ChemSpider – A Community Platform for Chemistry and Resources Supporting the Life Sciences

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US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure

ChemSpider was developed with the intention of aggregating and indexing available sources of chemical structures and their associated information into a single searchable repository and making it available to everybody, at no charge. There are many tens of chemical structure databases such as literature data, chemical vendor catalogs, molecular properties, environmental data, toxicity data, analytical data etc. and no single way to search across them. Despite the diversity of databases available online their inherent quality, accuracy and completeness is lacking in many regards. ChemSpider was established to provide a platform whereby the chemistry community could contribute to cleaning up the data, improving the quality of data online and expanding the information available to include data such as reaction syntheses, analytical data and experimental properties. ChemSpider has now grown into a database of over 20 million chemical substances integrated with over 300 disparate data sources, many of these directly supporting the Life Sciences. This presentation will provide an overview of our efforts to improve the quality of data online, to provide a foundation for the semantic web for chemistry and to provide access to a set online tools and services to support access to these data. I will also discuss how ChemSpider is being used to enhance Semantic Publishing in Chemistry at RSC.

Technologie Formation

ChemSpider – A Community Platform for Chemistry and Resources Supporting the Life Sciences

Chemistry on the Internet TODAY ,[object Object],[object Object],[object Object]

All Those Names, One Structure A problem to solve…

Trustworthy Chemistry? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Where Would You look? What Do You Trust?

Question Everything online: www.dhmo.org

Di-Hydrogen Monoxide ,[object Object],[object Object]

Vancomycin ,[object Object],[object Object],[object Object]

Wikipedia, C&E News, PubChem ,[object Object]

Feedback from C&E Senior Editor ,[object Object],[object Object]

Structural Data for LifeSciences DailyMed

Just “Public Compound” Databases ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

media.obsessable.com ,[object Object],What do humans want?

A Pragmatic Vision ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Answer Questions ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Statistics for Today ,[object Object],[object Object],[object Object],[object Object]

Searching Chemistry on the Internet ,[object Object],[object Object],[object Object]

Link the Internet with InChIKeys! Taken from: Rafael Sidis’ Blog

Vancomycin Search Molecular SKELETON Search Full Molecule

Vancomycin on ChemSpider 1 compound – 3 days

InChIKeys Make the internet searchable by adding InChIKeys Publishers add InChIKeys to papers now…

InChIKeys Make the internet searchable by adding InChIKeys Publishers add InChIKeys to papers now… is what???

InChI Resolver to DOIs Structure Search the Web

Most Chemistry is NOT Published ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Crowd-sourcing Curation and Deposition ,[object Object]

Multi-level Curation and Approval Building a Structure Centric Community for Chemists

Success Depends on Dictionaries Link to a Structure or the Right Structure?

Semantic Linking of Structures ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Chemistry on the Internet FUTURE ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Thank you [email_address] Twitter: ChemSpiderman www.chemspider.com/blog SLIDES: www.slideshare.net/AntonyWilliams

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The original abstract for the talk is below BUT the talk changed based on a big interest in InChI and the possibilities to use in a Semantic Web for Chemistry The increasing availability of free and open access resources for scientists on the internet presents us with a revolution in data availability. However, freedom costs and in many cases the cost is quality. ChemSpider is a free access website for chemists built with the intention of providing a structure centric community for chemists. As an aggregator of chemistry related information from many sources, at present over 21.5 million unique chemical entities from over 150 separate data sources, ChemSpider has taken on the task of both robotically and manually curating publicly available data sources. This presentation will provide an overview of how a curated platform can become the centralized hub for resourcing information about chemical entities. We will also present ChemMantis, an entity extraction platform for extracting chemical names and scientific terms in documents and providing a platform for structure-based searching of Open Access chemistry literature.

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ChemSpider is a free access website for chemists built with the vision of providing a structure centric community for chemists. Vision is great…execution is better. ChemSpider is now one of the internet’s primary portals for chemistry offering access to over 23 million unique chemical structures from over 200 data sources and expanding daily. Even though there are tens if not hundreds of chemical structure databases such as literature data, chemical vendor catalogs, molecular properties, environmental data, toxicity data, analytical data etc. there has been no single way to search across them. Despite the fact that there are a large number of databases containing chemical compounds and data available online their inherent quality, accuracy and completeness remains lacking in many regards. With ChemSpider we have provided a platform whereby the chemistry community could contribute to cleaning up the data, improving the quality of data online and expanding the information available to include data such as reaction syntheses, analytical data, experimental properties and linking to other valuable resources. This presentation will provide an overview of ChemSpider and its value to chemists as a search tool, as a public repository of information and how it can become one of the primary foundations of internet-based chemistry. I will also discuss the vision for ChemSpider and some of the exciting goals we are setting for the system moving forward.

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This was a presentation I gave to an audience at Nature Publishing Group in New York on May 7th 2009. It's a long presentation and over an hour in length. Not much new here relative to other presentations...just a knitting together of many of the others on here. There is an increasing availability of free and open access resources for scientists to use on the internet. Coupled with an increasing number of Open Source software programs we are in the middle of a revolution in data availability and tools to manipulate these data. ChemSpider is a free access website built with the intention of providing a structure centric community for chemists. As an aggregator of chemistry related information from many sources, at present over 21.5 million unique chemical entities from over 190 separate data sources, ChemSpider has taken on the task of both robotically and manually integrating and curating publicly available data sources. ChemSpider has also provided an environment for users to deposit, curate and annotate chemistry-related information. This has allowed the community to enhance ChemSpider by adding analytical data, associating synthetic pathways and publications and connecting to social networking resources. I will discuss how ChemSpider is fast becoming the premier curated platform and centralized hub for resourcing information about chemical entities and how the platform provides the foundation data for services allowing the analysis of analytical data and collaborative science.

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RSC|ChemSpider is one of the world’s largest online resources for chemistry related data and services. Developed with the intention of delivering access to structure-based chemistry data via the internet the ChemSpider platform hosts over 26 million unique chemical compounds aggregated from over 400 data sources and provides an environment for the community to both annotate and curate these existing data as well as deposit new data to the system. The search system delivers flexible querying capabilities together with links to external sites for publication and patent data. This presentation will review the present capabilities of the ChemSpider system providing direct examples of how to use the system to source high quality data of value to chemists. We will discuss some of the challenges associated with validating data quality and examine how ChemSpider is a part of the new “semantic web for chemistry”. ChemSpider has also spawned a number of additional projects include ChemSpider SyntheticPages for hosting openly peer-reviewed chemical synthesis articles, Learn Chemistry Wiki for students learning chemistry and SpectraSchool for learning spectroscopy.

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The internet has revolutionized the sharing of data and information and in the domain of chemistry there are many resources available to help with our research. In recent years various online resources have been introduced that allow users to access information, properties and data associated with chemical entities. At a time when CAS has declared that they now have over 50 million unique chemical entities in the registry the number of chemical structures distributed across the internet also measures in the tens of millions. There are many tens of databases on the internet hosting chemical structures associated with data focused on the specific nature of the collection – metabolic pathways, spectral data collections, chemical vendor collections, biological assay data and crystal structures are examples. Unfortunately there has been no single way to search across all of these resources. ChemSpider has taken on the task of integrating the multiple online resources of information into a single database using the chemical structure as the primary key and retaining the link out and attribution to the original datasource. In this manner ChemSpider intends to become a structure-centric hub for the chemistry community. This talk will provide an overview of the ChemSpider platform, how it is being used as a crowdsourcing platform for community-based curation of the data and the future vision of ChemSpider as one of the pillars of the semantic web of chemistry.

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Our access to scientific information has changed in ways that were hardly imagined even by the early pioneers of the internet. The immense quantities of data and the array of tools available to search and analyze online content continues to expand while the pace of change does not appear to be slowing. ChemSpider is one of the chemistry community’s primary online public compound databases. Containing tens of millions of chemical compounds and its associated data ChemSpider serves data tens of thousands of chemists every day and it serves as the foundation for many important international projects to integrate chemistry and biology data, facilitate drug discovery efforts and help to identify new chemicals from under the ocean. This presentation will provide an overview of the expanding reach of the ChemSpider platform and the nature of the solutions that it helps to enable. We will also discuss the possibilities it offers in the domain of crowdsourcing and open data sharing. The future of scientific information and communication will be underpinned by these efforts, influenced by increasing participation from the scientific community and facilitated collaboration and ultimately accelerate scientific progress.

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Scientists commonly find themselves in a state of overwhelm in regards to the availability of information accessible to them. The distribution of resources now includes the entire space of the worldwide web, access to primary databases such as CAS and, commonly, a plethora of internally developed systems. While the web has provided improved access to chemistry-related information there has not been an online central resource allowing integrated chemical structure-searching of chemistry databases, chemistry articles, patents and web pages such as blogs and wikis. ChemSpider has built a structure centric community for chemists by providing free access to an online database and collaboration tool for chemists. The online database offers an environment for curating the data on ChemSpider as well as the deposition of chemical structures, analytical data and associated information and provides a significant knowledge base and resource for chemists working in different domains. An overview of present and future capabilities is given.

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Six Myths about Ontologies: The Basics of Formal Ontology

johnbeverley2021

Effective data discovery is crucial for maintaining compliance and mitigating risks in today's rapidly evolving privacy landscape. However, traditional manual approaches often struggle to keep pace with the growing volume and complexity of data. Join us for an insightful webinar where industry leaders from TrustArc and Privya will share their expertise on leveraging AI-powered solutions to revolutionize data discovery. You'll learn how to: - Effortlessly maintain a comprehensive, up-to-date data inventory - Harness code scanning insights to gain complete visibility into data flows leveraging the advantages of code scanning over DB scanning - Simplify compliance by leveraging Privya's integration with TrustArc - Implement proven strategies to mitigate third-party risks Our panel of experts will discuss real-world case studies and share practical strategies for overcoming common data discovery challenges. They'll also explore the latest trends and innovations in AI-driven data management, and how these technologies can help organizations stay ahead of the curve in an ever-changing privacy landscape.

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Scaling API-first – The story of a global engineering organization Ian Reasor, Senior Computer Scientist - Adobe Radu Cotescu, Senior Computer Scientist - Adobe Apidays New York 2024: The API Economy in the AI Era (April 30 & May 1, 2024) ------ Check out our conferences at https://www.apidays.global/ Do you want to sponsor or talk at one of our conferences? https://apidays.typeform.com/to/ILJeAaV8 Learn more on APIscene, the global media made by the community for the community: https://www.apiscene.io Explore the API ecosystem with the API Landscape: https://apilandscape.apiscene.io/

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apidays

Tracing the root cause of a performance issue requires a lot of patience, experience, and focus. It’s so hard that we sometimes attempt to guess by trying out tentative fixes, but that usually results in frustration, messy code, and a considerable waste of time and money. This talk explains how to correctly zoom in on a performance bottleneck using three levels of profiling: distributed tracing, metrics, and method profiling. After we learn to read the JVM profiler output as a flame graph, we explore a series of bottlenecks typical for backend systems, like connection/thread pool starvation, invisible aspects, blocking code, hot CPU methods, lock contention, and Virtual Thread pinning, and we learn to trace them even if they occur in library code you are not familiar with. Attend this talk and prepare for the performance issues that will eventually hit any successful system. About authorWith two decades of experience, Victor is a Java Champion working as a trainer for top companies in Europe. Five thousands developers in 120 companies attended his workshops, so he gets to debate every week the challenges that various projects struggle with. In return, Victor summarizes key points from these workshops in conference talks and online meetups for the European Software Crafters, the world’s largest developer community around architecture, refactoring, and testing. Discover how Victor can help you on victorrentea.ro : company training catalog, consultancy and YouTube playlists.

Finding Java's Hidden Performance Traps @ DevoxxUK 2024

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Webinar Recording: https://www.panagenda.com/webinars/why-teams-call-analytics-is-critical-to-your-entire-business Nothing is as frustrating and noticeable as being in an important call and being unable to see or hear the other person. Not surprising then, that issues with Teams calls are among the most common problems users call their helpdesk for. Having in depth insight into everything relevant going on at the user’s device, local network, ISP and Microsoft itself during the call is crucial for good Microsoft Teams Call quality support. To ensure a quick and adequate solution and to ensure your users get the most out of their Microsoft 365. But did you know that ‘bad calls’ are also an excellent indicator of other problems arising? Precisely because it is so noticeable!? Like the canary in the mine, bad calls can be early indicators of problems. Problems that might otherwise not have been noticed for a while but can have a big impact on productivity and satisfaction. Join this session by Christoph Adler to learn how true Microsoft Teams call quality analytics helped other organizations troubleshoot bad calls and identify and fix problems that impacted Teams calls or the use of Microsoft365 in general. See what it can do to keep your users happy and productive! In this session we will cover - Why CQD data alone is not enough to troubleshoot call problems - The importance of attributing call problems to the right call participant - What call quality analytics can do to help you quickly find, fix-, and prevent problems - Why having retrospective detailed insights matters - Real life examples of how others have used Microsoft Teams call quality monitoring to problem shoot problems with their ISP, network, device health and more.

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EMPOWERMENT TECHNOLOGY GRADE 11 QUARTER 2 REVIEWER

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Following the popularity of "Cloud Revolution: Exploring the New Wave of Serverless Spatial Data," we're thrilled to announce this much-anticipated encore webinar. In this sequel, we'll dive deeper into the Cloud-Native realm by uncovering practical applications and FME support for these new formats, including COGs, COPC, FlatGeoBuf, GeoParquet, STAC, and ZARR. Building on the foundation laid by industry leaders Michelle Roby of Radiant Earth and Chris Holmes of Planet in the first webinar, this second part offers an in-depth look at the real-world application and behind-the-scenes dynamics of these cutting-edge formats. We will spotlight specific use-cases and workflows, showcasing their efficiency and relevance in practical scenarios. Discover the vast possibilities each format holds, highlighted through detailed discussions and demonstrations. Our expert speakers will dissect the key aspects and provide critical takeaways for effective use, ensuring attendees leave with a thorough understanding of how to apply these formats in their own projects. Elevate your understanding of how FME supports these cutting-edge technologies, enhancing your ability to manage, share, and analyze spatial data. Whether you're building on knowledge from our initial session or are new to the serverless spatial data landscape, this webinar is your gateway to mastering cloud-native formats in your workflows.

Cloud Frontiers: A Deep Dive into Serverless Spatial Data and FME

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The value of a flexible API Management solution for Open Banking Steve Melan, Manager for IT Innovation and Architecture - State's and Saving's Bank of Luxembourg Apidays New York 2024: The API Economy in the AI Era (April 30 & May 1, 2024) ------ Check out our conferences at https://www.apidays.global/ Do you want to sponsor or talk at one of our conferences? https://apidays.typeform.com/to/ILJeAaV8 Learn more on APIscene, the global media made by the community for the community: https://www.apiscene.io Explore the API ecosystem with the API Landscape: https://apilandscape.apiscene.io/

Apidays New York 2024 - The value of a flexible API Management solution for O...

apidays

In this keynote, Asanka Abeysinghe, CTO,WSO2 will explore the shift towards platformless technology ecosystems and their importance in driving digital adaptability and innovation. We will discuss strategies for leveraging decentralized architectures and integrating diverse technologies, with a focus on building resilient, flexible, and future-ready IT infrastructures. We will also highlight WSO2's roadmap, emphasizing our commitment to supporting this transformative journey with our evolving product suite.

Platformless Horizons for Digital Adaptability

WSO2

The Good, the Bad and the Governed - Why is governance a dirty word? David O'Neill, Chief Operating Officer - APIContext Apidays New York 2024: The API Economy in the AI Era (April 30 & May 1, 2024) ------ Check out our conferences at https://www.apidays.global/ Do you want to sponsor or talk at one of our conferences? https://apidays.typeform.com/to/ILJeAaV8 Learn more on APIscene, the global media made by the community for the community: https://www.apiscene.io Explore the API ecosystem with the API Landscape: https://apilandscape.apiscene.io/

Apidays New York 2024 - The Good, the Bad and the Governed by David O'Neill, ...

apidays

Dubai, often portrayed as a shimmering oasis in the desert, faces its own set of challenges, including the occasional threat of flooding. Despite its reputation for opulence and modernity, the emirate is not immune to the forces of nature. In recent years, Dubai has experienced sporadic but significant floods, testing the resilience of its infrastructure and communities. Among the critical lifelines in this bustling metropolis is the Dubai International Airport, a bustling hub that connects the city to the world. This article explores the intersection of Dubai flood events and the resilience demonstrated by the Dubai International Airport in the face of such challenges.

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ChemSpider – A Community Platform for Chemistry and Resources Supporting the Life Sciences

1. ChemSpider – A Community Platform for Chemistry and Resources Supporting the Life Sciences

6. The Final Search Strategy

7. All Those Names, One Structure A problem to solve…

10. Where Would You look? What Do You Trust?

11. Question Everything online: www.dhmo.org

12.

13.

14.

15.

16. It’s all on Wikipedia…

17. Chemistry on The Internet Is Messy

18. It’s Methane…

19. What’s Methane?

20. What’s Methane?

21. What ELSE is Methane???

22. Drugs are REALLY Messy

23.

24. The EXPERTS must get it right?!

25.

26.

27. Structural Data for LifeSciences DailyMed

28. Lack of Stereochemisty

29. Incorrect Structures

30. Ugh…

31.

32.

33.

34.

35.

36. ChemSpider Searches

37. Search Cholesterol

38. Search Cholesterol

39. Search Cholesterol

40. Search Cholesterol

41. Search Cholesterol

42. A Link Farm to Content

43. Linked across the internet

44. Kyoto Encyclopedia of Genes and Genomes

45. Linking SMPDB

46. Links to Patents based on structure

47. Articles Linked

48.

49. Search “OEA”

50. Search OEA

51. Search OEA

52. Search OEA

53. Linked Patents for OEA

54.

55.

56.

57. The InChI Identifier

58. Multiple Layers

59. InChIStrings Hash to InChIKeys

60. Link the Internet with InChIKeys! Taken from: Rafael Sidis’ Blog

61. Vancomycin – Search the Internet

62. Vancomycin Search Molecular SKELETON Search Full Molecule

63. Full Molecule Search: 4 Hits

64. Full Skeleton Search: 104 Hits

65.

66.

67.

68. Vancomycin

69. Vancomycin on ChemSpider 1 compound – 3 days

70. InChIKeys Make the internet searchable by adding InChIKeys Publishers add InChIKeys to papers now…

71. InChIKeys Make the internet searchable by adding InChIKeys Publishers add InChIKeys to papers now… is what???

72. The InChI “Resolver”

73. InChI Resolver to DOIs Structure Search the Web

74.

75. The CAS Registry

76. CAS Registry

77.

78. Multi-level Curation and Approval Building a Structure Centric Community for Chemists

79. Entity-Extraction, Mark-up, Annotate

80. Semantic Markup: Project Prospect

81. Success Depends on Dictionaries Link to a Structure or the Right Structure?

82. Name-Structure Pairs

83.

84. Org Prep Daily (Blog)

85. ChemSpider SyntheticPages

86.

87. ChemSpider Web Services

88.

89. Thank you [email_address] Twitter: ChemSpiderman www.chemspider.com/blog SLIDES: www.slideshare.net/AntonyWilliams

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