Literature-data integration in the life sciences – Jo McEntyre, EMBL-EBI
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OpenAIREplus workshop - “Linking Open Access publications to data – policy development and implementation” (June 11, 2012)
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http://www.seek4science.org
CrossRef DOIs for African Journal Partnership Journals
This document discusses CrossRef and the services it provides to scholarly publishers and journals. CrossRef is a not-for-profit organization that provides Digital Object Identifiers (DOIs) and linking services to over 5,000 member publications. It summarizes CrossRef's reference linking, metadata, and plagiarism checking services. It also provides information for African journals on how to get CrossRef DOIs and participate in CrossRef programs and services.
The royal society of chemistry and its adoption of semantic web technologies ...
Semantic web technologies have quickly penetrated all areas of traditional and new database systems and have become the de facto standard in information exchange and communication. The Royal Society of Chemistry has built a new chemistry data repository with the semantic web at the core of the system. Every module of the data repository contains a semantic web layer and is able to interact internally and externally using standard approaches and formats including RDF, appropriate ontologies, SPARQL querying and so on. In this presentation we will review the challenges associated with developing this new system based on semantic web technologies and how the approach that we have taken offers distinct advantages over the original data model designed to produce the ChemSpider database. Its advantages include extensibility, an ontological underpinning, federated integration and the adoption of modern standards rather than the constraints of a standard SQL model.
20140327 rda plazi_final
This document summarizes a presentation about the Plazi Treatment Repository project. It discusses how Plazi aims to make over 1 million taxonomic treatments openly accessible by semantically enhancing and linking content from biodiversity literature. A major challenge is copyright restrictions on publications, which Plazi addresses by only including non-copyrighted content and material for internal use. The presentation argues for legal changes like mandatory research licenses to further remove barriers to information exchange.
Proteomics and the "big data" trend: challenges and new possibilitites (Talk ...
Proteomics and the "big data" trend: challenges and new possibilitites (Talk ...Juan Antonio Vizcaino
The document discusses the challenges and opportunities of big data in proteomics. It describes how proteomics data volumes are growing rapidly due to technological advances, creating both computational challenges for data analysis and opportunities to reuse large amounts of public data. The PRIDE Archive at EBI stores over 4,000 proteomics datasets and provides tools like PRIDE Inspector to help analyze and validate large datasets. However, challenges remain around data standardization, metadata completeness, and the need for greater computational infrastructure and expertise to fully leverage the large amounts of shared proteomics data.Semantics as a service at EMBL-EBI
This document discusses using ontologies to make biological and biomedical data more interoperable and FAIR (Findable, Accessible, Interoperable, Reusable). It describes several ontology services and tools provided by EMBL-EBI to help with tasks like annotating data, mapping data to ontologies, searching and accessing ontologies, and publishing structured data. It also uses the example of the BioSamples database to illustrate challenges in working with large, heterogeneous datasets and how ontologies can help address issues like normalizing descriptions and attributes to enable better searching and data integration.
China: Journal Publishing, DOI and CrossCheck (2011 CrossRef Workshops)
This document summarizes information about journal publishing in China. It notes that China publishes around 5,000 scientific journals annually, with around 220 having English editions. Major digital databases that index Chinese journals are also discussed, including CNKI and WanFang Data, which together index over 170 million articles. The use of digital identifiers like DOI in China is still developing, with challenges around integrating Chinese-language journals and databases with international identifiers and services like CrossRef and CrossCheck.
The UK National Chemical Database Service – an integration of commercial and ...
The UK National Chemical Database Service – an integration of commercial and ...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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. BioDBCore: Current Status and Next Developments
The document discusses BioDBCore, a collaborative project aimed at gathering and standardizing metadata about biological databases. It provides an overview of BioDBCore's goals of improving data integration, encouraging standards, and maximizing resources. BioDBCore is led by Pascale Gaudet and Philippe Rocca-Serra and implemented on the BioSharing website. The document outlines the BioDBCore descriptors for databases and provides an example entry for the dictyBase database. It discusses maintaining and expanding BioDBCore records with the help of database providers and journals.
Tools and approaches for data deposition into nanomaterial databases
This document summarizes tools and approaches for depositing nanomaterial data into databases. It discusses the need for organized nanomaterial data and describes objectives to develop an interactive notebook called NanoBook for capturing characterization data. It aims to enhance the Nanomaterial Registry ontology and implement computational tools for quantitative structure-property relationship modeling to guide experimental design of novel nanomaterials. Challenges include developing descriptors for diverse nanoparticle structures and conducting systematic studies. The proposed solution is an open science data repository to map, import, export and analyze nanomaterial documents and data.
OSFair2017 Workshop | How FAIR friendly is the FAIRDOM Hub? Exposing metadata...
Carole Goble presents the FAIRDOM | OSFair2017 Workshop
Workshop title: How FAIR friendly is your data catalogue?
Workshop overview:
This workshop will build upon the work planned by the EOSCpilot data interoperability task and the BlueBridge workshop held on April 3 at the RDA meeting. We will investigate common mechanisms for interoperation of data catalogues that preserve established community standards, norms and resources, while simplifying the process of being/becoming FAIR. Can we have a simple interoperability architecture based on a common set of metadata types? What are the minimum metadata requirements to expose FAIR data to EOSC services and EOSC users?
DAY 3 - PARALLEL SESSION 6 & 7
Proteomics public data resources: enabling "big data" analysis in proteomics
Presentation given during the International de.NBI Symposium: "Bioinformatics for human Health and Disease" (Heidelberg, November 2016)
FAIR data and model management for systems biology.
Written and presented by Carole Goble (University of Manchester) as part of Intelligent Systems for Molecular Biology (ISMB), Dublin. July 10th - 14th 2015.
Royal society of chemistry activities to develop a data repository for chemis...
Royal society of chemistry activities to develop a data repository for chemis...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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. A chemistry data repository to serve them all
A chemistry data repository to serve them allUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Over the past five years the Royal Society of Chemistry has become world renowned for its public domain compound database that integrates chemical structures with online resources and available data. ChemSpider regularly serves over 50,000 users per day who are seeking chemistry related data. In parallel we have used ChemSpider and available software services to underpin a number of grant-based projects that we have been involved with: Open PHACTS – a semantic web project integrating chemistry and biology data, PharmaSea – seeking out new natural products from the ocean and the National Chemical Database Service for the United Kingdom. We are presently developing a new architecture that will offer broader scope in terms of the types of chemistry data that can be hosted. This presentation will provide an overview of our Cheminformatics activities at RSC, the development of a new architecture for a data repository that will underpin a global chemistry network, and the challenges ahead, as well as our activities in releasing software and data to the chemistry community. Big data challenges associated with building a national data repository for c...
Big data challenges associated with building a national data repository for c...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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. Embracing Semantic Technology for Better Metadata Authoring in Biomedicine (S...
Embracing Semantic Technology for Better Metadata Authoring in Biomedicine (S...CEDAR: Center for Expanded Data Annotation and Retrieval
The Center for Expanded Data Annotation and Retrieval (CEDAR) has developed a suite of tools and services that allow scientists to create and publish metadata describing scientific experiments. Using these tools and services—referred to collectively as the CEDAR Workbench—scientists can collaboratively author metadata and submit them to public repositories. A key focus of our software is semantically enriching metadata with ontology terms. The system combines emerging technologies, such as JSON-LD and graph databases, with modern software development technologies, such as microservices and container platforms. The result is a suite of user-friendly, Web-based tools and REST APIs that provide a versatile end-to-end solution to the problems of metadata authoring and management. This talk presents the architecture of the CEDAR Workbench and focuses on the technology choices made to construct an easily usable, open system that allows users to create and publish semantically enriched metadata in standard Web formats.Dealing with the complex challenge of managing diverse analytical chemistry d...
Dealing with the complex challenge of managing diverse analytical chemistry d...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This document discusses ChemSpider, an online database of chemical compounds. It summarizes ChemSpider's capabilities, including searching by mass or formula for structure identification. ChemSpider contains over 34 million chemicals from various sources that can be searched and filtered. The document outlines how ChemSpider provides value to mass spectrometrists and discusses efforts to integrate more spectral data like NMR spectra directly into ChemSpider from publications and individual submissions. Future goals include hosting over a million spectra online and improving visualization of spectral data.What's hot (20)
Clustering the royal society of chemistry chemical repository to enable enhan...
Clustering the royal society of chemistry chemical repository to enable enhan...
Building a semantic chemistry platform with the royal society of chemistry
Building a semantic chemistry platform with the royal society of chemistry
FAIR Data and Model Management for Systems Biology (and SOPs too!)
FAIR Data and Model Management for Systems Biology (and SOPs too!)
CrossRef DOIs for African Journal Partnership Journals
CrossRef DOIs for African Journal Partnership Journals
The royal society of chemistry and its adoption of semantic web technologies ...
The royal society of chemistry and its adoption of semantic web technologies ...
Proteomics and the "big data" trend: challenges and new possibilitites (Talk ...
Proteomics and the "big data" trend: challenges and new possibilitites (Talk ...
China: Journal Publishing, DOI and CrossCheck (2011 CrossRef Workshops)
China: Journal Publishing, DOI and CrossCheck (2011 CrossRef Workshops)
The UK National Chemical Database Service – an integration of commercial and ...
The UK National Chemical Database Service – an integration of commercial and ...
Tools and approaches for data deposition into nanomaterial databases
Tools and approaches for data deposition into nanomaterial databases
OSFair2017 Workshop | How FAIR friendly is the FAIRDOM Hub? Exposing metadata...
OSFair2017 Workshop | How FAIR friendly is the FAIRDOM Hub? Exposing metadata...
Proteomics public data resources: enabling "big data" analysis in proteomics
Proteomics public data resources: enabling "big data" analysis in proteomics
FAIR data and model management for systems biology.
FAIR data and model management for systems biology.
Royal society of chemistry activities to develop a data repository for chemis...
Royal society of chemistry activities to develop a data repository for chemis...
Big data challenges associated with building a national data repository for c...
Big data challenges associated with building a national data repository for c...
Embracing Semantic Technology for Better Metadata Authoring in Biomedicine (S...
Embracing Semantic Technology for Better Metadata Authoring in Biomedicine (S...
Dealing with the complex challenge of managing diverse analytical chemistry d...
Dealing with the complex challenge of managing diverse analytical chemistry d...
Similar to Literature-data integration in the life sciences – Jo McEntyre, EMBL-EBI
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.
Mcentyre dryad-orcid_may2013
This document provides an overview of Europe PubMed Central, a repository for life science literature built in collaboration with PubMed Central USA and Canada. It contains over 28 million abstracts and 2.5 million full text articles, with 600k open access articles. The document outlines reasons to use Europe PMC including integrated searching of abstracts and full text, semantic enrichment of text, and citation linking. It also discusses providing credit for authors, funders, and data through features like author search and linking publications to ORCID profiles. Tools are being developed for database curators to monitor when data is cited in articles.
Activities at the Royal Society of Chemistry to gather, extract and analyze b...
Activities at the Royal Society of Chemistry to gather, extract and analyze b...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The phrase “Big Data” is generally used to describe a large volume of structured and/or unstructured data that cannot be processed using traditional database and software techniques. In the domain of chemistry the Royal Society of Chemistry certainly hosts large structured databases of chemistry data, for example ChemSpider, as well as unstructured content, in the form of our collection of scientific articles. Our research literature provides value to their readership and, at present, as an example of one of our databases, ChemSpider is accessed by many tens of thousands of scientists every day. But do these collections constitute “Big Data” or is it the potential which lies within the collections that can contribute to the Big Data movement. This presentation will discuss our activities to contribute both data, and service-based access to our data sets, to support grant-based projects such as the Innovative Medicines Initiative Open PHACTS project (to support drug discovery) and the PharmaSea initiative (to identify novel natural products from the ocean). We will also provide an overview of our activities to perform data mining of public patent collections and examine what can be done with the data. We are presently extracting physicochemical properties and textual forms of NMR spectra and, with the resulting data, are building predictive models (for melting points at present) and assembling a large NMR spectral database containing many hundreds of thousands of spectral-structure pairs. Our experiences to date have demonstrated that we are working at the edge of current algorithmic and computing capabilities for predictive model building, with over a quarter of a million melting points producing a matrix of over 200 billion descriptors. Our work to produce the NMR spectral database will necessitate batch processing of the data to examine consistency between the spectral-structure pairs and other forms of data validation. The intention is to take our experiences in this work applied to a public patents corpus and apply it to the RSC back file of publications to mine data and enable new paths to the discoverability of both data and the associated publications. Dealing with the complex challenge of managing diverse chemistry data online
Dealing with the complex challenge of managing diverse chemistry data onlineUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The Royal Society of Chemistry has provided access to data associated with millions of chemical compounds via our ChemSpider database for over 5 years. During this period the richness and complexity of the data has continued to expand dramatically and the original vision for providing an integrated hub for structure-centric data has been delivered across the world to hundreds of thousands of users. With an intention of expanding the reach to cover more diverse aspects of chemistry-related data including compounds, reactions and analytical data, to name just a few data-types, we are in the process of implementing a new architecture to build a Chemistry Data Repository. The data repository will manage the challenges of associated metadata, the various levels of required security (private, shared and public) and exposing the data as appropriate using semantic web technologies. Ultimately this platform will become the host for all chemicals, reactions and analytical data contained within RSC publications and specifically supplementary information. This presentation will report on how our efforts to manage chemistry related data has impacted chemists and projects across the world and will review specifically our contributions to projects involving natural products for collaborators in Brazil and China, for the Open Source Drug Discovery project in India, and our collaborations with scientists in Russia.
Dealing with the complex challenge of managing diverse chemistry data online
This document discusses the challenges of managing chemistry data online and the development of an open data repository to address these challenges. It proposes a new architecture for a data repository that would integrate diverse chemistry data types through APIs and user interfaces. The repository would standardize data, enable deposition from various sources, and provide metrics and recognition to encourage participation. However, challenges remain around data formats, encouraging data sharing, and meeting scientists' needs. The document advocates for continued testing and collaboration to develop effective solutions.
The application of cloud computing to royal society of chemistry data platforms
Cloud computing offers significant advantages for the hosting of RSC chemistry databases in terms of reliability, performance and access to large scale computational power. The ChemSpider database contains almost 30 million unique chemical compounds and access to compute power to regenerate properties and add new properties is essential for efficient delivery on a manageable timescale. The use of cloud-based facilities reduces the needs for internal infrastructure and enhances performance generally at the cost of significant recoding of the platforms. This presentation will review our move of our ChemSpider related projects to the cloud, the associated challenges and both the obvious and unforeseen benefits. We will also discuss our use of parallelization technologies for mass calculation using Hadoop.
Globus in European Life Science
This presentation was given at the 2019 GlobusWorld Conference in Chicago, IL by Steven Newhouse from European Bioinformatics Institute.
Data integration
This document provides an overview of data integration in biology, including why it is needed, common problems, and popular approaches. It discusses the many different biological data sources and standards that have been developed for integration. Different architectures for data integration are described, including data warehousing, federation, and view integration. Key variables that affect integration like scope, domain, and interfaces are outlined. Important standards, ontologies, guidelines and tools that support integration are also reviewed.
NEBASE Hour - August 2008 - What's New At OCLC?
This document summarizes a presentation given by Christa Burns from OCLC about updates and new developments. It notes that OCLC has over 69,000 member libraries in 112 countries. It then summarizes some of the new initiatives and programs discussed, including the new governance structure, WorldCat Local pilot program, increased ebook offerings, and partnerships to share library data with Google and load national library records from countries around the world into WorldCat. It concludes by emphasizing OCLC's goal of further connecting the world's libraries through more collaboration, members, countries, and innovation.
ChemSpider – disseminating data and enabling an abundance of chemistry platforms
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.
Ontology Web Services for Semantic Applications
The document summarizes the Ontology Web Services provided by the National Center for Biomedical Ontology (NCBO) including the BioPortal Ontology Web services, NCBO Annotator Web service, and NCBO Resource Index Web service. These services allow programmatic access and traversal of ontologies, annotation of text with ontology terms, and searching of public biomedical data repositories indexed with ontology terms. The services aim to facilitate integration and interpretation of biomedical data on the Semantic Web.
Prototype Phase Kick-off Event and Ceremony
On Monday 7 December 2020, the selected consortia for the ARCHIVER prototype phase have been announced during a Public Award Ceremony.
The Kick-off marks the beginning of the Prototype implementation Phase, where the three selected to move forward will build prototypes of their solutions including all components, and basic functionality, interoperability, and security tests will be performed by IT specialists from the buyers’ group.
2013 CrossRef Annual Meeting Flash Update CrossCheck and CrossMark Rachael La...
This document summarizes statistics from CrossRef including that they index over 38 million content items from 527 publishers and screen over 80,000 documents per month. It also outlines features of CrossRef like CrossMark which tracks updates to articles and has over 270,000 deposits and 2,700 updates. Finally, it lists some publisher members that participate in CrossRef like major publishers Elsevier, Wiley, and Cambridge University Press.
ICIC 2017: Tutorial - Digging bioactive chemistry out of patents using open r...
Christopher Southan (The IUPHAR/BPS Guide to PHARMACOLOGY, UK)
While the raison d'être of patents is Intellectual Property (IP) there is a growing awareness of the scientific value of their data content. This is particularly so in medicinal chemistry and associated bioactivity domains where disclosed compounds and associated data not only exceeds that published in papers by several-fold and surfaces years earlier, but is also, paradoxically; completely open (i.e. no paywalls). Scientists have traditionally extracted their own relationships or used commercial sources but the last few years have seen a “big bang” in patent extractions submitted to open databases, including nearly 20 million structures now in PubChem.
This tutorial will:
Outline the statistics of patent chemistry in various open sources
Introduce a spectrum of open resources and tools
Enable an understanding of target identification, bioactivity and SAR extraction from patents and connecting these relationships to papers
Cover aspects of medicinal chemistry patent mining
Include hands on exercises using open source antimalarial research as examples
The focus will be on public databases and patent office portals, since these can be transparently demonstrated. However, the essential complementarity with commercial resources will be touched on. Those engaged in Competitive Intelligence will also find the material relevant.
iMicrobe_ASLO_2015
An Overview of the iMicrobe Project and available tools in the iPlant Cyberinfrastructure. This talk was given at a workshop at ASLO in Granada, Spain focused on applications in Oceanography and Limnology.
Semantic Web & Web 3.0 empowering real world outcomes in biomedical research ...
Talk presented in Spain (WiMS 2013/UAM-Madrid, UMA-Malaga), June 2013.
Replaces earlier version at: http://www.slideshare.net/apsheth/semantic-technology-empowering-real-world-outcomes-in-biomedical-research-and-clinical-practices
Biomedical and translational research as well as clinical practice are increasingly data driven. Activities routinely involve large number of devices, data and people, resulting in the challenges associated with volume, velocity (change), variety (heterogeneity) and veracity (provenance, quality). Equally important is to realize the challenge of serving the needs of broader ecosystems of people and organizations, extending traditional stakeholders like drug makers, clinicians and policy makers, to increasingly technology savvy and information empowered patients. We believe that semantics is becoming centerpiece of informatics solutions that convert data into meaningful, contextually relevant information and insights that lead to optimal decisions for translational research and 360 degree health, fitness and well-being.
In this talk, I will provide a series of snapshots of efforts in which semantic approach and technology is the key enabler. I will emphasize real-world and in-use projects, technologies and systems, involving significant collaborations between my team and biomedical researchers or practicing clinicians. Examples include:
• Active Semantic Electronic Medical Record
• Semantics and Services enabled Problem Solving Environment for T.cruzi (SPSE)
• Data Mining of Cardiology data
• Semantic Search, Browsing and Literature Based Discovery
• PREscription Drug abuse Online Surveillance and Epidemiology (PREDOSE)
• kHealth: development of a knowledge-enhanced sensing and mobile computing applications (using low cost sensors and smartphone), along with ability to convert low level observations into clinically relevant abstractions
Further details are at http://knoesis.org/amit/hcls
Connecting life sciences data at the European Bioinformatics Institute
Tony Burdett's slides from his talk at Connected Data London. Tony is a Senior Software Engineer at The European Bioinformatics Institute. He presented the complexity of data at the EMBL-EBI and what is their solution to make sense of all this data.
Biological Database (1)pptxpdfpdfpdf.pdf
Biological databases store and organize large amounts of biological data for research use. There are many types of biological databases that classify data by type, such as nucleotide sequences, protein sequences, genomes, protein structures, gene expression, and metabolic pathways. Databases can also be classified by their data source as primary databases containing experimental results or secondary databases that analyze primary database results. Database availability varies, with some publicly open and others proprietary. Common biological databases discussed include GenBank, UniProt, PDB, KEGG, and FlyBase.
Data integration
This document discusses data integration in bioinformatics. It begins by explaining why data integration is needed due to the large number of specialized databases and diversity of data types. It then defines data integration as combining data from different sources into a unified view. Some of the challenges of data integration mentioned include different data schemas, interfaces and vocabularies between databases. Several common approaches to data integration are described, including data centralization, federated databases and view integration. Important variables that affect integration approaches are also outlined, such as the domain, architecture and query interface. Finally, some examples of commonly used tools for tasks like workflow management, web services and format standards are provided.
Health Datapalooza 2013: Open Government Data - Natasha Noy
Health Datapalooza IV: June 3rd-4th, 2013
Open Government Data
Moderator:
George Thomas, Enterprise Architect, Office of the Chief Information Officer (CIO), U.S. Department of Health & Human Services
Speakers:
John Erickson, Director of Web Science Operations, Tetherless Word Constellation, Rensselaer Polytechnic Institute
James P. McCusker, Ph.D Student, Dept. of Computer Science, Rensselaer Polytechnic Institute
Mark Musen, Professor, Stanford University and Principal Investigator, National Center for Biomedical Ontologies
Natasha Noy, Senior Research Scientist, Stanford University and Executive Committee Member, National Center for Biomedical Ontologies
Michael Pendleton, Linked Open Data Manager, US Environmental Protection Agency
The session will open with an overview of trends affecting open data sharing, including ‘broad data’ challenges that emerge when application developers have millions of open government datasets available. We will explore issues of web-scale data discovery, rapid and potentially ad hoc integration, visualization, and analysis of partially modeled datasets as well as issues arising from combining different data use policies. We will present emerging solution standards and transitioning academic technologies, including innovative work conducted by the ‘Watson’ research group at Rensselaer Polytechnic Institute on using Watson as a ‘data advisor’. Panelists will synthesize session topics including optimal steps toward an open health knowledge graph facilitating ‘data liquidity’ (as defined by the ability to easily combine and refine data from disparate publishers). Panelists will discuss enabling the implementation of effective ‘lifting schemes’ by leveraging ‘collaboration without coordination’ processes to produce efficient data access techniques that drive innovative new application development tools, products, and services.
Similar to Literature-data integration in the life sciences – Jo McEntyre, EMBL-EBI (20)
ICIC 2013 Conference Proceedings Antony Williams Royal Society of Chemistry
ICIC 2013 Conference Proceedings Antony Williams Royal Society of Chemistry
Activities at the Royal Society of Chemistry to gather, extract and analyze b...
Activities at the Royal Society of Chemistry to gather, extract and analyze b...
Dealing with the complex challenge of managing diverse chemistry data online
Dealing with the complex challenge of managing diverse chemistry data online
Dealing with the complex challenge of managing diverse chemistry data online
Dealing with the complex challenge of managing diverse chemistry data online
The application of cloud computing to royal society of chemistry data platforms
The application of cloud computing to royal society of chemistry data platforms
ChemSpider – disseminating data and enabling an abundance of chemistry platforms
ChemSpider – disseminating data and enabling an abundance of chemistry platforms
2013 CrossRef Annual Meeting Flash Update CrossCheck and CrossMark Rachael La...
2013 CrossRef Annual Meeting Flash Update CrossCheck and CrossMark Rachael La...
ICIC 2017: Tutorial - Digging bioactive chemistry out of patents using open r...
ICIC 2017: Tutorial - Digging bioactive chemistry out of patents using open r...
Semantic Web & Web 3.0 empowering real world outcomes in biomedical research ...
Semantic Web & Web 3.0 empowering real world outcomes in biomedical research ...
Connecting life sciences data at the European Bioinformatics Institute
Connecting life sciences data at the European Bioinformatics Institute
Health Datapalooza 2013: Open Government Data - Natasha Noy
Health Datapalooza 2013: Open Government Data - Natasha Noy
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- 2. Overview • • • • What literature? What data? How we make literature-data connections Case study Challenges and future directions
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- 11. Links • by the author - on submission, as metadata (primary databases) • by database curators - information and links from the literature • expensive, slow, but high quality Text mining • by algorithms that use terminologies (can be subject to lag) • post publication – can find new associations • variable quality, but high throughput
- 12. Links from Literature to Databases • • • • • • • • • 800 K 370 K 110 K Proteins Nucleotides OMIM Chemicals Structure Clinical reviews Protein families Protein-protein interactions Gene expression experiments …
- 13. Text Mining in UKPMC (2.2 million articles) Semantic Type Gene/Protein Unique Terms Articles Annotations 225,905 1,288,809 15,021,502 GO Terms 32,486 1,806,539 15,016,957 Organism 178,847 1,689,251 12,322,782 Disease 170,592 1,743,212 16,201,198 Accession No. 232,950 65,640 331,329 76,350 1,669,500 22,438,980 Chemical
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- 15. 3.9 billion years ago
- 16. E. Coli meets humans Human colon cancer DNA repair
- 17. 07/21/10 17
- 19. Protein structure in PDBe
- 20. Link to the literature from the PDBe record
- 21. Algorithms that find similar structures
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- 23. Towards understanding DNA repair mechanisms
- 24. Challenges and future directions
- 25. Data-driven science Data re-use: biology is post publication Linking: citing papers and data (provenance and integration) Metrics and attribution Hard decisions about value of keeping complete data sets
- 26. Data landscape - possibilities analysis Research articles Unstructured Data Structured links Big Data: Deposition Primary Big Data: Curated Annotation reuse?
- 27. PDF HTML GIF JPG TIF MOV DOC Analysis supplied by Mimas, University of Manchester XSL
- 28. Solutions that make sense to scientists