| 1. |
- Bradley, Jean-Claude, et al.
(författare)
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Beautifying Data in the Real World
- 2009. - 1
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Ingår i: Beautiful Data. - Sebastol, USA : O'Reilly. - 9780596157111 ; , s. 259-278
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Bokkapitel (populärvet., debatt m.m.)
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| 2. |
- Guha, Rajarshi, et al.
(författare)
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Collaborative Cheminformatics Applications
- 2011
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Ingår i: Collaborative Computational Technologies for Biomedical Research. - Hoboken, N.J. : John Wiley & Sons. - 9780470638033
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Bokkapitel (övrigt vetenskapligt/konstnärligt)
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| 3. |
- O'Boyle, Noel, et al.
(författare)
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Open Data, Open Source and Open Standards in chemistry : The Blue Obelisk five years on
- 2011
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Ingår i: Journal of Cheminformatics. - : BioMed Central. - 1758-2946. ; 3, s. 37-
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Tidskriftsartikel (refereegranskat)abstract
- Background: The Blue Obelisk movement was established in 2005 as a response to the lack of Open Data,Open Standards and Open Source (ODOSOS) in chemistry. It aims to make it easier to carry out chemistryresearch by promoting interoperability between chemistry software, encouraging cooperation between OpenSource developers, and developing community resources and Open Standards. Results: This contribution looks back on the work carried out by the Blue Obelisk in the past 5 years and surveysprogress and remaining challenges in the areas of Open Data, Open Standards, and Open Source in chemistry. Conclusions: We show that the Blue Obelisk has been very successful in bringing together researchers anddevelopers with common interests in ODOSOS, leading to development of many useful resources freely availableto the chemistry community
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| 4. |
- Spjuth, Ola, 1977-, et al.
(författare)
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Towards interoperable and reproducible QSAR analyses : Exchange of data sets
- 2010
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Ingår i: Journal of Cheminformatics. - : BioMed Central. - 1758-2946. ; 2
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: QSAR/QSPR is a widely used method to relate chemical structures and responses based on ex- perimental observations. In QSAR, chemical structures are expressed as descriptors, which are mathematical representations like calculated properties or enumerated fragments. Many existing QSAR data sets are based on a combination of different software tools mixed with in-house developed solutions, with datasets manually assembled in spreadsheets. Currently there exists no agreed-upon definition of descriptors and no standard for exchanging data sets in QSAR, which together with numerous different descriptor implementations makes it a virtually impossible task to reproduce and validate analyses, and significantly hinders collaborations and re-use of data.RESULTS: We present a step towards standardizing QSAR analyses by defining interoperable and reproducible QSAR/QSPR data sets, comprising an open XML format (QSAR-ML) and an open extensible descriptor ontology (Blue Obelisk Descriptor Ontology). The ontology provides an extensible way of uniquely defining descriptors for use in QSAR experiments, and the exchange format supports multiple versioned implementations of these descriptors. Hence, a data set described by QSAR-ML makes its setup completely reproducible. We also provide an implementation as a set of plugins for Bioclipse that simplifies QSAR data set formation, and allows for exporting in QSAR-ML as well as traditional CSV formats. The implementation facilitates addition of new descriptor implementations, from locally installed software and remote Web services; the latter is demonstrated with REST and XMPP Web services.CONCLUSIONS: Standardized QSAR data sets opens up new ways to store, query, and exchange data for subsequent analyses. QSAR-ML supports completely reproducible dataset formation, solving the problems of defining which software components were used, their versions, and the case of multiple names for the same descriptor. This makes is easy to join, extend, combine data sets and also to work collectively. The presented Bioclipse plugins equip scientists with intuitive tools that make QSAR-ML widely available for the community.
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| 5. |
- Willighagen, Egon L., et al.
(författare)
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The Chemistry Development Kit (CDK) v2.0 : atom typing, depiction, molecular formulas, and substructure searching
- 2017
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Ingår i: Journal of Cheminformatics. - : Springer Science and Business Media LLC. - 1758-2946. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Background: The Chemistry Development Kit (CDK) is a widely used open source cheminformatics toolkit, providing data structures to represent chemical concepts along with methods to manipulate such structures and perform computations on them. The library implements a wide variety of cheminformatics algorithms ranging from chemical structure canonicalization to molecular descriptor calculations and pharmacophore perception. It is used in drug discovery, metabolomics, and toxicology. Over the last 10 years, the code base has grown significantly, however, resulting in many complex interdependencies among components and poor performance of many algorithms.Results: We report improvements to the CDK v2.0 since the v1.2 release series, specifically addressing the increased functional complexity and poor performance. We first summarize the addition of new functionality, such atom typing and molecular formula handling, and improvement to existing functionality that has led to significantly better performance for substructure searching, molecular fingerprints, and rendering of molecules. Second, we outline how the CDK has evolved with respect to quality control and the approaches we have adopted to ensure stability, including a code review mechanism.Conclusions: This paper highlights our continued efforts to provide a community driven, open source cheminformatics library, and shows that such collaborative projects can thrive over extended periods of time, resulting in a high-quality and performant library. By taking advantage of community support and contributions, we show that an open source cheminformatics project can act as a peer reviewed publishing platform for scientific computing software.
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| 6. |
- Willighagen, Egon, et al.
(författare)
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Userscripts for the Life Sciences
- 2007
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Ingår i: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 8, s. 487-
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Tidskriftsartikel (refereegranskat)abstract
- Background The web has seen an explosion of chemistry and biology related resources in the last 15 years: thousands of scientific journals, databases, wikis, blogs and resources are available with a wide variety of types of information. There is a huge need to aggregate and organise this information. However, the sheer number of resources makes it unrealistic to link them all in a centralised manner. Instead, search engines to find information in those resources flourish, and formal languages like Resource Description Framework and Web Ontology Language are increasingly used to allow linking of resources. A recent development is the use of userscripts to change the appearance of web pages, by on-the-fly modification of the web content. This opens possibilities to aggregate information and computational results from different web resources into the web page of one of those resources. Results Several userscripts are presented that enrich biology and chemistry related web resources by incorporating or linking to other computational or data sources on the web. The scripts make use of Greasemonkey-like plugins for web browsers and are written in JavaScript. Information from third-party resources are extracted using open Application Programming Interfaces, while common Universal Resource Locator schemes are used to make deep links to related information in that external resource. The userscripts presented here use a variety of techniques and resources, and show the potential of such scripts. Conclusion This paper discusses a number of userscripts that aggregate information from two or more web resources. Examples are shown that enrich web pages with information from other resources, and show how information from web pages can be used to link to, search, and process information in other resources. Due to the nature of userscripts, scientists are able to select those scripts they find useful on a daily basis, as the scripts run directly in their own web browser rather than on the web server. This flexibility allows the scientists to tune the features of web resources to optimise their productivity.
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