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知识发现与PUBMED信息检索平台实现对接

已有 4087 次阅读 2012-3-13 09:21 |个人分类:知识发现|系统分类:科研笔记| 信息, class, 艾滋病, method, action

ARROWSMITH知识发现平台已与PUBMED医学信息检索平台实现了对接，比以前的信息检索分析和知识发现更为方便，直观。
 
具体操作方法如下：
 
进入ARROWSMITH知识发现平台，切换到PUBMED检索平台，例如检索AIDS（艾滋病）：
检索结果（知识发现的A集文献） Search Results (184940篇) 有两个选项：
1  你是否想做AIDS的知识发现？Use AIDS for ARROWSMITH?
 
Yes 是

2  你是否需要免费全文或综述文献？Filter by Free Full Text or Review

选择1，进行知识发现

http://arrowsmith.psych.uic.edu/cgi-bin/arrowsmith_uic/pubsmith.cgi?term=AIDS+++&ID=1365&AC=A&cmd=ARROWSMITH

检索gene therapy （基因治疗）

检索结果(知识发现的C集文献）  Search Results (134438篇)
你是否想做艾滋病基因治疗的知识发现？Use gene therapy for ARROWSMITH?

Yes 是

http://arrowsmith.psych.uic.edu/cgi-bin/arrowsmith_uic/pubsmith.cgi?term=gene++therapy+++&ID=1365&AC=C&cmd=ARROWSMITH&GO=0

得到A与C文献集中的B-list（词汇）

Start A-Literature C-Literature B-list Filter Literature
A-query: AIDS
C-query: gene therapy
The B-list contains title words and phrases (terms) that appeared in both the A and the C literature. 2221 articles appeared in both literatures and were not included in the process of computing the B-list but can be viewed here. The results of this search are saved under id # 1365 and can be accessed from the start page after you leave this session. There are 40674 terms on the current B-list (7912 are predicted to be relevant), which is shown ranked according to predicted relevance. The list can be further trimmed down using the filters listed in the left margin.

To assess whether there appears to be a biologically significant relationship between the AB and BC literatures for specific B-terms, please select one or more B-terms and then click the button to view the corresponding AB and BC literatures. Use Ctrl to select multiple B-terms.

http://arrowsmith.psych.uic.edu/cgi-bin/arrowsmith_uic/edit_b.cgi?refresh=T&ID=1365

 

需要对B词汇进行语义分类限制吗？Restrict by semantic categories?

  是

对B词汇进行分类选择和语义过滤（Semantic Filters）

http://arrowsmith.psych.uic.edu/cgi-bin/arrowsmith_uic/umls.cgi?task=filter&ID=1365

按相关度列出知识发现（词汇）表：

http://arrowsmith.psych.uic.edu/cgi-bin/arrowsmith_uic/view_b_txt.cgi?ID=1365

 

job id # 1365 started Mon Mar 12 18:28:11 2012
Max_citations: 50000
Stoplist: /var/www/html/arrowsmith_uic/data/stopwords_pubmed
Ngram_max: 3
A_query_raw: AIDS Mon Mar 12 18:28:25 2012

A query = AIDS started Mon Mar 12 18:28:25 2012
A query resulted in 50000 titles
C_query_raw: AIDS Mon Mar 12 18:46:07 2012

C: AIDS 184940

A: pubmed_query_A 184940

AC: ( AIDS ) AND ( AIDS ) 184940

A_query_raw: AIDS Mon Mar 12 18:46:33 2012

A query = AIDS started Mon Mar 12 18:46:34 2012
A query resulted in 50000 titles
C_query_raw: gene therapy Mon Mar 12 18:48:48 2012

C: gene therapy 134438

A: pubmed_query_A 184940

AC: ( AIDS ) AND ( gene therapy ) 2221

A_query_raw: AIDS Mon Mar 12 18:49:22 2012

A query = AIDS started Mon Mar 12 18:49:22 2012
A query resulted in 50000 titles
C_query_raw: gene therapy Mon Mar 12 18:51:39 2012

C: gene therapy 134438

A: pubmed_query_A 184940

AC: ( AIDS ) AND ( gene therapy ) 2221

C query = gene therapy started Mon Mar 12 18:51:40 2012
C query resulted in 50000 titles
A AND C query resulted in 2221 titles
C_query_raw: gene therapy Mon Mar 12 18:55:18 2012

C: gene therapy 134438

A: pubmed_query_A 184940

AC: ( AIDS ) AND ( gene therapy ) 2221

C_query_raw: gene therapy Mon Mar 12 18:56:26 2012

C: gene therapy 134438

A: pubmed_query_A 184940

AC: ( AIDS ) AND ( gene therapy ) 2221

40674 B-terms ready on Mon Mar 12 18:59:00 2012

A_query_raw: AIDS Mon Mar 12 18:59:21 2012

A query = AIDS started Mon Mar 12 18:59:22 2012
A query resulted in 50000 titles
A_query_raw: AIDS Mon Mar 12 19:00:42 2012

A query = AIDS started Mon Mar 12 19:00:42 2012
A query resulted in 50000 titles
Sem_filter:
Genes & Molecular Sequences, and Gene & Protein Names
A_query_raw: AIDS Mon Mar 12 19:12:01 2012

A query = AIDS started Mon Mar 12 19:12:01 2012
A query resulted in 50000 titles
C_query_raw: AIDS Mon Mar 12 19:12:21 2012

C: AIDS 184940

A: pubmed_query_A 184940

AC: ( AIDS ) AND ( AIDS ) 184940

C_query_raw: gene[title] Mon Mar 12 19:14:23 2012

C: gene[title] 332114

A: pubmed_query_A 184940

AC: ( AIDS ) AND ( gene[title] ) 1337

C_query_raw: gene[title] Mon Mar 12 19:14:48 2012

C: gene[title] 332114

A: pubmed_query_A 184940

AC: ( AIDS ) AND ( gene[title] ) 1337

C query = gene[title] started Mon Mar 12 19:14:49 2012
C query resulted in 50000 titles
A AND C query resulted in 1337 titles
36407 B-terms ready on Mon Mar 12 19:20:27 2012

Viewed A AND C titles Mon Mar 12 19:22:21 2012
Sem_filter:
Concepts & Ideas
Disorders
Genes & Molecular Sequences, and Gene & Protein Names
C_query_raw: Mon Mar 12 19:43:51 2012

C:

A: pubmed_query_A 184940

AC: ( AIDS ) AND ( ) 184940

13734 B-terms left after filter executed Mon Mar 12 19:51:54 2012

Sem_filter:
Chemicals & Drugs
Concepts & Ideas
Disorders
Genes & Molecular Sequences, and Gene & Protein Names
A_query_raw: AIDS Mon Mar 12 20:05:48 2012

A query = AIDS started Mon Mar 12 20:05:48 2012
A query resulted in 50000 titles
13734 B-terms left after filter executed Mon Mar 12 20:07:47 2012

A_query_raw: AIDS Mon Mar 12 20:12:36 2012

A query = AIDS started Mon Mar 12 20:12:36 2012
A query resulted in 50000 titles

B-list on Mon Mar 12 20:15:04 2012
1 brca2
2 adiponectin
3 brca1
4 toll receptor
5 stat5
6 rankl
7 lentiviral vector
8 dc sign
9 wnt
10 tlr4
11 related macular degeneration
12 jak2
13 suppressor cytokine signaling
14 quantitative trait loci
15 carotid intima media
16 e2f1
17 akt
18 vegf
19 stat1
20 mrsa
21 drb1
22 codon polymorphism
23 sybr green
24 antiretroviral therapy
25 therapy hiv
26 neural stem cell
27 suppressor cytokine
28 zinc finger protein
29 baff
30 single nucleotide polymorphism
31 mtor
32 age related macular
33 splice site
34 zinc finger
35 sybr green i
36 associated virus vector
37 loop mediated isothermal
38 stat3
39 viral load
40 highly active antiretroviral
41 cox-2
42 web server
43 c virus hcv
44 risk human papillomavirus
45 nod2
46 papillomavirus infection
47 microsatellite
48 beta catenin
49 jnk
50 vascular endothelial growth
51 nfat
52 cyp2c19
53 ppargamma
54 ryanodine receptor
55 repeat polymorphism
56 chronic hepatitis c
57 intima media thickness
58 transducer activator transcription
59 tlr7
60 signal transducer activator
61 c ebp
62 neural stem
63 hla g
64 hypoxia inducible
65 differentially expressed gene
66 ctla-4
67 adenoviral vector
68 cannabinoid receptor
69 comparative genomic
70 hepatitis c patient
71 cyclophilin
72 hiv-1 subtype
73 specific primer
74 chronic hepatitis b
75 time pcr assay
76 cloning expression
77 solid lipid nanoparticle
78 memory cd8 t
79 hypoxia inducible factor
80 feline immunodeficiency
81 promoter polymorphism
82 tp53
83 tandem repeat
84 smad3
85 hla drb1
86 inflammatory cytokine
87 pi3k
88 nod scid
89 sp1
90 real time pcr
91 ccaat enhancer
92 c ebpbeta
93 memory cd8
94 cd14
95 spacer region
96 active antiretroviral
97 tlr9
98 ghrelin
99 socs
100 cxcr4

选择相关知识概念（词汇）

可以查看：

AB literature AB集文献

B-term B-词汇

BC literature BC集文献

相关研究文献，可以作为科研选题或研究工作参考。

http://arrowsmith.psych.uic.edu/cgi-bin/arrowsmith_uic/show_sentences.cgi

 

Start A-Literature C-Literature B-list Filter Literature
AB literature

B-term

BC literature

AIDS brca2 gene[title]
1: BRCA2 Fine-Tunes the Spindle Assembly Checkpoint through Reinforcement of BubR1 Acetylation. 2012
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2: Telephone genetic counseling for high-risk women undergoing BRCA1 and BRCA2 testing: rationale and development of a randomized controlled trial. 2008
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1: Epigenetic modulation of BRCA1 and BRCA2 gene expression by equol in breast cancer cell lines. 2012
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2: Spectra of BRCA1 and BRCA2 mutations in Korean patients with breast cancer: the importance of whole-gene sequencing. 2012
Add to clipboard

3: Molecular and clinical characterization of an in frame deletion of uncertain clinical significance in the BRCA2 gene. 2012
Add to clipboard

4: Improved survival in non-Ashkenazi Jewish ovarian cancer patients with BRCA1 and BRCA2 gene mutations. 2011
Add to clipboard

5: Evaluation of the XRCC1 gene as a phenotypic modifier in BRCA1/2 mutation carriers. Results from the consortium of investigators of modifiers of BRCA1/BRCA2. 2011
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6: Two new CHEK2 germ-line variants detected in breast cancer/sarcoma families negative for BRCA1, BRCA2, and TP53 gene mutations. 2011
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7: The rs2910164:G>C SNP in the MIR146A gene is not associated with breast cancer risk in BRCA1 and BRCA2 mutation carriers. 2011
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8: Altered BRCA1 and BRCA2 responses and mutation of BRCA1 gene in mice exposed chronically and transgenerationally to aqueous extract of betel nut (AEBN). 2011
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9: Annual screening strategies in BRCA1 and BRCA2 gene mutation carriers: A comparative effectiveness analysis. 2011
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10: An entire exon 3 germ-line rearrangement in the BRCA2 gene: pathogenic relevance of exon 3 deletion in breast cancer predisposition. 2011
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11: BRCA2 is a moderate penetrance gene contributing to young-onset prostate cancer: implications for genetic testing in prostate cancer patients. 2011
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12: Ileal metastasis of breast cancer in a patient with a BRCA2 gene mutation: Report of a case. 2011
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13: US court reverses gene patent ruling for BRCA1 and BRCA2. 2011
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14: Association of BRCA1 and BRCA2 mutations with survival, chemotherapy sensitivity, and gene mutator phenotype in patients with ovarian cancer. 2011
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15: Variation in the BRCA2 gene in a child with medulloblastoma and a family history of breast cancer. 2011
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16: Frequent Germline Mutation in the BRCA2 Gene in Esophageal Squamous Cell Carcinoma Patients from a Low-risk Chinese Population. 2011
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17: BRCA2 is required for the maintenance of telomere homeostasis. 2011
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18: The Leu33Pro polymorphism in the ITGB3 gene does not modify BRCA1/2-associated breast or ovarian cancer risks: results from a multicenter study among 15,542 BRCA1 and BRCA2 mutation carriers. 2010
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19: Altered gene expression in morphologically normal epithelial cells from heterozygous carriers of BRCA1 or BRCA2 mutations. 2010
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20: Gene methylation in breast ductal fluid from BRCA1 and BRCA2 mutation carriers. 2010
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21: Screening for genomic rearrangements in BRCA1 and BRCA2 genes in Czech high-risk breast/ovarian cancer patients: high proportion of population specific alterations in BRCA1 gene. 2010
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22: Identification of a new complex deleterious mutation in exon 18 of the BRCA2 gene in a hereditary male/female breast cancer family. 2010
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23: Characteristics, treatment, and outcome of breast cancers diagnosed in BRCA1 and BRCA2 gene mutation carriers in intensive screening programs including magnetic resonance imaging. 2010
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24: Four new cases of double heterozygosity for BRCA1 and BRCA2 gene mutations: clinical, pathological, and family characteristics. 2010
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25: Novel germline mutations in BRCA2 gene among breast and breast-ovarian cancer families from Poland. 2010
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26: BRCA1 and BRCA2: breast/ovarian cancer susceptibility gene products and participants in DNA double strand break repair. 2010
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27: CCND1 and ZNF217 gene amplification is equally frequent in BRCA1 and BRCA2 associated and non-BRCA breast cancer. 2010
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28: Predicting BRCA1 and BRCA2 gene mutation carriers: comparison of PENN II model to previous study. 2010
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29: Slip-sliding away: serial changes and homoplasy in repeat number in the Drosophila yakuba homolog of human cancer susceptibility gene BRCA2. 2010
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30: A new mutation of BRCA2 gene in an Italian healthy woman with familial breast cancer history. 2010
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31: Allelic Imbalance in BRCA1 and BRCA2 Gene Expression and Familial Ovarian Cancer. 2010
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32: Arabidopsis BRCA2 and RAD51 proteins are specifically involved in defense gene transcription during plant immune responses. 2010
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33: Breast and ovarian cancer risk perception after prophylactic salpingo-oophorectomy due to an inherited mutation in the BRCA1 or BRCA2 gene. 2009
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34: Age at onset of bilateral breast cancer, the presence of hereditary BRCA1, BRCA2, CHEK2 gene mutations and positive family history of cancer. 2009
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35: Prevalence of BRCA1 and BRCA2 gene mutations in families with medium and high risk of breast and ovarian cancer in Brazil. 2009
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36: Detecting BRCA2 protein truncation in tissue biopsies to identify breast cancers that arise in BRCA2 gene mutation carriers. 2009
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37: Case report: de novo BRCA2 gene mutation in a 35-year-old woman with breast cancer. 2009
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38: Association between polymorphisms of the brca2 gene and clinical parameters in breast cancer. 2009
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