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Additional file 1: Supplement 01 (v03) to “The Translational Medicine Ontology and Knowledge Base: Driving personalized medicine by bridging the gap between bench and bedside” A supplemental document containing the TMKB SPARQL queries and results created for this manuscript. (PDF 476 KB)

Ontologies have a wide range of uses beyond the semantic web. If you have had a productive conversation with an intelligent assistant such as Siri or Alexa, then you have used an ontology, perhaps without realising it. In this talk I talk about some of the varied ways ontologies are used in practice and what we’ve done at the Royal Society of Chemistry.

What is BridgeDb? Biological systems consist of many thousands of genes, proteins, and metabolites. Our collective knowledge about these entities is collected in many hundreds of disparate databases, each focusing on particular themes of knowledge or types of experiments. Importantly, to capture this focus, each database uses its own definition of the key entities and have a matching collection of entity identifiers. Linking all these identifiers requires a flexible tool that provides identifier mappings (IDmaps) but that also knows about these complexities. BridgeDb (bridgedb.org) offer IDmaps and understands the difference between a gene, a DNA sequence, a microarray probe, and a protein. Likewise, it understands the difference between stereoisomers, protonation states, and compound classes for metabolites and other small molecules. Modules and plugins are available to use BridgeDb in many bioinformatics toolsets.

Additional file 1. The supporting information for the paper entitled: PubChemRDF: towards the semantic annotation of PubChem compound and substance databases.

The Royal Society of Chemistry publishes many thousands of articles per year, the majority of these containing rich chemistry data that, in general, in limited in its value when isolated only to the HTML or PDF form of the articles commonly consumed by readers. RSC also has an archive of over 300,000 articles containing rich chemistry data especially in the form of chemicals, reactions, property data and analytical spectra. RSC is developing a platform integrating these various forms of chemistry data. The data will be aggregated both during the manuscript deposition process as well as the result of text-mining and extraction of data from across the RSC archive. This presentation will report on the development of the platform including our success in extracting compounds, reactions and spectral data from articles. We will also discuss our developing process for handling data at manuscript deposition and the integration and support of eLab Notebooks (ELNS) in terms of facilitating data deposition and sourcing data. Each of these processes is intended to ensure long-term access to research data with the intention of facilitating improved discovery.

We provide an overview of the use we make of ontologies at the Royal Society of Chemistry. Our engagement with the ontology community began in 2006 with preparations for Project Prospect, which used ChEBI and other Open Biomedical Ontologies to mark up journal articles. Subsequently Project Prospect has evolved into DERA (Digitally Enhancing the RSC Archive) and we have developed further ontologies for text markup, covering analytical methods and name reactions. Most recently we have been contributing to CHEMINF, an open-source cheminformatics ontology, as part of our work on disseminating calculated physicochemical properties of molecules via the Open PHACTS. We show how we represent these properties and how it can serve as a template for disseminating different sorts of chemical information.

In recent years the Royal Society of Chemistry has become known for our development of freely accessible data platforms including ChemSpider, ChemSpider Reactions and our new chemistry data repository. In order to support drug discovery RSC participates in a number of projects including the Open PHACTS semantic web project, the PharmaSea natural products discovery project and the Open Source Drug Discovery project in collaboration with a team in India. Our most recent developments include extending our efforts to support neglected diseases by the provision of high quality datasets resulting from our curation efforts to support modeling, the delivery of enhanced application programming interfaces to allow open source drug discovery teams to both source and deposit data from our chemistry databases and the provision of a micropublishing platform to report on various aspects of work supporting neglected disease drug discovery. This presentation will review our existing efforts and our plans for extended development.

The Royal Society of Chemistry has an archive of hundreds of thousands of published articles containing various types of chemistry related data – compounds, reactions, property data, spectral data etc. RSC has a vision of extracting as much of these data as possible and providing access via ChemSpider and its related projects. To this end we have applied a combination of text-mining extraction, image conversion and chemical validation and standardization approaches. The outcome of this project will result in new chemistry related data being added to our chemical and reaction databases and in the ability to more tightly couple web-based versions of the articles with these extracted data. The ability to search across the archive will be enhanced as a result. This presentation will report on our progress in this data extraction project and discuss how we will ultimately use similar approaches in our publishing pipeline to enhance article markup for new publications.

"The traditional perception of the publishing process has been that it culminates in a print article. The Royal Society of Chemistry (RSC) has for many years been acutely aware that there is a wealth of information contained in scientific communications that we publish and that its true value can only be unlocked by enabling the discovery of the data within them. This is challenging due to the variety of ways that scientists provide data, textually, graphically, and increasingly in supplementary information. This talk will outline how the RSC has applied innovative approaches, developed both internally and externally, to identifying important chemical data within the literature and provides tools to anyone using chemical data to analyse and improve its quality. Examples will include: Project Prospect, the Experimental Data Checker, our CIF data importer, ChemSpider and our structure validation and standardization service."

The production of valid and appropriate chemical structure representations which are appropriate for deposition into chemical structure databases and for inclusion into scientific publications requires adoption of a set of pre-processing filters and standardization procedures. As part of our ongoing effort to improve the quality of data for deposition into the RSC ChemSpider database, to provide a manner by which to validate and prepare data for publication and to provide a valuable service to the chemistry community, we have delivered the ChemValidator online service. This website provides access to an intuitive user interface for the upload of chemical compounds in various formats, pre-processing and standardization relative to a defined set of standards and validation checking of the chemicals according to a number of rules including hypervalency, absence of stereochemistry and charge balance. This presentation will report on the development of ChemValidator. This presentation was given by David Sharpe at the ACS Fall Meeting in 2012

Presentation delivered by Colin Batchelor from the RSC eScience team at ACS New Orleans Spring Meeting April 2013. There are dozens of public compound databases now available online, some of these providing access to tens of millions of chemical compounds. However, very little effort has been put into the delivery of databases of chemical reactions with the majority of large resources being commercial in nature. In our five years of delivering chemical based data resources to the chemistry community one of the primary requests has been that chemists want to know how to synthesize many of the chemicals they are researching. This presentation will provide an overview of our concerted efforts to enhance access to freely available chemistry data and will discuss the ChemSpider Reactions as an integrating hub of content including data extracted from US patents, from RSC Journals and databases and from our micro-publishing platform ChemSpider Synthetic Pages (CSSP).

As a result of the advent of internet technologies supporting participation on the internet via blogs, wikis and other social networking approaches, chemists now have an opportunity to contribute to the growing chemistry content on the web. As scientists an important skill to develop is the ability to succinctly report in a published format the details of scientific experimentation. The Royal Society of Chemistry provides a number of online systems to share chemistry data, the most well known of these being the ChemSpider database. In parallel the ChemSpider SyntheticPages (CSSP) platform is an online publishing platform for scientists, and especially students, to publish the details of chemical syntheses that they have performed. Using the rich capabilities of internet platforms, including the ability to display interactive spectral data and movies, CSSP is an ideal environment for students to publish their work, especially syntheses that might not support mainstream publication.

High quality chemical databases are struggling with protecting their data from the flow of wild machine-generated chemistry and lower-quality data. The period of primarily human curation prior to deposition in a database is gone and quality-conscious databases need to heavily rely on automated validation checks. An automated chemical validation system is being developed by the cheminformatics team at the Royal Society of Chemistry to be the “quality gatekeeper” of databases at the point of deposition. ChemSpider is leading a community-wide standardization approach starting with our support of the Open PHACTS semantic web project, an Innovative Medicines Initiative. The Chemical Validation and Standardization Platform (CVSP) is being designed as an open, flexible chemical validation and standardization platform that validates and standardizes chemical records. This presentation will review the existing beta version of the system and work in progress.

The Royal Society of Chemistry has an archive of published journals and books stretching back to 1841. In the past decade we have digitized this archive and semantically enriched our frontfile data with chemical structures linked to our free online chemical compound database, ChemSpider. In this talk we will survey our recent efforts to extract all kinds of data – chemical structures, experimental and bibliographic data – from both our backfile and frontfile. We will also discuss our future work to extract chemical reactions to host in our ChemSpider Reactions database and will discuss the potential applications of optical structure recognition technologies for converting structure images to structures as well as using similar techniques to convert experimental spectral data into interactive data formats. A key aspect of this project is the delivery of a crowdsourcing platform for the interactive annotation and validation of the extracted data.

ChemSpider is one of the chemistry community’s primary public compound databases. Containing tens of millions of chemical compounds and its associated data ChemSpider serves data to many tens of websites and software applications at this point. This presentation will provide an overview of the expanding reach of the ChemSpider platform and the nature of solutions that it helps to enable. We will also discuss some of the future directions for the project that are envisaged and how we intend to continue expanding the impact for the platform.

We present two complementary annotation schemes for sentence based annotation of full scientific papers, CoreSC and AZ-II, which have been applied to primary research articles in chemistry. The AZ scheme is based on the rhetorical structure of a scientific paper and follows the knowledge claims made by the authors. It has been shown to be reliably annotated by independent human coders and has proven useful for various information access tasks. AZ-II is its extended version, which has been successfully applied to chemistry. The CoreSC scheme takes a different view of scientific papers, treating them as the humanly readable representations of scientific investigations.\ud It therefore seeks to retrieve the structure of the investigation from the paper as generic high-level Core Scientific Concepts (CoreSC). CoreSCs have been annotated by 16 chemistry experts over a total of 265 full papers in physical chemistry and biochemistry. We describe the differences and similarities between the two schemes in detail and present the two corpora produced using each scheme. There are 36 shared papers in the corpora, which allows us to quantitatively compare aspects of the annotation schemes. We show the correlation between the two schemes, their strengths and weaknesses and discuss the benefits of combining a rhetorical based analysis of the papers\ud with a content-based one.

The paper describes initial work on an ontology based tool, ART, for the semantic annotation of papers stored in digital repositories. ART is intended for the annotation not only of data and metadata about a paper, but also the main elements of the described scientific investigation, such as goals, hypotheses, and observations. ART will also be able to aid in the expression of research results directly in a semantic format, through the composition of text using ontology-based templates and stored typical key phrases for the description of basic elements of the research. ART's system design, its functionality, and related projects are discussed. An example annotated paper is presented in order to demonstrate the expected output of the tool.