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The Chemical Translation Service--a web-based tool to improve standardization of metabolomic reports

G. Wohlgemuth, P. K. Haldiya, E. Willighagen, T. Kind, O. Fiehn
2010 Bioinformatics  
Metabolomic publications and databases use different database identifiers or even trivial names which disable queries across databases or between studies.  ...  Source Code: The source code is hosted as a Google Code Project at http://code.google.com/p/chemical-compound-repository/ Web Front End: The database is freely available under: http://cts.fiehnlab.ucdavis.edu  ...  In other cases, authors merely use compound names without referencing to databases.  ... 
doi:10.1093/bioinformatics/btq476 pmid:20829444 pmcid:PMC2951090 fatcat:2m6drcyklzbexatts3tcr5tj3u

Comprehensive database of secondary metabolites from cyanobacteria [article]

Martin R. Jones, Ernani Pinto, Mariana A. Torres, Fabiane Dörr, Hanna Mazur-Marzec, Karolina Szubert, Luciana Tartaglione, Carmela Dell'Aversano, Christopher O. Miles, Daniel G. Beach, Pearse McCarron, Kaarina Sivonen (+3 others)
2020 bioRxiv   pre-print
A comprehensive database is necessary to correctly identify cyanobacterial metabolites and advance research on their abundance, persistence and toxicity in natural environments.  ...  This approach demonstrated, for example, that 65% of the compounds carry at least one peptide bond, 57% are cyclic compounds, and 30% carry at least one halogen atom.  ...  Compound identifier (key) Continuous numbering of compounds in database (CyanoMetBD_xxxx) CyanoMetBD_0760 Compound Name Most common name for the compound Anabaenopeptin A Synonyms Alternative  ... 
doi:10.1101/2020.04.16.038703 fatcat:cgzy7qj7tjavhkm523w5mpwoma

ClassyFire: automated chemical classification with a comprehensive, computable taxonomy

Yannick Djoumbou Feunang, Roman Eisner, Craig Knox, Leonid Chepelev, Janna Hastings, Gareth Owen, Eoin Fahy, Christoph Steinbeck, Shankar Subramanian, Evan Bolton, Russell Greiner, David S. Wishart
2016 Journal of Cheminformatics  
This is regrettable as comprehensive chemical classification and description tools could not only improve our understanding of chemistry but also improve the linkage between chemistry and many other fields  ...  Furthermore each category is named using a consensus-based nomenclature and described (in English) based on the characteristic common structural properties of the compounds it contains.  ...  MW, AM, ST, and VM all provided contributions and suggestions in improving and refining ClassyFire.  ... 
doi:10.1186/s13321-016-0174-y pmid:27867422 pmcid:PMC5096306 fatcat:5oarznaf6zcvjpcsdgple7x4qi

Can Better Identifier Splitting Techniques Help Feature Location?

Bogdan Dit, Latifa Guerrouj, Denys Poshyvanyk, Giuliano Antoniol
2011 2011 IEEE 19th International Conference on Program Comprehension  
Overall, our findings outline potential benefits of putting additional research efforts into defining more sophisticated source code preprocessing techniques as they can still be useful in situations where  ...  The main research question that we ask in this study is if we had a perfect technique for splitting identifiers, would it still help improve accuracy of feature location techniques applied in different  ...  in compound (or abbreviated) identifiers.  ... 
doi:10.1109/icpc.2011.47 dblp:conf/iwpc/DitGPA11 fatcat:edw4xswdjrd6pncc3fb62xmuv4

Relating developers' concepts and artefact vocabulary in a financial software module

Tezcan Dilshener, Michel Wermelinger
2011 2011 27th IEEE International Conference on Software Maintenance (ICSM)  
Developers working on unfamiliar systems are challenged to accurately identify where and how high-level concepts are implemented in the source code.  ...  We compared the relative importance of the domain concepts, as understood by developers, in the user manual and in the source code.  ...  They extracted identifier names and comments representing those concepts from the source code.  ... 
doi:10.1109/icsm.2011.6080808 dblp:conf/icsm/DilshenerW11 fatcat:fetdf5vofraztn6tzzs5bjexga

Minimizing Medication Errors from Electronic Prescription Transmission—Digitizing Compounded Drug Preparations

Richard H. Parrish, Lucy Gilak, Donna Bohannon, Steven P. Emrick, Brian Serumaga, Roy Guharoy
2019 Pharmacy  
Included in this work are identifying authorized compounding monographs, surveying provider and end-user groups for information about data specificity during e-prescribing, and generating guidelines for  ...  the development of a compatible data model for clinical formulation identifiers (CF-IDs).  ...  elements that uniquely identify a CNSP name and its monograph.  ... 
doi:10.3390/pharmacy7040149 pmid:31703306 pmcid:PMC6958393 fatcat:fjglzcq47bex5ioyvah5ezj5ei

EvoPat – Pattern-Based Evolution and Refactoring of RDF Knowledge Bases [chapter]

Christoph Rieß, Norman Heino, Sebastian Tramp, Sören Auer
2010 Lecture Notes in Computer Science  
For more advanced and domain-specific evolution and refactorings, several simple evolution patterns can be combined into a compound one.  ...  We performed a comprehensive survey of possible evolution patterns with a combinatorial analysis of all possible before/after combinations, resulting in an extensive catalog of usable evolution patterns  ...  Refactoring is based on two key concepts: code smells and refactorings. Code smells are an informal but still useful characterization of patterns of bad source code.  ... 
doi:10.1007/978-3-642-17746-0_41 fatcat:ehhvjdwycjewrjscaqhjuvkxlq

CyanoMetDB, a comprehensive public database of secondary metabolites from cyanobacteria

Martin R. Jones, Ernani Pinto, Mariana A. Torres, Fabiane Dörr, Hanna Mazur-Marzec, Karolina Szubert, Luciana Tartaglione, Carmela Dell'Aversano, Christopher O. Miles, Daniel G. Beach, Pearse McCarron, Kaarina Sivonen (+3 others)
2021 Water Research  
CyanoMetDB contains 2010 cyanobacterial metabolites and 99 structurally related compounds.  ...  More than two thousand cyanobacterial secondary metabolites have been reported from diverse sources over the past fifty years.  ...  sources and chemical structural descriptors (SMILES, InChI, InChIKey and IUPAC name).  ... 
doi:10.1016/j.watres.2021.117017 pmid:33765498 fatcat:wwzvakdzujffdd6zpck3fttt7e

Description of a drug hierarchy in a concept-based reference terminology

J M Kim, P Frosdick
2001 Proceedings. AMIA Symposium  
It promises to be the most comprehensive terminology available.  ...  SNOMED Clinical Terms (CT), scheduled for release in December 2001, integrates the relative strengths of SNOMED RT, and the United Kingdom s Clinical Terms Version 3, formerly known as the Read Codes Version  ...  Due to the high granularity and lack of a central source for the codes, it is quite difficult and laborious to maintain the database.  ... 
pmid:11825202 pmcid:PMC2243540 fatcat:ja7d4ustcjbzxmgwzo5gbgr6hm

Comprehending Test Code: An Empirical Study

Chak Shun Yu, Christoph Treude, Mauricio Aniche
2019 2019 IEEE International Conference on Software Maintenance and Evolution (ICSME)  
Developers spend a large portion of their time and effort on comprehending source code.  ...  While many studies have investigated how developers approach these comprehension tasks and what factors influence their success, less is known about how developers comprehend test code specifically, despite  ...  [35] Comparing the impact of compound and short identifier names on program comprehension. [11] Impact of code smells on program comprehension. II.  ... 
doi:10.1109/icsme.2019.00084 dblp:conf/icsm/YuTA19 fatcat:hxrvnobqibboxhhkwq7mci7aqi

Comprehending Test Code: An Empirical Study [article]

Chak Shun Yu, Christoph Treude, Maurício Aniche
2019 arXiv   pre-print
Developers spend a large portion of their time and effort on comprehending source code.  ...  While many studies have investigated how developers approach these comprehension tasks and what factors influence their success, less is known about how developers comprehend test code specifically, despite  ...  [35] Comparing the impact of compound and short identifier names on program comprehension. [11] Impact of code smells on program comprehension. II.  ... 
arXiv:1907.13365v1 fatcat:k7xqtlxkr5dkhdk5m56atmhm54

Potential of metabolomics as a functional genomics tool

Raoul J. Bino, Robert D. Hall, Oliver Fiehn, Joachim Kopka, Kazuki Saito, John Draper, Basil J. Nikolau, Pedro Mendes, Ute Roessner-Tunali, Michael H. Beale, Richard N. Trethewey, B. Markus Lange (+2 others)
2004 Trends in Plant Science  
For the continued maturation of metabolomics, the following three objectives need to be achieved: (i) improvement in the comprehensive coverage of the plant metabolome, (ii) facilitation of comparison  ...  Metabolomics (comprehensive analysis in which all the metabolites of an organism are identified and quantified [1]) has emerged as a functional genomics methodology that contributes to our understanding  ...  or absolute quantification value. † The metabolite identifiers should consist of descriptive codes, such as the International Union of Pure and Applied Chemistry (IUPAC) name, chemical abstract number  ... 
doi:10.1016/j.tplants.2004.07.004 pmid:15337491 fatcat:e4fsk5rt4bcrpllsdbug7wfyju

An Architecture-Centric Approach to Detecting Security Patterns in Software [chapter]

Michaela Bunke, Karsten Sohr
2011 Lecture Notes in Computer Science  
Utilizing security patterns already improves the security of software in early software development stages.  ...  In this paper, we show how to detect security patterns in code with the help of a reverse engineering tool-suite Bauhaus.  ...  Some descriptions make use of UML diagrams or rarely source code snippets to clarify the security pattern modeling during the design phase.  ... 
doi:10.1007/978-3-642-19125-1_12 fatcat:u6mcstpgkbca5kcu3qidvounby

Online Metabolomics Databases and Pipelines [chapter]

Adam J.
2012 Metabolomics  
Description: A study design database for GC/MS metabolomics experiments. Species: Plant species Reference data: Provides raw and processed GC/MS data for download together with metadata.  ...  Online tools for generating InChI codes from structures or other identifiers are listed in Table 1 .  ...  ., 2010) since this tool is capable of batch translations of miscellaneous metabolite identifiers and synonyms to standard InChI codes and other common identifiers.  ... 
doi:10.5772/31021 fatcat:7nkgmwx72nesleacrrulcrwf4a

Improving the Tokenisation of Identifier Names [chapter]

Simon Butler, Michel Wermelinger, Yijun Yu, Helen Sharp
2011 Lecture Notes in Computer Science  
Identifier names are the main vehicle for semantic information during program comprehension.  ...  into naming conventions in industrial-scale object-oriented code.  ...  Acknowledgements We would like to thank the anonymous reviewers on the ECOOP 2011 Program Committee, and Tiago Alves and Eric Bouwers for their thoughtful comments that have helped improve this paper.  ... 
doi:10.1007/978-3-642-22655-7_7 fatcat:n7cyw7ohhrctzio5gc4djhnvie
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