-
1
-
-
68249087607
-
Semantic similarity in biomedical ontologies
-
Pesquita C, Faria D, Falcao AO, Lord P, Couto FM. Semantic similarity in biomedical ontologies. PLoS Comput Biol. 2009; 5(7):1000443.
-
(2009)
PLoS Comput Biol
, vol.5
, Issue.7
, pp. 1000443
-
-
Pesquita, C.1
Faria, D.2
Falcao, A.O.3
Lord, P.4
Couto, F.M.5
-
2
-
-
84984979145
-
-
In: Carugo O, Eisenhaber F, (eds). New York: Springer
-
Hoehndorf R, Gkoutos GV, Schofield PN. In: Carugo O, Eisenhaber F, (eds).Datamining with Ontologies. New York: Springer; 2016, pp. 385-97.
-
(2016)
Datamining with Ontologies
, pp. 385-397
-
-
Hoehndorf, R.1
Gkoutos, G.V.2
Schofield, P.N.3
-
3
-
-
84963491282
-
Semantic similarity from natural language and ontology analysis
-
Harispe S, et al. Semantic similarity from natural language and ontology analysis. Synth Lect Hum Lang Technol. 2015; 8(1):1-254.
-
(2015)
Synth Lect Hum Lang Technol
, vol.8
, Issue.1
, pp. 1-254
-
-
Harispe, S.1
-
4
-
-
78049446066
-
Semantic similarity for automatic classification of chemical compounds
-
Ferreira JD, Couto FM. Semantic similarity for automatic classification of chemical compounds. PLoS Comput Biol. 2010; 6(9):1000937. doi: 10.1371/journal.pcbi.1000937.
-
(2010)
PLoS Comput Biol
, vol.6
, Issue.9
, pp. 1000937
-
-
Ferreira, J.D.1
Couto, F.M.2
-
5
-
-
84930038930
-
Discovering novel protein-protein interactions by measuring the protein semantic similarity from the biomedical literature
-
Chiang JH, Ju JH. Discovering novel protein-protein interactions by measuring the protein semantic similarity from the biomedical literature. J Bioinform Comput Biol. 2014; 12(06):1442008.
-
(2014)
J Bioinform Comput Biol
, vol.12
, Issue.6
, pp. 1442008
-
-
Chiang, J.H.1
Ju, J.H.2
-
6
-
-
80054087451
-
Phenomenet: a whole-phenome approach to disease gene discovery
-
Hoehndorf R, Schofield PN, Gkoutos GV. Phenomenet: a whole-phenome approach to disease gene discovery. Nucleic Acids Res. 2011; 39(18):119-9.
-
(2011)
Nucleic Acids Res
, vol.39
, Issue.18
, pp. 119-119
-
-
Hoehndorf, R.1
Schofield, P.N.2
Gkoutos, G.V.3
-
7
-
-
70350474767
-
Clinical diagnostics in human genetics with semantic similarity searches in ontologies
-
Köhler S, et al. Clinical diagnostics in human genetics with semantic similarity searches in ontologies. Am J Hum Genet. 2009; 85(4):457-64.
-
(2009)
Am J Hum Genet
, vol.85
, Issue.4
, pp. 457-464
-
-
Köhler, S.1
-
8
-
-
33947308770
-
Finding genomic ontology terms in text using evidence content
-
Couto FM, Silva MJ, Coutinho PM. Finding genomic ontology terms in text using evidence content. BMC Bioinforma. 2005; (6 Suppl 1):S21.
-
(2005)
BMC Bioinforma
, vol.6
, pp. S21
-
-
Couto, F.M.1
Silva, M.J.2
Coutinho, P.M.3
-
9
-
-
33646358998
-
Prediction of yeast protein-protein interaction network: insights from the gene ontology and annotations
-
Wu X, et al. Prediction of yeast protein-protein interaction network: insights from the gene ontology and annotations. Nucleic Acids Res. 2006; 34(7):2137-50.
-
(2006)
Nucleic Acids Res
, vol.34
, Issue.7
, pp. 2137-2150
-
-
Wu, X.1
-
10
-
-
58149312546
-
Evaluation of go-based functional similarity measures using s. cerevisiae protein interaction and expression profile data
-
Xu T, Du L, Zhou Y. Evaluation of go-based functional similarity measures using s. cerevisiae protein interaction and expression profile data. BMC Bioinforma. 2008; 9(1):1-10.
-
(2008)
BMC Bioinforma
, vol.9
, Issue.1
, pp. 1-10
-
-
Xu, T.1
Du, L.2
Zhou, Y.3
-
11
-
-
84897695340
-
The semantic measures library and toolkit: fast computation of semantic similarity and relatedness using biomedical ontologies
-
Harispe S, et al. The semantic measures library and toolkit: fast computation of semantic similarity and relatedness using biomedical ontologies. Bioinformatics. 2014; 30(5):740-2.
-
(2014)
Bioinformatics
, vol.30
, Issue.5
, pp. 740-742
-
-
Harispe, S.1
-
12
-
-
84861179768
-
"Guilt by Association" is the exception rather than the rule in gene networks
-
Gillis J, Pavlidis P. "Guilt by Association" is the exception rather than the rule in gene networks. PLoS Comput Biol. 2012; 8(3):1002444.
-
(2012)
PLoS Comput Biol
, vol.8
, Issue.3
, pp. 1002444
-
-
Gillis, J.1
Pavlidis, P.2
-
13
-
-
0034069495
-
Gene ontology: tool for the unification of biology
-
Ashburner M, et al. Gene ontology: tool for the unification of biology. Nat Genet. 2000; 25(1):25-9.
-
(2000)
Nat Genet
, vol.25
, Issue.1
, pp. 25-29
-
-
Ashburner, M.1
-
14
-
-
84891749517
-
The human phenotype ontology project: linking molecular biology and disease through phenotype data
-
Köhler S, Doelken SC, Mungall CJ, Bauer S, Firth HV, Bailleul-Forestier I, Black GCM, Brown DL, Brudno M, Campbell J, FitzPatrick DR, Eppig JT, Jackson AP, Freson K, Girdea M, Helbig I, Hurst JA, Jähn J, Jackson LG, Kelly AM, Ledbetter DH, Mansour S, Martin CL, Moss C, Mumford A, Ouwehand WH, Park SM, Riggs ER, Scott RH, Sisodiya S, Vooren SV, Wapner RJ, Wilkie AOM, Wright CF, Vulto-van Silfhout AT, Leeuw Nd, de Vries BBA, Washingthon NL, Smith CL, Westerfield M, Schofield P, Ruef BJ, Gkoutos GV, Haendel M, Smedley D, Lewis SE, Robinson PN. The human phenotype ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res. 2014; 42(D1):966-74.
-
(2014)
Nucleic Acids Res
, vol.42
, Issue.D1
, pp. 966-974
-
-
Köhler, S.1
Doelken, S.C.2
Mungall, C.J.3
Bauer, S.4
Firth, H.V.5
Bailleul-Forestier, I.6
Black, G.C.M.7
Brown, D.L.8
Brudno, M.9
Campbell, J.10
FitzPatrick, D.R.11
Eppig, J.T.12
Jackson, A.P.13
Freson, K.14
Girdea, M.15
Helbig, I.16
Hurst, J.A.17
Jähn, J.18
Jackson, L.G.19
Kelly, A.M.20
Ledbetter, D.H.21
Mansour, S.22
Martin, C.L.23
Moss, C.24
Mumford, A.25
Ouwehand, W.H.26
Park, S.M.27
Riggs, E.R.28
Scott, R.H.29
Sisodiya, S.30
Vooren, S.V.31
Wapner, R.J.32
Wilkie, A.O.M.33
Wright, C.F.34
Vulto-van Silfhout, A.T.35
Leeuw, N.36
de Vries, B.B.A.37
Washingthon, N.L.38
Smith, C.L.39
Westerfield, M.40
Schofield, P.41
Ruef, B.J.42
Gkoutos, G.V.43
Haendel, M.44
Smedley, D.45
Lewis, S.E.46
Robinson, P.N.47
more..
-
15
-
-
79952022327
-
An ontology-based measure to compute semantic similarity in biomedicine
-
Batet M, Sánchez D, Valls A. An ontology-based measure to compute semantic similarity in biomedicine. J Biomed Inform. 2011; 44(1):118-25. Ontologies for Clinical and Translational Research.
-
(2011)
J Biomed Inform
, vol.44
, Issue.1
, pp. 118-125
-
-
Batet, M.1
Sánchez, D.2
Valls, A.3
-
16
-
-
22044433259
-
Relations in biomedical ontologies
-
Smith B, Ceusters W, Klagges B, Köhler J, Kumar A, Lomax J, Mungall C, Neuhaus F, Rector AL, Rosse C. Relations in biomedical ontologies. Genome Biol. 2005; 6(5):46.
-
(2005)
Genome Biol
, vol.6
, Issue.5
, pp. 46
-
-
Smith, B.1
Ceusters, W.2
Klagges, B.3
Köhler, J.4
Kumar, A.5
Lomax, J.6
Mungall, C.7
Neuhaus, F.8
Rector, A.L.9
Rosse, C.10
-
17
-
-
77956477258
-
Relations as patterns: Bridging the gap between OBO and OWL
-
Hoehndorf R, Oellrich A, Dumontier M, Kelso J, Rebholz-Schuhmann D, Herre H. Relations as patterns: Bridging the gap between OBO and OWL. BMC Bioinforma. 2010; 11(1):441.
-
(2010)
BMC Bioinforma
, vol.11
, Issue.1
, pp. 441
-
-
Hoehndorf, R.1
Oellrich, A.2
Dumontier, M.3
Kelso, J.4
Rebholz-Schuhmann, D.5
Herre, H.6
-
18
-
-
23744500479
-
SciPy: Open source scientific tools for Python
-
Accessed 2016-04-06
-
Jones E, Oliphant T, Peterson P, et al. SciPy: Open source scientific tools for Python. 2001. http://www.scipy.org/. Accessed 2016-04-06.
-
(2001)
-
-
Jones, E.1
Oliphant, T.2
Peterson, P.3
-
19
-
-
33644873184
-
BioGRID: a general repository for interaction datasets
-
Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. BioGRID: a general repository for interaction datasets. Nucleic Acids Res. 2006; 34(suppl 1):535-9. doi: 10.1093/nar/gkj109. http://nar.oxfordjournals.org/content/34/suppl_1/D535.full.pdf+html.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 535-539
-
-
Stark, C.1
Breitkreutz, B.J.2
Reguly, T.3
Boucher, L.4
Breitkreutz, A.5
Tyers, M.6
-
20
-
-
0002016474
-
Semantic similarity in a taxonomy: An Information-Based measure and its application to problems of ambiguity in natural language
-
Resnik P. Semantic similarity in a taxonomy: An Information-Based measure and its application to problems of ambiguity in natural language. J Artif Intell Res. 1999; 11:95-130.
-
(1999)
J Artif Intell Res
, vol.11
, pp. 95-130
-
-
Resnik, P.1
-
21
-
-
33646023117
-
An introduction to ROC analysis
-
Fawcett T. An introduction to ROC analysis. Pattern Recogn Lett. 2006; 27(8):861-74. doi: 10.1016/j.patrec.2005.10.010.
-
(2006)
Pattern Recogn Lett
, vol.27
, Issue.8
, pp. 861-874
-
-
Fawcett, T.1
-
22
-
-
84864072163
-
Disease model curation improvements at mouse genome informatics
-
Bello SM, Richardson JE, Davis AP, Wiegers TC, Mattingly CJ, Dolan ME, Smith CL, Blake JA, Eppig JT. Disease model curation improvements at mouse genome informatics. Database. 2012; 2012:63.
-
(2012)
Database
, vol.2012
, pp. 63
-
-
Bello, S.M.1
Richardson, J.E.2
Davis, A.P.3
Wiegers, T.C.4
Mattingly, C.J.5
Dolan, M.E.6
Smith, C.L.7
Blake, J.A.8
Eppig, J.T.9
-
23
-
-
47149083877
-
Metrics for GO based protein semantic similarity: a systematic evaluation
-
Pesquita C, Faria D, Bastos H, Ferreira AEN, Falcão AO, Couto FM. Metrics for GO based protein semantic similarity: a systematic evaluation. BMC Bioinforma. 2008; (9 Suppl 5):S4. doi: 10.1186/1471-2105-9-S5-S4.
-
(2008)
BMC Bioinforma.
, vol.9
, pp. S4
-
-
Pesquita, C.1
Faria, D.2
Bastos, H.3
Ferreira, A.E.N.4
Falcão, A.O.5
Couto, F.M.6
-
24
-
-
49949096013
-
Gene ontology term overlap as a measure of gene functional similarity
-
Mistry M, Pavlidis P. Gene ontology term overlap as a measure of gene functional similarity. BMC Bioinforma. 2008; 9(1):1-11.
-
(2008)
BMC Bioinforma
, vol.9
, Issue.1
, pp. 1-11
-
-
Mistry, M.1
Pavlidis, P.2
-
25
-
-
77956497662
-
Improving disease gene prioritization using the semantic similarity of gene ontology terms
-
Schlicker A, Lengauer T, Albrecht M. Improving disease gene prioritization using the semantic similarity of gene ontology terms. Bioinformatics. 2010; 26(18):561-7.
-
(2010)
Bioinformatics
, vol.26
, Issue.18
, pp. 561-567
-
-
Schlicker, A.1
Lengauer, T.2
Albrecht, M.3
-
26
-
-
84875449584
-
An integrative, translational approach to understanding rare and orphan genetically based diseases
-
Hoehndorf R, Schofield PN, Gkoutos GV. An integrative, translational approach to understanding rare and orphan genetically based diseases. Interface Focus. 2013; 3(2):20120055. doi: 10.1098/rsfs.2012.0055.
-
(2013)
Interface Focus
, vol.3
, Issue.2
, pp. 20120055
-
-
Hoehndorf, R.1
Schofield, P.N.2
Gkoutos, G.V.3
-
27
-
-
84946224963
-
Improving chemical entity recognition through h-index based semantic similarity
-
Lamurias A, Ferreira JD, Couto FM. Improving chemical entity recognition through h-index based semantic similarity. J Cheminformatics. 2015; 7(1):13. doi: 10.1186/1758-2946-7-S1-S13.
-
(2015)
J Cheminformatics
, vol.7
, Issue.1
, pp. 13
-
-
Lamurias, A.1
Ferreira, J.D.2
Couto, F.M.3
-
28
-
-
84885997808
-
Exploiting disjointness axioms to improve semantic similarity measures
-
Ferreira JD, Hastings J, Couto FM. Exploiting disjointness axioms to improve semantic similarity measures. Bioinformatics. 2013; 29(21):2781-787. doi: 10.1093/bioinformatics/btt491. http://bioinformatics.oxfordjournals.org/content/29/21/2781.full.pdf+html.
-
(2013)
Bioinformatics
, vol.29
, Issue.21
, pp. 2781-2787
-
-
Ferreira, J.D.1
Hastings, J.2
Couto, F.M.3
-
29
-
-
81055149924
-
Exact score distribution computation for ontological similarity searches
-
Schulz MH, Köhler S, Bauer S, Robinson PN. Exact score distribution computation for ontological similarity searches. BMC Bioinforma. 2011; 12(1):441. doi: 10.1186/1471-2105-12-441.
-
(2011)
BMC Bioinforma
, vol.12
, Issue.1
, pp. 441
-
-
Schulz, M.H.1
Köhler, S.2
Bauer, S.3
Robinson, P.N.4
|