Rb1 mutations ?"
889Meta Candidates (5):
890   861 C0026882:Mutations (Mutation) [Genetic Function]
891   827 C1705285:Mutation (Mutation Abnormality) [Cell or Molecular Dysfunction]
892   777 C0596988:Mutant [Cell or Molecular Dysfunction]
893   694 C0080113:RB1 (Retinoblastoma Protein) [Amino Acid, Peptide, or Protein,Biologically Active Substance]
894   694 C0694889:RB1 (RB1 gene) [Gene or Genome]
895Meta Mapping (888):
896   694 C0694889:RB1 (RB1 gene) [Gene or Genome]
897   861 C0026882:Mutations (Mutation) [Genetic Function]
898Meta Mapping (888):
899   694 C0080113:RB1 (Retinoblastoma Protein) [Amino Acid, Peptide, or Protein,Biologically Active Substance]
900   861 C0026882:Mutations (Mutation) [Genetic Function]