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Volumn 55, Issue 3, 2015, Pages 510-528

New publicly available chemical query language, CSRML, to support chemotype representations for application to data mining and modeling

Author keywords

[No Author keywords available]

Indexed keywords

APPLICATION PROGRAMS; ESSENTIAL OILS; HYPERTEXT SYSTEMS; KNOWLEDGE MANAGEMENT; MODELING LANGUAGES; MOLECULES; QUERY LANGUAGES; SPECIFICATIONS; XML;

EID: 84925436995     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci500667v     Document Type: Article
Times cited : (153)

References (74)
  • 1
  • 2
    • 0033217178 scopus 로고    scopus 로고
    • Implementation of a System for Reagent Selection and Library Enumeration, Profiling, and Design
    • Leach, A. R.; Bradshaw, J.; Green, D. V. S.; Hann, M. M.; Delany, J. J. Implementation of a System for Reagent Selection and Library Enumeration, Profiling, and Design J. Chem. Inf. Model. 1999, 39, 1161-1172
    • (1999) J. Chem. Inf. Model. , vol.39 , pp. 1161-1172
    • Leach, A.R.1    Bradshaw, J.2    Green, D.V.S.3    Hann, M.M.4    Delany, J.J.5
  • 3
    • 84879976551 scopus 로고    scopus 로고
    • Interaction Design of Generic Chemical Patterns
    • Schomburg, K. T.; Wetzer, L.; Rarey, M. Interaction Design of Generic Chemical Patterns Drug Discovery Today 2013, 18, 651-658
    • (2013) Drug Discovery Today , vol.18 , pp. 651-658
    • Schomburg, K.T.1    Wetzer, L.2    Rarey, M.3
  • 4
    • 0343869724 scopus 로고    scopus 로고
    • SYBYL Line Notation (SLN): A Versatile Language for Chemical Structure Representation
    • Ash, S.; Cline, M. A.; Homer, R. W.; Hurst, T.; Smith, G. B. SYBYL Line Notation (SLN): A Versatile Language for Chemical Structure Representation J. Chem. Inf. Model. 1997, 37, 71-79
    • (1997) J. Chem. Inf. Model. , vol.37 , pp. 71-79
    • Ash, S.1    Cline, M.A.2    Homer, R.W.3    Hurst, T.4    Smith, G.B.5
  • 5
    • 58149119670 scopus 로고    scopus 로고
    • SYBYL Line Notation (SLN): A Single Notation to Represent Chemical Structures, Queries, Reactions, and Virtual Libraries
    • Homer, R. W.; Swanson, J.; Jilek, R. J.; Hurst, T.; Clark, R. D. SYBYL Line Notation (SLN): A Single Notation To Represent Chemical Structures, Queries, Reactions, and Virtual Libraries J. Chem. Inf. Model. 2008, 48, 2294-2307
    • (2008) J. Chem. Inf. Model. , vol.48 , pp. 2294-2307
    • Homer, R.W.1    Swanson, J.2    Jilek, R.J.3    Hurst, T.4    Clark, R.D.5
  • 6
    • 84925448781 scopus 로고    scopus 로고
    • MDL Information Systems, Inc. (accessed Nov 2)
    • CTfile Formats. MDL Information Systems, Inc. http://accelrys.com/products/informatics/cheminformatics/ctfile-formats/no-fee.php (accessed Nov 2, 2014).
    • (2014) CTfile Formats
  • 7
    • 84925388493 scopus 로고    scopus 로고
    • PerkinElmer Inc. (accessed Nov 2)
    • ChemDraw. PerkinElmer Inc. http://www.cambridgesoft.com/Ensemble-for-Chemistry/ChemDraw/ (accessed Nov 2, 2014).
    • (2014) ChemDraw
  • 9
    • 84925409371 scopus 로고    scopus 로고
    • ChemAxon-cheminformatics platforms and desktop applications. (accessed Nov 2)
    • MarvinSketch. ChemAxon-cheminformatics platforms and desktop applications. http://www.chemaxon.com/products/marvin/marvinsketch/ (accessed Nov 2, 2014).
    • (2014) MarvinSketch
  • 12
    • 84870497766 scopus 로고    scopus 로고
    • Classification Models for Safe Drug Molecules
    • Methods in Molecular Biology; Springer: New York, Vol
    • Madan, A. K.; Bajaj, S.; Dureja, H. Classification Models for Safe Drug Molecules. Computational Toxicology Volume II; Methods in Molecular Biology; Springer: New York, 2013; Vol. 930, pp 99-124.
    • (2013) Computational Toxicology Volume II , vol.930 , pp. 99-124
    • Madan, A.K.1    Bajaj, S.2    Dureja, H.3
  • 13
    • 8644248268 scopus 로고    scopus 로고
    • Building Predictive Models for Protein Tyrosine Phosphatase 1B Inhibitors Based on Discriminating Structural Features by Reassembling Medicinal Chemistry Building Blocks
    • Yang, C.; Cross, K.; Myatt, G. J.; Blower, P. E.; Rathman, J. F. Building Predictive Models for Protein Tyrosine Phosphatase 1B Inhibitors Based on Discriminating Structural Features by Reassembling Medicinal Chemistry Building Blocks J. Med. Chem. 2004, 47, 5984-5994
    • (2004) J. Med. Chem. , vol.47 , pp. 5984-5994
    • Yang, C.1    Cross, K.2    Myatt, G.J.3    Blower, P.E.4    Rathman, J.F.5
  • 14
    • 0025863682 scopus 로고
    • Computer Prediction of Possible Toxic Action from Chemical Structure; The DEREK System
    • Sanderson, D. M.; Earnshaw, C. G. Computer Prediction of Possible Toxic Action from Chemical Structure; The DEREK System Human & Experimental Toxicology 1991, 10, 261-273
    • (1991) Human & Experimental Toxicology , vol.10 , pp. 261-273
    • Sanderson, D.M.1    Earnshaw, C.G.2
  • 15
    • 84867811626 scopus 로고    scopus 로고
    • Optimizing Predictive Performance of CASE Ultra Expert System Models Using the Applicability Domains of Individual Toxicity Alerts
    • Chakravarti, S. K.; Saiakhov, R. D.; Klopman, G. Optimizing Predictive Performance of CASE Ultra Expert System Models Using the Applicability Domains of Individual Toxicity Alerts J. Chem. Inf. Model. 2012, 52, 2609-2618
    • (2012) J. Chem. Inf. Model. , vol.52 , pp. 2609-2618
    • Chakravarti, S.K.1    Saiakhov, R.D.2    Klopman, G.3
  • 16
    • 84925382502 scopus 로고    scopus 로고
    • (accessed Nov 2)
    • Daylight > SMARTS Examples. http://www.daylight.com/dayhtml-tutorials/languages/smarts/smarts-examples.html#P (accessed Nov 2, 2014).
    • (2014) Daylight > SMARTS Examples
  • 19
    • 84865485155 scopus 로고    scopus 로고
    • ToxAlerts: A Web Server of Structural Alerts for Toxic Chemicals and Compounds with Potential Adverse Reactions
    • Sushko, I.; Salmina, E.; Potemkin, V. A.; Poda, G.; Tetko, I. V. ToxAlerts: A Web Server of Structural Alerts for Toxic Chemicals and Compounds with Potential Adverse Reactions J. Chem. Inf. Model. 2012, 52, 2310-2316
    • (2012) J. Chem. Inf. Model. , vol.52 , pp. 2310-2316
    • Sushko, I.1    Salmina, E.2    Potemkin, V.A.3    Poda, G.4    Tetko, I.V.5
  • 22
    • 84925387736 scopus 로고    scopus 로고
    • (accessed Nov 2)
    • KNIME. http://www.knime.org/ (accessed Nov 2, 2014).
    • (2014) KNIME
  • 23
    • 0034699054 scopus 로고    scopus 로고
    • A Universal Approach to Web-Based Chemistry Using XML and CML
    • Murray-Rust, P.; Rzepa, H. S.; Wright, M.; Zara, S. A Universal Approach to Web-Based Chemistry Using XML and CML Chem. Commun. 2000, 1471-1472
    • (2000) Chem. Commun. , pp. 1471-1472
    • Murray-Rust, P.1    Rzepa, H.S.2    Wright, M.3    Zara, S.4
  • 24
    • 33947478901 scopus 로고
    • The valence-shell electron-pair repulsion (VSEPR) theory of directed valency
    • Gillepsie, R. J. The valence-shell electron-pair repulsion (VSEPR) theory of directed valency J. Chem. Educ. 1963, 40, 295-301
    • (1963) J. Chem. Educ. , vol.40 , pp. 295-301
    • Gillepsie, R.J.1
  • 25
    • 84925383014 scopus 로고    scopus 로고
    • ToxPrint ChemoTypes. ChemoTyper Community Website. https://chemotyper.org/ (accessed Dec 19)
    • ToxPrint ChemoTypes. https://toxprint.org/; ChemoTyper Community Website. https://chemotyper.org/ (accessed Dec 19, 2014).
    • (2014)
  • 26
    • 84925383013 scopus 로고    scopus 로고
    • Java Architecture for XML Binding (JAXB). (accessed Nov 2)
    • Java Architecture for XML Binding (JAXB). http://www.oracle.com/technetwork/articles/javase/index-140168.html (accessed Nov 2, 2014).
    • (2014)
  • 28
    • 0004027344 scopus 로고    scopus 로고
    • 3 rd ed. Addison-Wesley: Reading, Mass, ISBN 0-201-88954-4 OCLC 59193992
    • Stroustrup, B. The C++ Programming Language, 3 rd ed.; Addison-Wesley: Reading, Mass, 1997; ISBN 0-201-88954-4 OCLC 59193992.
    • (1997) The C++ Programming Language
    • Stroustrup, B.1
  • 29
    • 84925383012 scopus 로고    scopus 로고
    • Xerces-C++ XML Parser. (accessed Nov 2)
    • Xerces-C++ XML Parser. https://xerces.apache.org/xerces-c/ (accessed Nov 2, 2014).
    • (2014)
  • 30
    • 84925383011 scopus 로고    scopus 로고
    • Apache License, Version 2.0. (accessed Nov 2)
    • Apache License, Version 2.0. https://www.apache.org/licenses/LICENSE-2.0.html (accessed Nov 2, 2014).
    • (2014)
  • 31
    • 84925383010 scopus 로고    scopus 로고
    • US FDA/Center for Drug Evaluation and Research. (accessed Nov 2)
    • US FDA/Center for Drug Evaluation and Research. http://www.accessdata.fda.gov/scripts/cder/drugsatfda/index.cfm (accessed Nov 2, 2014).
    • (2014)
  • 32
    • 0026319831 scopus 로고
    • Priority-Based Assessment of Food Additives Database of the U.S. Food and Drug Administration Center for Food Safety and Applied Nutrition
    • Benz, R. D.; Irausquin, H. Priority-Based Assessment of Food Additives Database of the U.S. Food and Drug Administration Center for Food Safety and Applied Nutrition Environ. Health Perspect. 1991, 96, 85-89
    • (1991) Environ. Health Perspect. , vol.96 , pp. 85-89
    • Benz, R.D.1    Irausquin, H.2
  • 33
    • 84925383009 scopus 로고    scopus 로고
    • National Toxicology Program - NTP. (accessed Nov 2)
    • National Toxicology Program - NTP. http://ntp.niehs.nih.gov/ (accessed Nov 2, 2014).
    • (2014)
  • 34
    • 84925383008 scopus 로고    scopus 로고
    • Chemical Carcinogenesis Research Information System Fact Sheet. (accessed Nov 2)
    • Chemical Carcinogenesis Research Information System Fact Sheet. http://www.nlm.nih.gov/pubs/factsheets/ccrisfs.html (accessed Nov 2, 2014).
    • (2014)
  • 35
    • 84925383007 scopus 로고    scopus 로고
    • Integrated Risk Information System Fact Sheet. (accessed Nov 2)
    • Integrated Risk Information System Fact Sheet. http://www.nlm.nih.gov/pubs/factsheets/irisfs.html (accessed Nov 2, 2014).
    • (2014)
  • 36
    • 84925383006 scopus 로고    scopus 로고
    • GENETOX. (accessed Nov 2)
    • GENETOX. http://toxnet.nlm.nih.gov/newtoxnet/genetox.htm (accessed Nov 2, 2014).
    • (2014)
  • 37
    • 84925383005 scopus 로고    scopus 로고
    • Developmental and Reproductive Toxicology Database Fact Sheet. (accessed Nov 2)
    • Developmental and Reproductive Toxicology Database Fact Sheet. http://www.nlm.nih.gov/pubs/factsheets/dartfs.html (accessed Nov 2, 2014).
    • (2014)
  • 38
    • 84925383004 scopus 로고    scopus 로고
    • TERIS, Teratogen Information System. (accessed Nov 2)
    • TERIS, Teratogen Information System. https://depts.washington.edu/terisweb/teris/ (accessed Nov 2, 2014).
    • (2014)
  • 39
    • 84925383003 scopus 로고    scopus 로고
    • US EPA ECOTOX Database. (accessed Nov 2)
    • US EPA ECOTOX Database. http://cfpub.epa.gov/ecotox/ (accessed Nov 2, 2014).
    • (2014)
  • 40
    • 84925383002 scopus 로고    scopus 로고
    • US FDA Endocrine Disruptor Knowledge Base. (accessed Nov 2)
    • US FDA Endocrine Disruptor Knowledge Base. http://www.fda.gov/ScienceResearch/BioinformaticsTools/EndocrineDisruptorKnowledgebase/default.htm (accessed Nov 2, 2014).
    • (2014)
  • 41
    • 84925383001 scopus 로고    scopus 로고
    • The Carcinogenic Potency Project (CPDB). (accessed Nov 2)
    • The Carcinogenic Potency Project (CPDB). http://toxnet.nlm.nih.gov/cpdb/ (accessed Nov 2, 2014).
    • (2014)
  • 42
    • 84925383000 scopus 로고    scopus 로고
    • US EPA DSSTox, Computational Toxicology Research Program(CompTox). (accessed Nov 2)
    • US EPA DSSTox, Computational Toxicology Research Program(CompTox). http://www.epa.gov/ncct/dsstox/index.html (accessed Nov 2, 2014).
    • (2014)
  • 43
    • 84925382999 scopus 로고    scopus 로고
    • US EPA ACToR. (accessed Nov 2)
    • US EPA ACToR. http://actor.epa.gov/actor/faces/ACToRHome.jsp (accessed Nov 2, 2014).
    • (2014)
  • 44
    • 84925382998 scopus 로고    scopus 로고
    • US EPA ToxRefDB,Computational Toxicology Research Program(CompTox). (accessed Nov 2)
    • US EPA ToxRefDB,Computational Toxicology Research Program(CompTox). http://www.epa.gov/ncct/toxrefdb/ (accessed Nov 2, 2014).
    • (2014)
  • 45
    • 45749117943 scopus 로고    scopus 로고
    • A novel approach: Chemical relational databases, and the role of the ISS CAN database on assessing chemical carcinogenicity
    • Benigni, R.; Bossa, C.; Richard, A.; Yang, C. A novel approach: chemical relational databases, and the role of the ISS CAN database on assessing chemical carcinogenicity Ann. Ist Super Sanita 2008, 44 (1) 48-56
    • (2008) Ann. Ist Super Sanita , vol.44 , Issue.1 , pp. 48-56
    • Benigni, R.1    Bossa, C.2    Richard, A.3    Yang, C.4
  • 46
    • 84925382997 scopus 로고    scopus 로고
    • ECHA REACH Substance Registration Database. (accessed Nov 2)
    • ECHA REACH Substance Registration Database. http://echa.europa.eu/information-on-chemicals/registered-substances (accessed Nov 2, 2014).
    • (2014)
  • 47
    • 84925382996 scopus 로고    scopus 로고
    • Scientific Committee on Consumer Safety (SCCS). (accessed Nov 2)
    • Scientific Committee on Consumer Safety (SCCS). http://ec.europa.eu/health/scientific-committees/consumer-safety/index-en.htm (accessed Nov 2, 2014).
    • (2014)
  • 48
    • 84925382995 scopus 로고    scopus 로고
    • US EPA TSCA Chemical Substance Inventory. (accessed Nov 2)
    • US EPA TSCA Chemical Substance Inventory. http://www.epa.gov/oppt/existingchemicals/pubs/tscainventory/index.html (accessed Nov 2, 2014).
    • (2014)
  • 49
    • 84925382994 scopus 로고    scopus 로고
    • US EPA Pesticide Inert Ingredients.
    • US EPA Pesticide Inert Ingredients. http://www.epa.gov/opprd001/inerts/ and http://www2.epa.gov/pesticide-registration/inert-ingredients-overview-and-guidance (accessed Nov 2, 2014).
    • (2014)
  • 50
    • 84925382993 scopus 로고    scopus 로고
    • PAN Pesticide Database. (accessed Nov 2)
    • PAN Pesticide Database. http://pesticideinfo.org/ (accessed Nov 2, 2014).
    • (2014)
  • 51
    • 84879599189 scopus 로고    scopus 로고
    • Improving the Human Hazard Characterization of Chemicals: A Tox21 Update
    • Tice, R.; Austin, C.; Kavlock, R. J.; Bucher, J. R. Improving the Human Hazard Characterization of Chemicals: A Tox21 Update Environ. Health Perspect. 2013, 121, 756-765
    • (2013) Environ. Health Perspect. , vol.121 , pp. 756-765
    • Tice, R.1    Austin, C.2    Kavlock, R.J.3    Bucher, J.R.4
  • 52
    • 84925382992 scopus 로고    scopus 로고
    • Domestic Substances List - Acts & Regulations - Environment Canada. (accessed Nov 2)
    • Domestic Substances List - Acts & Regulations - Environment Canada. http://www.ec.gc.ca/lcpe-cepa/default.asp (accessed Nov 2, 2014).
    • (2014)
  • 53
    • 84925382991 scopus 로고    scopus 로고
    • CosIng Database. (accessed Nov 2)
    • CosIng Database. http://ec.europa.eu/consumers/cosmetics/cosing/ (accessed Nov 2, 2014).
    • (2014)
  • 54
    • 84925382990 scopus 로고    scopus 로고
    • ChemIDplus. (accessed Nov 2)
    • ChemIDplus. http://chem.sis.nlm.nih.gov/chemidplus/ (accessed Nov 2, 2014).
    • (2014)
  • 55
    • 84925382989 scopus 로고    scopus 로고
    • ChemSpider. (accessed Nov 2)
    • ChemSpider. http://www.chemspider.com/ (accessed Nov 2, 2014).
    • (2014)
  • 56
    • 84925382988 scopus 로고    scopus 로고
    • Chemical Evaluation and Risk Estimation System (CERES). (accessed Nov 2)
    • Chemical Evaluation and Risk Estimation System (CERES). http://www.accessdata.fda.gov/FDATrack/track-proj?program=cfsan&id=CFSAN-OFAS-Chemical-Evaluation-and-Risk-Estimation-System (accessed Nov 2, 2014).
    • (2014)
  • 57
    • 24044545913 scopus 로고    scopus 로고
    • CO: A Chemical Ontology for Identification of Functional Groups and Semantic Comparison of Small Molecules
    • Aug 29
    • Feldman, H. J.; Dumontier, M.; Ling, S.; Haider, N.; Hoque, C. W. CO: A Chemical Ontology for Identification of Functional Groups and Semantic Comparison of Small Molecules FEBS Lett. 2005, 579 (21) 4685-4691 Aug 29
    • (2005) FEBS Lett. , vol.579 , Issue.21 , pp. 4685-4691
    • Feldman, H.J.1    Dumontier, M.2    Ling, S.3    Haider, N.4    Hoque, C.W.5
  • 58
    • 84925382987 scopus 로고    scopus 로고
    • PubChem structure search (includes SMARTS search capability), National Center for Biotechnology Information
    • PubChem structure search (includes SMARTS search capability), National Center for Biotechnology Information. https://pubchem.ncbi.nlm.nih.gov/search/search.cgi#.
  • 59
    • 84925382889 scopus 로고    scopus 로고
    • Heterocylic ring classificitaon (Genetontology). (accessed Nov 2)
    • Heterocylic ring classificitaon (Genetontology). https://database.riken.jp/sw/en/heterocycle-biosynthetic-process/cria250u18130i/ (accessed Nov 2, 2014).
    • (2014)
  • 61
    • 84925382888 scopus 로고    scopus 로고
    • Database and ontology of Chemical Entities of Biological Interest (ChEBI)
    • Database and ontology of Chemical Entities of Biological Interest (ChEBI). http://www.ebi.ac.uk/chebi/.
  • 62
    • 84925382887 scopus 로고    scopus 로고
    • US EPA Office of Pesticide Programs chemical classes
    • US EPA Office of Pesticide Programs chemical classes. http://www.epa.gov/oppsrrd1/registration-review/explanation.htm.
  • 64
    • 0037439447 scopus 로고    scopus 로고
    • Nonleadlikeness and Leadlikeness in Biochemical Screening
    • Rishton, G. M. Nonleadlikeness and Leadlikeness in Biochemical Screening Drug Discovery Today 2003, 8, 86-96
    • (2003) Drug Discovery Today , vol.8 , pp. 86-96
    • Rishton, G.M.1
  • 65
    • 84925382886 scopus 로고    scopus 로고
    • RDKit. (accessed Nov 2)
    • RDKit. http://rdkit.org/ (accessed Nov 2, 2014).
    • (2014)
  • 66
    • 84925382885 scopus 로고    scopus 로고
    • The Chemistry Development Kit. (accessed Nov 2)
    • The Chemistry Development Kit. http://sourceforge.net/projects/cdk/ (accessed Nov 2, 2014).
    • (2014)
  • 67
    • 0000661751 scopus 로고
    • Aromaticity and Conjugation
    • Randic, M. Aromaticity and Conjugation J. Am. Chem. Soc. 1977, 99 (2) 444-450
    • (1977) J. Am. Chem. Soc. , vol.99 , Issue.2 , pp. 444-450
    • Randic, M.1
  • 68
    • 0001296548 scopus 로고    scopus 로고
    • Overcoming the Limitations of a Connection Table Description: A Universal Representation of Chemical Species
    • Bauerschmidt, S.; Gasteiger, J. Overcoming the Limitations of a Connection Table Description: A Universal Representation of Chemical Species J. Chem. Inf. Model. 1997, 37, 705-714
    • (1997) J. Chem. Inf. Model. , vol.37 , pp. 705-714
    • Bauerschmidt, S.1    Gasteiger, J.2
  • 69
    • 0023856614 scopus 로고
    • Chemical Structure, Salmonella Mutagenicity and Extent of Carcinogenicity as Indicators of Genotoxic Carcinogenesis among 222 Chemicals Tested in Rodents by the U.S. NCI/NTP
    • Ashby, J.; Tennant, R. W. Chemical Structure, Salmonella Mutagenicity and Extent of Carcinogenicity as Indicators of Genotoxic Carcinogenesis among 222 Chemicals Tested in Rodents by the U.S. NCI/NTP Mutation Research/Genetic Toxicology 1988, 204, 17-115
    • (1988) Mutation Research/Genetic Toxicology , vol.204 , pp. 17-115
    • Ashby, J.1    Tennant, R.W.2


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