Cheta 25 may
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CheTA aims to automate the generation of metadata for chemistry documents using text mining tools. It will add chemistry annotations to the largest text mining repository, U-Compare, and design chemistry-specific workflows. This will make the annotation process more efficient and reduce the need for expensive human annotations.
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The extraction of chemical entities from documents such as patents and publications has been pursued for a number of years. We wish to report on ChemMantis, an integrated system for chemistry-based entity extraction and document mark-up enabling access to the rich resource of online chemistry know as ChemSpider. We will discuss the development of the platform from its inception as a series of dictionaries to the integration of an entity extraction algorithm and its expansion to a public deposition and publishing platform for chemistry. Chemistry articles can now be deposited, marked-up and exposed to the public within a few minutes in many cases making it an ideal platform for communicating research and providing integrated access to data sources including PubChem, ChEBI, Wikipedia and Entrez.The UK National Chemical Database Service – an integration of commercial and ...
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At a time when the data explosion has simply been redefined as “Big”, the hurdles associated with building a subject-specific data repository for chemistry are daunting. Combining a multitude of non-standard data formats for chemicals, related properties, reactions, spectra etc., together with the confusion of licensing and embargoing, and providing for data exchange and integration with services and platforms external to the repository, the challenge is significant. This all at a time when semantic technologies are touted as the fundamental technology to enhance integration and discoverability. Funding agencies are demanding change, especially a change towards access to open data to parallel their expectations around Open Access publishing. The Royal Society of Chemistry has been funded by the Engineering and Physical Science Research of the UK to deliver a “chemical database service” for UK scientists. This presentation will provide an overview of the challenges associated with this project and our progress in delivering a chemistry repository capable of handling the complex data types associated with chemistry. The benefits of such a repository in terms of providing data to develop prediction models to further enable scientific discovery will be discussed and the potential impact on the future of scientific publishing will also be examined. 2013 CrossRef Workshops Text Data Mining Geoffrey Bilder
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The internet now offers access to a myriad of online resources that can be of value to chemists working in the Life Sciences. While finding information online is, in many cases, a simple search away, the accuracy and validity of the associated data and information should be questioned. As more databases and resources are introduced online, and commonly not integrated to other resources, a scientist must perform multiple searches and then undertake the task of meshing and merging data. ChemSpider is a freely accessible online database that has taken on the challenge of meshing together distributed resources across the internet to provide a structure-based hub. It is a crowdsourcing environment hosting over 26 million unique compounds linked out to over 400 data sources. With well defined programming interfaces for integration ChemSpider has been integrated to many commercial and open software packages and is presently serving as the chemistry foundation for the IMI Open PHACTS project.
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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.
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The document discusses ChemSpider, a free online chemical database, and its efforts to engage the chemistry community to help build and curate its database. It describes ChemSpider's roles in hosting and exposing chemical data as well as curating submitted data. It acknowledges that while crowdsourcing engagement has been low, more collaboration across databases could help improve overall data quality. Continued growth will depend on better engaging the community to contribute to and help shape the resource.Presentation of ChemSPider at PubChem Public Meeting
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ChemSpider is an online database of over 20 million chemical structures that aims to build a structure-centric community for chemists. It provides tools for structure drawing, searching databases of chemicals from various sources, and accessing related analytical data. Usage has grown to over 1200 unique users per day. ChemSpider plans to further enhance integration with other databases and literature, expand curation efforts, and generate predicted chemical properties to improve the resource.Dealing with the complex challenge of managing diverse analytical chemistry d...
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At a time when the data explosion has simply been redefined as “Big”, the hurdles associated with building a subject-specific data repository for chemistry are daunting. Combining a multitude of non-standard data formats for chemicals, related properties, reactions, spectra etc., together with the confusion of licensing and embargoing, and providing for data exchange and integration with services and platforms external to the repository, the challenge is significant. This all at a time when semantic technologies are touted as the fundamental technology to enhance integration and discoverability. Funding agencies are demanding change, especially a change towards access to open data to parallel their expectations around Open Access publishing. The Royal Society of Chemistry has been funded by the Engineering and Physical Science Research of the UK to deliver a “chemical database service” for UK scientists. This presentation will provide an overview of the challenges associated with this project and our progress in delivering a chemistry repository capable of handling the complex data types ssociated with chemistry. The benefits of such a repository in terms of providing data to develop prediction models to further enable scientific discovery will be discussed and the potential impact on the future of scientific publishing will also be examined. ChemSpider as a Foundation for Crowdsourcing and Collaborations in Open Chemi...
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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.2013 CrossRef Annual Meeting Strategic Update Geoffrey Bilder
1) The Prospect working group collaborating on a common API to enable text and data mining across publishers through content negotiation and licensing verification.
2) CrossRef metadata services like search, funding data through FundRef, and a proposed click-through licensing service for text mining.
3) Tools and services for small publishers around DOIs, archiving, and identifying member needs and interests.
CrossRef Text & Data Mining - UKSG 2015
CrossRef provides a text and data mining hub for researchers. It has built a cross-publisher API to allow researchers to access full text content from participating publishers for open access or subscribed content using a common protocol. The API addresses issues like negotiating permissions by including licensing information in article metadata and a registry of text and data mining terms and conditions. Over 14 million articles from publishers now include full-text links and license information to enable text and data mining through the CrossRef API.
Ifla 2010
The document discusses Arizona State University's home-grown online usage statistics website. It provides an overview of the website which librarians use as a valuable tool for collection assessment and decision making. The website displays usage reports from various electronic resources that the librarians gather from vendors. It outlines the steps taken to create the website, including compiling data, naming files, storing reports, and transferring files to a web server. The tool has helped ASU librarians in tasks like a collection realignment project aimed at reducing costs while minimizing impacts.
ICIC 2013 Conference Proceedings Antony Williams Royal Society of Chemistry
The Big Data Challenges Associated with Building a National Data Repository for Chemistry
Antony Williams (Royal Society of Chemistry , USA)
At a time when the data explosion has simply been redefined as “Big”, the hurdles associated with building a subject-specific data repository for chemistry are daunting. Combining a multitude of non-standard data formats for chemicals, related properties, reactions, spectra etc., together with the confusion of licensing and embargoing, and providing for data exchange and integration with services and platforms external to the repository, the challenge is significant. This all at a time when semantic technologies are touted as the fundamental technology to enhance integration and discoverability. Funding agencies are demanding change, especially a change towards access to open data to parallel their expectations around Open Access publishing. The Royal Society of Chemistry has been funded by the Engineering and Physical Science Research of the UK to deliver a “chemical database service” for UK scientists. This presentation will provide an overview of the challenges associated with this project and our progress in delivering a chemistry repository capable of handling the complex data types associated with chemistry. The benefits of such a repository in terms of providing data to develop prediction models to further enable scientific discovery will be discussed and the potential impact on the future of scientific publishing will also be examined.
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Cheta 25 may
- 1. Chemistry Using Text Annotation Lezan Hawizy, Peter Murray-Rust, Jun’ichi Tsujii, Bill Black, Jim Downing & Sophia Ananiadou Ba La
- 3. CheTA: issues Human annotations, especially in Chemistry, are • Accurate but labour-intensive • Very useful but expensive • Great benchmarks but time- consuming
- 5. CheTA: significance Automate the metadata generation for chemistry using text-mining tools
- 6. CheTA: significance Automate metadata generation for chemistry using text-mining tools
- 7. CheTA: significance Automate metadata generation for chemistry using text-mining tools Add chemistry to the largest repository of text-mining tools (U- Compare)
- 8. CheTA: significance Automate metadata generation for chemistry using text-mining tools Add chemistry to the largest repository of text-mining tools (U- Compare)
- 9. CheTA: significance Automate metadata generation for chemistry using text-mining tools Add chemistry to the largest repository of text-mining tools (U- Compare) Design chemistry specific workflows which are useful to all scientists in general.
- 10. CheTA: audience Annotators working on chemical documents Search engines wanting to incorporate new data into their indices Scientific community leaning towards using text-mining tools People responsible towards building corpora and evaluation standards
- 11. CheTA: currently … List of chemical entities Chemistry documents
- 12. CheTa: currently… Explore chemistry-text mining relation using OSCAR Examine new and efficient machine- learning techniques Design effective evaluation framework that can port to other domains as well
- 13. CheTA: oscarIT
- 14. CheTA: currently … Use U-Compare to Run applications User interface to compare different annotations Add chemistry to its repositories Implement the evaluation framework
Editor's Notes
- A typical view of annotation in Chemistry. Identify each entity, markup requisite labels and references. It is quite tedious and requires expert knowledge for efficient annotation.
- Why do we need these annotations? Because they are accurate! A human expert-knowledge is likely to very accurate. It is useful for automation such as training mathematical models for automatic named entity recognition. Once automation has been achieved, these human annotation can serve as great benchmarks!
- Combine text, process and visualisation
- Cheta aims to automate annotation
- Make chemistry accessible to other realms of Science
- Design mechanisms so that scientists can use various workflows without the need for programming acumen
- OSCAR reads a list of chemistry documents and returns a list of chemical entities such as chemical compounds, reaction, chemical adjectives etc.
- Napolean’s march graph of OSCAR. Describes how a document containing 4500 words is trimmed to a list of 467 entities.
- Tailor OSCAR into U-Compare components; design workflows. Add a user interface to compare several NERs.