Document (#30261)

Author

Toldo, L.
Rippmann, F.

Title

Integrated bioinformatics application for automated target discovery.

Source

Journal of the American Society for Information Science and Technology. 56(2005) no.5, S.483-492

Year

2005

Abstract

In this article we present an in silico method that automatically assigns putative functions to DNA sequences. The annotations are at an increasingly conceptual level, up to identifying general biomedical fields to which the sequences could contribute. This bioinformatics data-mining system makes substantial use of several resources: a locally stored MEDLINE® database; a manually built classification system; the MeSH® taxonomy; relational technology; and bioinformatics methods. Knowledge is generated from various data sources by using well-defined semantics, and by exploiting direct links between them. A two-dimensional Concept Map(TM) displays the knowledge graph, which allows causal connections to be followed. The use of this method has been valuable and has saved considerable time in our in-house projects, and can be generally exploited for any sequence-annotation or knowledge-condensation task.

Footnote

Beitrag in einem special issue on bioinformatics

Field

Molekularbiologie

Similar documents (content)

1. Rodríguez, A.; Carazo, J.M.; Trelles-Salazar, O.: Mining association rules from biological databases (2005) 0.29

   0.29403514 = sum of:
     0.29403514 = product of:
       0.91885984 = sum of:
         0.013193 = weight(abstract_txt:data in 5261) [ClassicSimilarity], result of:
           0.013193 = score(doc=5261,freq=1.0), product of:
             0.06326918 = queryWeight, product of:
               1.0105342 = boost
               3.3363478 = idf(docFreq=4274, maxDocs=44218)
               0.01876592 = queryNorm
             0.20852174 = fieldWeight in 5261, product of:
               1.0 = tf(freq=1.0), with freq of:
                 1.0 = termFreq=1.0
               3.3363478 = idf(docFreq=4274, maxDocs=44218)
               0.0625 = fieldNorm(doc=5261)
         0.079742625 = weight(abstract_txt:sequence in 5261) [ClassicSimilarity], result of:
           0.079742625 = score(doc=5261,freq=2.0), product of:
             0.1322524 = queryWeight, product of:
               1.0330983 = boost
               6.82169 = idf(docFreq=130, maxDocs=44218)
               0.01876592 = queryNorm
             0.6029579 = fieldWeight in 5261, product of:
               1.4142135 = tf(freq=2.0), with freq of:
                 2.0 = termFreq=2.0
               6.82169 = idf(docFreq=130, maxDocs=44218)
               0.0625 = fieldNorm(doc=5261)
         0.010588082 = weight(abstract_txt:this in 5261) [ClassicSimilarity], result of:
           0.010588082 = score(doc=5261,freq=2.0), product of:
             0.04964343 = queryWeight, product of:
               1.0963051 = boost
               2.4130175 = idf(docFreq=10762, maxDocs=44218)
               0.01876592 = queryNorm
             0.21328263 = fieldWeight in 5261, product of:
               1.4142135 = tf(freq=2.0), with freq of:
                 2.0 = termFreq=2.0
               2.4130175 = idf(docFreq=10762, maxDocs=44218)
               0.0625 = fieldNorm(doc=5261)
         0.07099404 = weight(abstract_txt:annotations in 5261) [ClassicSimilarity], result of:
           0.07099404 = score(doc=5261,freq=1.0), product of:
             0.15420595 = queryWeight, product of:
               1.1155536 = boost
               7.3661537 = idf(docFreq=75, maxDocs=44218)
               0.01876592 = queryNorm
             0.4603846 = fieldWeight in 5261, product of:
               1.0 = tf(freq=1.0), with freq of:
                 1.0 = termFreq=1.0
               7.3661537 = idf(docFreq=75, maxDocs=44218)
               0.0625 = fieldNorm(doc=5261)
         0.032392323 = weight(abstract_txt:method in 5261) [ClassicSimilarity], result of:
           0.032392323 = score(doc=5261,freq=1.0), product of:
             0.1151484 = queryWeight, product of:
               1.3632762 = boost
               4.50095 = idf(docFreq=1333, maxDocs=44218)
               0.01876592 = queryNorm
             0.28130937 = fieldWeight in 5261, product of:
               1.0 = tf(freq=1.0), with freq of:
                 1.0 = termFreq=1.0
               4.50095 = idf(docFreq=1333, maxDocs=44218)
               0.0625 = fieldNorm(doc=5261)
         0.033794343 = weight(abstract_txt:knowledge in 5261) [ClassicSimilarity], result of:
           0.033794343 = score(doc=5261,freq=2.0), product of:
             0.107616685 = queryWeight, product of:
               1.6141368 = boost
               3.5527887 = idf(docFreq=3442, maxDocs=44218)
               0.01876592 = queryNorm
             0.31402513 = fieldWeight in 5261, product of:
               1.4142135 = tf(freq=2.0), with freq of:
                 2.0 = termFreq=2.0
               3.5527887 = idf(docFreq=3442, maxDocs=44218)
               0.0625 = fieldNorm(doc=5261)
         0.20525566 = weight(abstract_txt:sequences in 5261) [ClassicSimilarity], result of:
           0.20525566 = score(doc=5261,freq=2.0), product of:
             0.312956 = queryWeight, product of:
               2.2474837 = boost
               7.4202213 = idf(docFreq=71, maxDocs=44218)
               0.01876592 = queryNorm
             0.6558611 = fieldWeight in 5261, product of:
               1.4142135 = tf(freq=2.0), with freq of:
                 2.0 = termFreq=2.0
               7.4202213 = idf(docFreq=71, maxDocs=44218)
               0.0625 = fieldNorm(doc=5261)
         0.4728998 = weight(abstract_txt:bioinformatics in 5261) [ClassicSimilarity], result of:
           0.4728998 = score(doc=5261,freq=2.0), product of:
             0.6249276 = queryWeight, product of:
               3.8896933 = boost
               8.561393 = idf(docFreq=22, maxDocs=44218)
               0.01876592 = queryNorm
             0.75672734 = fieldWeight in 5261, product of:
               1.4142135 = tf(freq=2.0), with freq of:
                 2.0 = termFreq=2.0
               8.561393 = idf(docFreq=22, maxDocs=44218)
               0.0625 = fieldNorm(doc=5261)
       0.32 = coord(8/25)
   

2. Shachak, A.: Diffusion pattern of the use of genomic databases and analysis of biological sequences from 1970-2003 : bibliographic record analysis of 12 journals (2006) 0.24

   0.2437191 = sum of:
     0.2437191 = product of:
       1.0154963 = sum of:
         0.01865772 = weight(abstract_txt:data in 4906) [ClassicSimilarity], result of:
           0.01865772 = score(doc=4906,freq=2.0), product of:
             0.06326918 = queryWeight, product of:
               1.0105342 = boost
               3.3363478 = idf(docFreq=4274, maxDocs=44218)
               0.01876592 = queryNorm
             0.29489428 = fieldWeight in 4906, product of:
               1.4142135 = tf(freq=2.0), with freq of:
                 2.0 = termFreq=2.0
               3.3363478 = idf(docFreq=4274, maxDocs=44218)
               0.0625 = fieldNorm(doc=4906)
         0.05582694 = weight(abstract_txt:medline in 4906) [ClassicSimilarity], result of:
           0.05582694 = score(doc=4906,freq=1.0), product of:
             0.13137591 = queryWeight, product of:
               1.0296693 = boost
               6.7990475 = idf(docFreq=133, maxDocs=44218)
               0.01876592 = queryNorm
             0.42494047 = fieldWeight in 4906, product of:
               1.0 = tf(freq=1.0), with freq of:
                 1.0 = termFreq=1.0
               6.7990475 = idf(docFreq=133, maxDocs=44218)
               0.0625 = fieldNorm(doc=4906)
         0.056386553 = weight(abstract_txt:sequence in 4906) [ClassicSimilarity], result of:
           0.056386553 = score(doc=4906,freq=1.0), product of:
             0.1322524 = queryWeight, product of:
               1.0330983 = boost
               6.82169 = idf(docFreq=130, maxDocs=44218)
               0.01876592 = queryNorm
             0.42635563 = fieldWeight in 4906, product of:
               1.0 = tf(freq=1.0), with freq of:
                 1.0 = termFreq=1.0
               6.82169 = idf(docFreq=130, maxDocs=44218)
               0.0625 = fieldNorm(doc=4906)
         0.010588082 = weight(abstract_txt:this in 4906) [ClassicSimilarity], result of:
           0.010588082 = score(doc=4906,freq=2.0), product of:
             0.04964343 = queryWeight, product of:
               1.0963051 = boost
               2.4130175 = idf(docFreq=10762, maxDocs=44218)
               0.01876592 = queryNorm
             0.21328263 = fieldWeight in 4906, product of:
               1.4142135 = tf(freq=2.0), with freq of:
                 2.0 = termFreq=2.0
               2.4130175 = idf(docFreq=10762, maxDocs=44218)
               0.0625 = fieldNorm(doc=4906)
         0.20525566 = weight(abstract_txt:sequences in 4906) [ClassicSimilarity], result of:
           0.20525566 = score(doc=4906,freq=2.0), product of:
             0.312956 = queryWeight, product of:
               2.2474837 = boost
               7.4202213 = idf(docFreq=71, maxDocs=44218)
               0.01876592 = queryNorm
             0.6558611 = fieldWeight in 4906, product of:
               1.4142135 = tf(freq=2.0), with freq of:
                 2.0 = termFreq=2.0
               7.4202213 = idf(docFreq=71, maxDocs=44218)
               0.0625 = fieldNorm(doc=4906)
         0.6687813 = weight(abstract_txt:bioinformatics in 4906) [ClassicSimilarity], result of:
           0.6687813 = score(doc=4906,freq=4.0), product of:
             0.6249276 = queryWeight, product of:
               3.8896933 = boost
               8.561393 = idf(docFreq=22, maxDocs=44218)
               0.01876592 = queryNorm
             1.0701741 = fieldWeight in 4906, product of:
               2.0 = tf(freq=4.0), with freq of:
                 4.0 = termFreq=4.0
               8.561393 = idf(docFreq=22, maxDocs=44218)
               0.0625 = fieldNorm(doc=4906)
       0.24 = coord(6/25)
   

3. Song, M.; Kim, S.Y.; Zhang, G.; Ding, Y.; Chambers, T.: Productivity and influence in bioinformatics : a bibliometric analysis using PubMed central (2014) 0.14

   0.13541439 = sum of:
     0.13541439 = product of:
       0.84634 = sum of:
         0.028563682 = weight(abstract_txt:data in 1202) [ClassicSimilarity], result of:
           0.028563682 = score(doc=1202,freq=3.0), product of:
             0.06326918 = queryWeight, product of:
               1.0105342 = boost
               3.3363478 = idf(docFreq=4274, maxDocs=44218)
               0.01876592 = queryNorm
             0.4514628 = fieldWeight in 1202, product of:
               1.7320508 = tf(freq=3.0), with freq of:
                 3.0 = termFreq=3.0
               3.3363478 = idf(docFreq=4274, maxDocs=44218)
               0.078125 = fieldNorm(doc=1202)
         0.08056419 = weight(abstract_txt:biomedical in 1202) [ClassicSimilarity], result of:
           0.08056419 = score(doc=1202,freq=1.0), product of:
             0.14457989 = queryWeight, product of:
               1.0801743 = boost
               7.132539 = idf(docFreq=95, maxDocs=44218)
               0.01876592 = queryNorm
             0.5572296 = fieldWeight in 1202, product of:
               1.0 = tf(freq=1.0), with freq of:
                 1.0 = termFreq=1.0
               7.132539 = idf(docFreq=95, maxDocs=44218)
               0.078125 = fieldNorm(doc=1202)
         0.013235102 = weight(abstract_txt:this in 1202) [ClassicSimilarity], result of:
           0.013235102 = score(doc=1202,freq=2.0), product of:
             0.04964343 = queryWeight, product of:
               1.0963051 = boost
               2.4130175 = idf(docFreq=10762, maxDocs=44218)
               0.01876592 = queryNorm
             0.2666033 = fieldWeight in 1202, product of:
               1.4142135 = tf(freq=2.0), with freq of:
                 2.0 = termFreq=2.0
               2.4130175 = idf(docFreq=10762, maxDocs=44218)
               0.078125 = fieldNorm(doc=1202)
         0.723977 = weight(abstract_txt:bioinformatics in 1202) [ClassicSimilarity], result of:
           0.723977 = score(doc=1202,freq=3.0), product of:
             0.6249276 = queryWeight, product of:
               3.8896933 = boost
               8.561393 = idf(docFreq=22, maxDocs=44218)
               0.01876592 = queryNorm
             1.1584975 = fieldWeight in 1202, product of:
               1.7320508 = tf(freq=3.0), with freq of:
                 3.0 = termFreq=3.0
               8.561393 = idf(docFreq=22, maxDocs=44218)
               0.078125 = fieldNorm(doc=1202)
       0.16 = coord(4/25)
   

4. Fenstermacher, D.A.: Introduction to bioinformatics. (2005) 0.13

   0.13123477 = sum of:
     0.13123477 = product of:
       0.8202173 = sum of:
         0.03231612 = weight(abstract_txt:data in 5257) [ClassicSimilarity], result of:
           0.03231612 = score(doc=5257,freq=6.0), product of:
             0.06326918 = queryWeight, product of:
               1.0105342 = boost
               3.3363478 = idf(docFreq=4274, maxDocs=44218)
               0.01876592 = queryNorm
             0.5107719 = fieldWeight in 5257, product of:
               2.4494898 = tf(freq=6.0), with freq of:
                 6.0 = termFreq=6.0
               3.3363478 = idf(docFreq=4274, maxDocs=44218)
               0.0625 = fieldNorm(doc=5257)
         0.11163301 = weight(abstract_txt:biomedical in 5257) [ClassicSimilarity], result of:
           0.11163301 = score(doc=5257,freq=3.0), product of:
             0.14457989 = queryWeight, product of:
               1.0801743 = boost
               7.132539 = idf(docFreq=95, maxDocs=44218)
               0.01876592 = queryNorm
             0.77211994 = fieldWeight in 5257, product of:
               1.7320508 = tf(freq=3.0), with freq of:
                 3.0 = termFreq=3.0
               7.132539 = idf(docFreq=95, maxDocs=44218)
               0.0625 = fieldNorm(doc=5257)
         0.007486904 = weight(abstract_txt:this in 5257) [ClassicSimilarity], result of:
           0.007486904 = score(doc=5257,freq=1.0), product of:
             0.04964343 = queryWeight, product of:
               1.0963051 = boost
               2.4130175 = idf(docFreq=10762, maxDocs=44218)
               0.01876592 = queryNorm
             0.1508136 = fieldWeight in 5257, product of:
               1.0 = tf(freq=1.0), with freq of:
                 1.0 = termFreq=1.0
               2.4130175 = idf(docFreq=10762, maxDocs=44218)
               0.0625 = fieldNorm(doc=5257)
         0.6687813 = weight(abstract_txt:bioinformatics in 5257) [ClassicSimilarity], result of:
           0.6687813 = score(doc=5257,freq=4.0), product of:
             0.6249276 = queryWeight, product of:
               3.8896933 = boost
               8.561393 = idf(docFreq=22, maxDocs=44218)
               0.01876592 = queryNorm
             1.0701741 = fieldWeight in 5257, product of:
               2.0 = tf(freq=4.0), with freq of:
                 4.0 = termFreq=4.0
               8.561393 = idf(docFreq=22, maxDocs=44218)
               0.0625 = fieldNorm(doc=5257)
       0.16 = coord(4/25)
   

5. Huang, H.; Andrews, J.; Tang, J.: Citation characterization and impact normalization in bioinformatics journals (2012) 0.13

   0.12676741 = sum of:
     0.12676741 = product of:
       0.79229635 = sum of:
         0.013193 = weight(abstract_txt:data in 69) [ClassicSimilarity], result of:
           0.013193 = score(doc=69,freq=1.0), product of:
             0.06326918 = queryWeight, product of:
               1.0105342 = boost
               3.3363478 = idf(docFreq=4274, maxDocs=44218)
               0.01876592 = queryNorm
             0.20852174 = fieldWeight in 69, product of:
               1.0 = tf(freq=1.0), with freq of:
                 1.0 = termFreq=1.0
               3.3363478 = idf(docFreq=4274, maxDocs=44218)
               0.0625 = fieldNorm(doc=69)
         0.007486904 = weight(abstract_txt:this in 69) [ClassicSimilarity], result of:
           0.007486904 = score(doc=69,freq=1.0), product of:
             0.04964343 = queryWeight, product of:
               1.0963051 = boost
               2.4130175 = idf(docFreq=10762, maxDocs=44218)
               0.01876592 = queryNorm
             0.1508136 = fieldWeight in 69, product of:
               1.0 = tf(freq=1.0), with freq of:
                 1.0 = termFreq=1.0
               2.4130175 = idf(docFreq=10762, maxDocs=44218)
               0.0625 = fieldNorm(doc=69)
         0.02389621 = weight(abstract_txt:knowledge in 69) [ClassicSimilarity], result of:
           0.02389621 = score(doc=69,freq=1.0), product of:
             0.107616685 = queryWeight, product of:
               1.6141368 = boost
               3.5527887 = idf(docFreq=3442, maxDocs=44218)
               0.01876592 = queryNorm
             0.2220493 = fieldWeight in 69, product of:
               1.0 = tf(freq=1.0), with freq of:
                 1.0 = termFreq=1.0
               3.5527887 = idf(docFreq=3442, maxDocs=44218)
               0.0625 = fieldNorm(doc=69)
         0.74772024 = weight(abstract_txt:bioinformatics in 69) [ClassicSimilarity], result of:
           0.74772024 = score(doc=69,freq=5.0), product of:
             0.6249276 = queryWeight, product of:
               3.8896933 = boost
               8.561393 = idf(docFreq=22, maxDocs=44218)
               0.01876592 = queryNorm
             1.196491 = fieldWeight in 69, product of:
               2.236068 = tf(freq=5.0), with freq of:
                 5.0 = termFreq=5.0
               8.561393 = idf(docFreq=22, maxDocs=44218)
               0.0625 = fieldNorm(doc=69)
       0.16 = coord(4/25)