BioIT 2009 BioCatalogue slides by Carole GobleBioCatalogue
Biocatalogue is a public, curated catalog of life science web services that allows users to register, find, and curate web services. It utilizes a community-sourced approach to annotation and expert oversight. The catalog is currently in a beta phase and contains over 465 services. It provides standardized descriptions, functional annotations, and metrics to help users understand what services are available and how they can be used.
Altmetrics to track the impact of datasetsPat Loria
There are many good reasons why researchers might track the impact of their datasets. To provide supplementary evidence of influence for the next grant application or performance review or promotional opportunity. Or to track impact on the academy, on industry, on society or public policy. Could people or organizations engaging with a dataset become potential partners or collaborators?
Altmetrics provide quantitative evidence of impact or influence by reporting scholarly and social online engagement with research datasets. They can be tracked using a range of services, from the more traditional citation databases to data and institutional repositories, and of course from altmetrics aggregator services.
But we need to be careful not to create additional administrative burdens on time-poor researchers and also of the limitations in data citation practices or the lack thereof. One way we can achieve the former is to harvest altmetrics into our institutional repositories or data discovery services, saving time for the researcher by providing a systems solution.
Cancer View Canada is a platform that aims to connect Canadians to cancer services, information and resources. It provides a centralized hub for knowledge management, collaboration and sharing of resources across the Canadian cancer control community. The platform features tools for collecting and uploading content, connecting with other users, and collaborating online. It also includes a federated search tool that allows simultaneous searching of multiple online databases related to Canadian cancer control. The goal is to make high-quality cancer information and services more accessible nationwide.
The Diversity of Biomedical Data, Databases and Standards (Research Data Alli...Peter McQuilton
A 10 minute presentation given in Denver (CO) on the 15th September as part of the IG Elixir Bridging Force, WG Biosharing Registry,WG Data Type Registries,WG Metadata Standards Catalog joint session of the Research Data Alliance 8th Plenary (part of International Data Week).
This presentation covers the proliferation of data, databases, and data standards in biomedicine, and how BioSharing can help inform and educate users on this landscape and relationships between data, databases and data standards.
Beacon: A Protocol for Federated Discovery and Sharing of Genomic DataMiro Cupak
The document summarizes Beacon, a protocol for federated discovery and sharing of genomic data across institutions. It allows institutions to share whether they have information on specific genetic mutations through a standardized web service API. Over 25 genomic organizations representing over 160 datasets totaling over 2 million queries participate in the Beacon Network, which searches across participating beacons and aggregates the results.
Beacon Network: A System for Global Genomic Data SharingMiro Cupak
A global federated network called the Beacon Network was created to share genomic data in order to drive discoveries and applications in medicine. The Beacon Network allows users to query beacons from various genomic organizations to discover if they have information about specific genetic mutations. It translates queries and intelligently distributes them across over 60 beacons from 25 organizations. Since launching, the Beacon Network has served over 400,000 queries from users in over 100 countries, resulting in over 2 million queries to participants of the network.
research participation as a social contractBrian Bot
Brian Bot discusses Sage Bionetworks' approach to promote open sharing of complex biological data through engaging communities of researchers and empowering citizens to contribute health data to research. The summary describes Sage Bionetworks' ResearchKit and mPower apps that have collected data from thousands of participants to study Parkinson's disease.
Beacon Network: A System for Global Genomic Data SharingMiro Cupak
The Beacon Network provides a system for global genomic data sharing by allowing users to query a network of genetic data sources to determine if a particular genetic variant or mutation exists in their databases. It began as a web service called Beacon that responds with "yes" or "no" to questions about genetic mutations. The Beacon Network expands this by distributing queries across multiple beacons and aggregating the results. It currently includes over 25 genomic organizations with access to over 2 million samples and 2 billion genetic variants, serving hundreds of thousands of queries from users around the world. The goal is to facilitate discovery of new links between genetic data and health conditions.
BioIT 2009 BioCatalogue slides by Carole GobleBioCatalogue
Biocatalogue is a public, curated catalog of life science web services that allows users to register, find, and curate web services. It utilizes a community-sourced approach to annotation and expert oversight. The catalog is currently in a beta phase and contains over 465 services. It provides standardized descriptions, functional annotations, and metrics to help users understand what services are available and how they can be used.
Altmetrics to track the impact of datasetsPat Loria
There are many good reasons why researchers might track the impact of their datasets. To provide supplementary evidence of influence for the next grant application or performance review or promotional opportunity. Or to track impact on the academy, on industry, on society or public policy. Could people or organizations engaging with a dataset become potential partners or collaborators?
Altmetrics provide quantitative evidence of impact or influence by reporting scholarly and social online engagement with research datasets. They can be tracked using a range of services, from the more traditional citation databases to data and institutional repositories, and of course from altmetrics aggregator services.
But we need to be careful not to create additional administrative burdens on time-poor researchers and also of the limitations in data citation practices or the lack thereof. One way we can achieve the former is to harvest altmetrics into our institutional repositories or data discovery services, saving time for the researcher by providing a systems solution.
Cancer View Canada is a platform that aims to connect Canadians to cancer services, information and resources. It provides a centralized hub for knowledge management, collaboration and sharing of resources across the Canadian cancer control community. The platform features tools for collecting and uploading content, connecting with other users, and collaborating online. It also includes a federated search tool that allows simultaneous searching of multiple online databases related to Canadian cancer control. The goal is to make high-quality cancer information and services more accessible nationwide.
The Diversity of Biomedical Data, Databases and Standards (Research Data Alli...Peter McQuilton
A 10 minute presentation given in Denver (CO) on the 15th September as part of the IG Elixir Bridging Force, WG Biosharing Registry,WG Data Type Registries,WG Metadata Standards Catalog joint session of the Research Data Alliance 8th Plenary (part of International Data Week).
This presentation covers the proliferation of data, databases, and data standards in biomedicine, and how BioSharing can help inform and educate users on this landscape and relationships between data, databases and data standards.
Beacon: A Protocol for Federated Discovery and Sharing of Genomic DataMiro Cupak
The document summarizes Beacon, a protocol for federated discovery and sharing of genomic data across institutions. It allows institutions to share whether they have information on specific genetic mutations through a standardized web service API. Over 25 genomic organizations representing over 160 datasets totaling over 2 million queries participate in the Beacon Network, which searches across participating beacons and aggregates the results.
Beacon Network: A System for Global Genomic Data SharingMiro Cupak
A global federated network called the Beacon Network was created to share genomic data in order to drive discoveries and applications in medicine. The Beacon Network allows users to query beacons from various genomic organizations to discover if they have information about specific genetic mutations. It translates queries and intelligently distributes them across over 60 beacons from 25 organizations. Since launching, the Beacon Network has served over 400,000 queries from users in over 100 countries, resulting in over 2 million queries to participants of the network.
research participation as a social contractBrian Bot
Brian Bot discusses Sage Bionetworks' approach to promote open sharing of complex biological data through engaging communities of researchers and empowering citizens to contribute health data to research. The summary describes Sage Bionetworks' ResearchKit and mPower apps that have collected data from thousands of participants to study Parkinson's disease.
Beacon Network: A System for Global Genomic Data SharingMiro Cupak
The Beacon Network provides a system for global genomic data sharing by allowing users to query a network of genetic data sources to determine if a particular genetic variant or mutation exists in their databases. It began as a web service called Beacon that responds with "yes" or "no" to questions about genetic mutations. The Beacon Network expands this by distributing queries across multiple beacons and aggregating the results. It currently includes over 25 genomic organizations with access to over 2 million samples and 2 billion genetic variants, serving hundreds of thousands of queries from users around the world. The goal is to facilitate discovery of new links between genetic data and health conditions.
BioCatalogue talk by Carole Goble. She outlines in these slides the reasons behind the BioCatalogue project. And present the BioCatalogue and its goals.
BioCatalogue DILS & Enfin 2009 by JitsBioCatalogue
Jiten Bhagat presented on the BioCatalogue, a public and curated catalogue of life science web services. The BioCatalogue allows anyone to register, discover, and curate web services. It provides rich metadata for over 3,000 publicly available life science web services. The BioCatalogue aims to make these services easier to find, advertise, understand, and use for various stakeholders like service providers, users, and curators. It utilizes a community-driven model where experts oversee annotation from both automated sources and crowdsourced user contributions.
A presentation by Nicole Harris, JISC given at licensing workshops run by JISC Collections. It focuses on the role of federation access management in relation to licensing terms.
The document summarizes an update on the NISO Open Discovery Initiative standards. It provides an overview of the ODI, which defines recommendations for data exchange between libraries, content providers, and discovery service vendors. The ODI aims to help libraries assess content provider participation in discovery services and ensure fair and unbiased indexing. It also outlines the roles and responsibilities of each party to ensure transparency and conformance with ODI practices. Recent updates to the ODI recommended practice in 2020 focused on metadata elements, fair linking, open access indicators, and statistical reporting.
Webinar: Preserving user privacy and protecting online contentOpenAthens
Adam Snook, OpenAthens product manager, discusses preserving user privacy and protecting online content. Adam also explains RA21 and what federated single sign-on is.
The document discusses BioCatalogue, a public registry of life science web services. It allows users to register, discover, and curate web services. Since its launch in 2009, BioCatalogue has grown to include over 1,000 web services and 50,000 annotations. Features have expanded to include improved monitoring, APIs, and tools to aid mass curation. The goals are to better support developers and provide more functional descriptions of services.
Webservices and Workflows. Taverna, Biocatalgue and myExperiment.Rafael C. Jimenez
This document summarizes web services and workflow solutions from myGrid, including Biocatalogue, Taverna, and myExperiment. Biocatalogue is a registry of life science web services that allows users to register, discover, and curate services. Taverna is a workflow management system that allows users to assemble workflows using available services from Biocatalogue and myExperiment. MyExperiment is a site for sharing, discovering, and reusing workflows. It supports reuse and repurposing of workflows across different scientific domains.
The webinar discusses quick wins for improving the user experience when accessing online library resources. It covers challenges users face with logins, the benefits of single sign-on via federated access management, and initiatives like RA21 that aim to create a seamless user experience across resources. Six quick wins are suggested: improving terminology, organisation discovery, deep linking, working with designers, user testing, and support team training on federated sign-on.
BioCatalogue Presentation @ Enabling Systems Biology 2011, by Jiten BhagatBioCatalogue
The BioCatalogue is a public, centralized registry of life science web services that allows users to register, discover, annotate, and monitor web services. It aims to address the challenges of discovering, understanding, and keeping track of the thousands of publicly available web services. Key features include web service registration, annotation with descriptions, tags, and categories, keyword search and filtering. The BioCatalogue has over 18,000 unique visitors from 130+ countries and provides APIs for programmatic access. It also includes tools for mass curation of web services and plans to release mobile apps. Lessons learned include that describing web services is difficult and comprehensive APIs and functional views are needed beyond technical SOAP/REST views.
User contributions have the potential to enrich WorldCat in several ways:
1) Over 160,000 user-created lists are already in WorldCat, allowing sharing of citations and recommendations.
2) User feedback like corrections, added content, and ratings can help improve WorldCat's quality and coverage.
3) Linking user contributions to related professional and external data could provide a more comprehensive view of identities, works, and topics in WorldCat.
However, challenges remain in encouraging contributions at scale while maintaining data quality, integrating social metadata with existing systems, and addressing users' reluctance to engage in some activities like ratings.
Better software, better service, better research: The Software Sustainabilit...Carole Goble
Ever spotted some great looking software only to discover you can’t get it, it doesn’t work, there is no documentation to help fix it and the developers don’t have the time or incentive to help? Ever produced some software that you want to be widely used or have folks contribute? What’s the sustainability of that key platform/library/tool /database your lab uses day in and day out? Are you helping the providers? The same issues stand for Data (or as we now say “FAIR” Findable, Accessible, Interoperable, Reusable Data) and its metadata. Is anyone looking out for Europe’s data services– the datasets and analysis systems you use and you make – the standards they use and the curators and developers who make them? Or is FAIR just a FAIRy story? I’ll tell how two organisations with quite different structures and approaches - the UK’s Software Sustainability Institute and the ELIXIR European Research Infrastructure for Life Science Data – are working for the common goal of better software, better service, and better research.
https://www.rothamsted.ac.uk/events/14th-international-symposium-integrative-bioinformatics
This presentation was provided by Violeta Ilik of Northwestern University during the NISO Virtual Conference held on Feb 15, 2017, entitled Institutional Repositories: Ensuring Yours is Populated, Useful and Thriving. The DOI for this presentation is http://dx.doi.org/10.18131/G3VP6R
InterEthos - making taxonomies interoperableswithins
InterEthos is a platform that allows users to create, modify, share, correlate, and internationalize different taxonomies through an open source API. The presentation discussed InterEthos' current services like taxonomy sharing and search, future plans like ontology development and versioning, and current projects applying the platform for social services organizations. Operations were outlined, including targeting the social services sector, being open source, and addressing open questions around business models, governance, and data storage.
Keeping pace with online publishing challengesptslides
Randy Petway discusses the challenges facing online publishing, including continuously evolving user expectations as new technologies and social media emerge, the rapid rate of change in the industry, and the need for revenue generation. He outlines a platform approach for publishers, providing a full suite of online content delivery, community building, personalization, search, and monetization tools to address these challenges and keep pace with the digital environment. The platform currently supports over 10,000 electronic publications across 300 international publishers and sees high monthly usage numbers.
Brief introduction to FAIRsharing work with industry (publishers, pharmas) and the FAIR Cookbook (for the Life Science): https://www.opensciencefair.eu/2021/workshops/applying-fair-principles-to-open-science-and-industry-to-drive-innovation-challenges-and-opportunities
The document discusses key concepts of Web 2.0 including that it focuses on content, community, and user experience through a paradigm shift. Web 2.0 enables new technologies like AJAX, widgets, APIs, and social networking to provide richer user experiences and allow users to generate, share, and collaborate on content. It emphasizes community features that let people connect and collaborate to build value through transparency and engagement.
Crossref for Ambassadors - Introductory webinarCrossref
This document provides an overview and agenda for a Crossref presentation. It introduces Crossref, its mission to make research outputs easy to find and link, and its role in tagging metadata and building infrastructure for scholarly communications. The presentation agenda covers Crossref services, members, content types, focus for 2018, and new developments like Event Data and tools to help members. It also provides links for brand guidelines, communications contacts, and product support.
BioCatalogue talk by Carole Goble. She outlines in these slides the reasons behind the BioCatalogue project. And present the BioCatalogue and its goals.
BioCatalogue DILS & Enfin 2009 by JitsBioCatalogue
Jiten Bhagat presented on the BioCatalogue, a public and curated catalogue of life science web services. The BioCatalogue allows anyone to register, discover, and curate web services. It provides rich metadata for over 3,000 publicly available life science web services. The BioCatalogue aims to make these services easier to find, advertise, understand, and use for various stakeholders like service providers, users, and curators. It utilizes a community-driven model where experts oversee annotation from both automated sources and crowdsourced user contributions.
A presentation by Nicole Harris, JISC given at licensing workshops run by JISC Collections. It focuses on the role of federation access management in relation to licensing terms.
The document summarizes an update on the NISO Open Discovery Initiative standards. It provides an overview of the ODI, which defines recommendations for data exchange between libraries, content providers, and discovery service vendors. The ODI aims to help libraries assess content provider participation in discovery services and ensure fair and unbiased indexing. It also outlines the roles and responsibilities of each party to ensure transparency and conformance with ODI practices. Recent updates to the ODI recommended practice in 2020 focused on metadata elements, fair linking, open access indicators, and statistical reporting.
Webinar: Preserving user privacy and protecting online contentOpenAthens
Adam Snook, OpenAthens product manager, discusses preserving user privacy and protecting online content. Adam also explains RA21 and what federated single sign-on is.
The document discusses BioCatalogue, a public registry of life science web services. It allows users to register, discover, and curate web services. Since its launch in 2009, BioCatalogue has grown to include over 1,000 web services and 50,000 annotations. Features have expanded to include improved monitoring, APIs, and tools to aid mass curation. The goals are to better support developers and provide more functional descriptions of services.
Webservices and Workflows. Taverna, Biocatalgue and myExperiment.Rafael C. Jimenez
This document summarizes web services and workflow solutions from myGrid, including Biocatalogue, Taverna, and myExperiment. Biocatalogue is a registry of life science web services that allows users to register, discover, and curate services. Taverna is a workflow management system that allows users to assemble workflows using available services from Biocatalogue and myExperiment. MyExperiment is a site for sharing, discovering, and reusing workflows. It supports reuse and repurposing of workflows across different scientific domains.
The webinar discusses quick wins for improving the user experience when accessing online library resources. It covers challenges users face with logins, the benefits of single sign-on via federated access management, and initiatives like RA21 that aim to create a seamless user experience across resources. Six quick wins are suggested: improving terminology, organisation discovery, deep linking, working with designers, user testing, and support team training on federated sign-on.
BioCatalogue Presentation @ Enabling Systems Biology 2011, by Jiten BhagatBioCatalogue
The BioCatalogue is a public, centralized registry of life science web services that allows users to register, discover, annotate, and monitor web services. It aims to address the challenges of discovering, understanding, and keeping track of the thousands of publicly available web services. Key features include web service registration, annotation with descriptions, tags, and categories, keyword search and filtering. The BioCatalogue has over 18,000 unique visitors from 130+ countries and provides APIs for programmatic access. It also includes tools for mass curation of web services and plans to release mobile apps. Lessons learned include that describing web services is difficult and comprehensive APIs and functional views are needed beyond technical SOAP/REST views.
User contributions have the potential to enrich WorldCat in several ways:
1) Over 160,000 user-created lists are already in WorldCat, allowing sharing of citations and recommendations.
2) User feedback like corrections, added content, and ratings can help improve WorldCat's quality and coverage.
3) Linking user contributions to related professional and external data could provide a more comprehensive view of identities, works, and topics in WorldCat.
However, challenges remain in encouraging contributions at scale while maintaining data quality, integrating social metadata with existing systems, and addressing users' reluctance to engage in some activities like ratings.
Better software, better service, better research: The Software Sustainabilit...Carole Goble
Ever spotted some great looking software only to discover you can’t get it, it doesn’t work, there is no documentation to help fix it and the developers don’t have the time or incentive to help? Ever produced some software that you want to be widely used or have folks contribute? What’s the sustainability of that key platform/library/tool /database your lab uses day in and day out? Are you helping the providers? The same issues stand for Data (or as we now say “FAIR” Findable, Accessible, Interoperable, Reusable Data) and its metadata. Is anyone looking out for Europe’s data services– the datasets and analysis systems you use and you make – the standards they use and the curators and developers who make them? Or is FAIR just a FAIRy story? I’ll tell how two organisations with quite different structures and approaches - the UK’s Software Sustainability Institute and the ELIXIR European Research Infrastructure for Life Science Data – are working for the common goal of better software, better service, and better research.
https://www.rothamsted.ac.uk/events/14th-international-symposium-integrative-bioinformatics
This presentation was provided by Violeta Ilik of Northwestern University during the NISO Virtual Conference held on Feb 15, 2017, entitled Institutional Repositories: Ensuring Yours is Populated, Useful and Thriving. The DOI for this presentation is http://dx.doi.org/10.18131/G3VP6R
InterEthos - making taxonomies interoperableswithins
InterEthos is a platform that allows users to create, modify, share, correlate, and internationalize different taxonomies through an open source API. The presentation discussed InterEthos' current services like taxonomy sharing and search, future plans like ontology development and versioning, and current projects applying the platform for social services organizations. Operations were outlined, including targeting the social services sector, being open source, and addressing open questions around business models, governance, and data storage.
Keeping pace with online publishing challengesptslides
Randy Petway discusses the challenges facing online publishing, including continuously evolving user expectations as new technologies and social media emerge, the rapid rate of change in the industry, and the need for revenue generation. He outlines a platform approach for publishers, providing a full suite of online content delivery, community building, personalization, search, and monetization tools to address these challenges and keep pace with the digital environment. The platform currently supports over 10,000 electronic publications across 300 international publishers and sees high monthly usage numbers.
Brief introduction to FAIRsharing work with industry (publishers, pharmas) and the FAIR Cookbook (for the Life Science): https://www.opensciencefair.eu/2021/workshops/applying-fair-principles-to-open-science-and-industry-to-drive-innovation-challenges-and-opportunities
The document discusses key concepts of Web 2.0 including that it focuses on content, community, and user experience through a paradigm shift. Web 2.0 enables new technologies like AJAX, widgets, APIs, and social networking to provide richer user experiences and allow users to generate, share, and collaborate on content. It emphasizes community features that let people connect and collaborate to build value through transparency and engagement.
Crossref for Ambassadors - Introductory webinarCrossref
This document provides an overview and agenda for a Crossref presentation. It introduces Crossref, its mission to make research outputs easy to find and link, and its role in tagging metadata and building infrastructure for scholarly communications. The presentation agenda covers Crossref services, members, content types, focus for 2018, and new developments like Event Data and tools to help members. It also provides links for brand guidelines, communications contacts, and product support.
12. Users Services Curation Monitoring Integration test scripts REST API Open Search myExperiment Instances and versioning QoS feeds notification ratings recommendations Identity management Content Provider engagement Policy identification Taverna Ownership account management BioMoby DAS Next? Curation tools Google gadget RSS/ATOM Try it first Level of curation Feedback providers curators More services Internal messaging www.biocatalogue.org wiki
13.
14. Credits Thomas Laurent Hamish McWilliams Franck Tanoh Jiten Bhagat Carole Goble Steve Pettifer Katy Wolstencroft Robert Stevens David De Roure Rodrigo Lopez Eric Nzuobontane
‘Web applications that interact with other web applications for the purpose of exchanging data’
We’ve built a catalogue for all of this… Cost Licensing
Who are the stake holder?
Automated monitoring & testing Test scripts, endpoint availability, meantime failure Partner feeds myExperiment.org Workflow profile Update feeds to users Develop incentives Expert for oversight How do we rank? How do we compare non-alike?
User management Registration of individuals using user/group registration model available in myExperiment/Wiki Identity managementManagement of identity life-cycle for entities (subjects or objects) Account managementCentralised administration as per myExperiment/Wiki AMS User profileSubject management of individual profiles Metadata annotation Data model; 4 levels of completeness (bronze, silver, gold and platinum) FunctionWeb Service operational description OperationDescription of operations, methods/actions Conditions of UseIf required, to describe usage limitations, etiquette, contract and licensing ProvenanceDescription of the service(s) hosting server Community StandingAnnotation (submitter/community) of institutional service host Operational MetricsLevel of Service, Availability, Q&A OntologymyGrid Ontology Service Submission Single and multiple (batch) submission of service. Only registered users are allowed to submit services. Service typesSOAP Service versionsAs services get re-developed or remodelled Service instancesMultiple instance of same, mirror or equivalent services geographically distributed sites Submission dashboardFigure X – Service submission interface allowing checking for duplications. Intuitive displays of available service information and cueing for descriptors that may be incomplete or missing. Applies to the qualification of annotation standards described in the metadata section. Ability to preview submission before committing to the back-end database. Service Curation TaggingKeyword-base curation driven by controlled vocabularies and ontologies. Service popularity quantification tagging. Community driven. WSDL parsingParsing of the Web Service Description Language services operational descriptions file. This will expose methods/action and their corresponding inputs and outputs in human readable descriptions Service Monitoring Interface monitoringChecks for consistency and change-tracking Availability monitoringChecks for service availability. Simple operational tests. QoS monitoringChecks for consistency, robustness and long-term availability of services. 3rd Party AggregationChecks for pipe-line and workflow integrity Service Discovery Simple/Advanced searchFull-text term searching. Available via the portal. Also to be made available via EB-eye and Google. Search of services matching free-text strings, filtering by date, type, provider, functionality, categories, tags and technologies. Tag searchSearch via tags – driven by annotation via ontologies (see above). RecommendationsBest-practise recommendation for service tagging and annotation to enable efficient and consistent searching across service types and service groups. Notification via RSS feeds (new and updated services, important service changes, status, BioCatalogue functionality, etc.) BrowserAmazon-like browsing interface with the capability to view details of services of interestSystem integration[with myExperiment? to complete] REST APIProgrammatic and non-programmatic access to service resources through URIs and HTTP verbs. Open SearchEnable addition of the BioCatalogue as a search engine in browsers that can handle the open search formatUse OpenSearch format as one of the formats for returning search queries myExperimentServices from BioCatalogue displayed in myExperiment so users of myExperiment can browse them. This includes a “Latest Services” and “Updated Services” list. Services within workflows in myExperiment reference the appropriate services in BioCatalogue so users can click through to the information in BioCatalogue.