Using community-defined metadata standards in the FAIR principles: how BioSha...Peter McQuilton
A 10 minute presentation given in Denver (CO) on the 16th September as part of the IG Elixir Bridging Force and Biosharing Registry WG joint session at the Research Data Alliance 8th Plenary (part of International Data Week).
This presentation covers the use of community-defined metadata standards in the life science, making these standards FAIR, and how BioSharing can help.
Cross-linked metadata standards, repositories and the data policies - The Bio...Peter McQuilton
A 20 minute presentation given in Denver (CO) on the 17th September as part of the Biosharing Registry WG, Metadata Standards Catalog WG, and Publishing Data Workflows WG joint session at the Research Data Alliance 8th Plenary (part of International Data Week).
This presentation covers the explosion of metadata standards and databases in the life, biomedical and environmental sciences and how BioSharing is helping to understand this landscape, both in terms of the relationship between standards and other standards and databases, and the life cycle and evolution of each resource. BioSharing also links these resources to the data policies that recommend them (for example, from funding agencies or journal publishers), enabling an understanding of the entire data cycle, from conception to publishing and storage.
A presentation on FAIR, FAIRsharing and the FAIR ecosystem for the ENVRI-FAIR community on the 13th December 2019. This presentation covers the basics of what FAIR is, how FAIRsharing can help 'FAIRify' standards, repositories, knowledgebases and data policies, and then the connections FAIRsharing has with other initiatives, such as the FAIR Evaluator, Data Stewardship Wizard, our RDA WG, GO-FAIR and EOSC-Life.
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.
2021 04 Introduction to FAIRsharing - cinecaAllyson Lister
Part of the The “How FAIR are you” webinar series and hackathon, which aim at increasing and facilitating the uptake of FAIR approaches into software, training materials and cohort data, to facilitate responsible and ethical data and resource sharing and implementation of federated applications for data analysis.
More information at
* the webinar page: https://www.cineca-project.eu/news-events-all/how-fair-are-you-hackathon
* the recording of the talk: https://www.youtube.com/watch?v=UdGZOynyuGo
Rafael Jimenez presents the FAIRSharing on behalf of Peter McQuilton, Susanna-Assunta Sansone & the FAIRsharing team | 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
FAIRsharing - Mapping the Landscape of Databases, Repositories, Standards and...Peter McQuilton
This document summarizes the work of the FAIRsharing project, which maps databases, standards, and policies to assess and improve their FAIRness. FAIRsharing aims to increase guidance for users and visibility for producers of these resources. It provides a registry of over 500 curated records describing digital assets. FAIRsharing also works to enable the FAIR principles by ensuring these resources are findable, accessible, interoperable, and reusable. Users are encouraged to claim records, provide feedback, and formally cite resources to support these goals.
Using community-defined metadata standards in the FAIR principles: how BioSha...Peter McQuilton
A 10 minute presentation given in Denver (CO) on the 16th September as part of the IG Elixir Bridging Force and Biosharing Registry WG joint session at the Research Data Alliance 8th Plenary (part of International Data Week).
This presentation covers the use of community-defined metadata standards in the life science, making these standards FAIR, and how BioSharing can help.
Cross-linked metadata standards, repositories and the data policies - The Bio...Peter McQuilton
A 20 minute presentation given in Denver (CO) on the 17th September as part of the Biosharing Registry WG, Metadata Standards Catalog WG, and Publishing Data Workflows WG joint session at the Research Data Alliance 8th Plenary (part of International Data Week).
This presentation covers the explosion of metadata standards and databases in the life, biomedical and environmental sciences and how BioSharing is helping to understand this landscape, both in terms of the relationship between standards and other standards and databases, and the life cycle and evolution of each resource. BioSharing also links these resources to the data policies that recommend them (for example, from funding agencies or journal publishers), enabling an understanding of the entire data cycle, from conception to publishing and storage.
A presentation on FAIR, FAIRsharing and the FAIR ecosystem for the ENVRI-FAIR community on the 13th December 2019. This presentation covers the basics of what FAIR is, how FAIRsharing can help 'FAIRify' standards, repositories, knowledgebases and data policies, and then the connections FAIRsharing has with other initiatives, such as the FAIR Evaluator, Data Stewardship Wizard, our RDA WG, GO-FAIR and EOSC-Life.
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.
2021 04 Introduction to FAIRsharing - cinecaAllyson Lister
Part of the The “How FAIR are you” webinar series and hackathon, which aim at increasing and facilitating the uptake of FAIR approaches into software, training materials and cohort data, to facilitate responsible and ethical data and resource sharing and implementation of federated applications for data analysis.
More information at
* the webinar page: https://www.cineca-project.eu/news-events-all/how-fair-are-you-hackathon
* the recording of the talk: https://www.youtube.com/watch?v=UdGZOynyuGo
Rafael Jimenez presents the FAIRSharing on behalf of Peter McQuilton, Susanna-Assunta Sansone & the FAIRsharing team | 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
FAIRsharing - Mapping the Landscape of Databases, Repositories, Standards and...Peter McQuilton
This document summarizes the work of the FAIRsharing project, which maps databases, standards, and policies to assess and improve their FAIRness. FAIRsharing aims to increase guidance for users and visibility for producers of these resources. It provides a registry of over 500 curated records describing digital assets. FAIRsharing also works to enable the FAIR principles by ensuring these resources are findable, accessible, interoperable, and reusable. Users are encouraged to claim records, provide feedback, and formally cite resources to support these goals.
BioSharing, an ELIXIR Interoperability Platform resourcePeter McQuilton
A 20 minute presentation given at the 9th RDA Plenary in Barcelona as part of the BioSharing WG - ELIXIR Bridging Force IG session. This presentation covers the basics of what BioSharing is, who it's for, and how it captures and connects information on data standards, databases and data policies from the life, biomedical and environmental sciences.
The FAIR Cookbook poster, as presented at the ELIXIR-UK Node and the UK Conference of Bioinformatics and Computational Biology 2021: https://www.earlham.ac.uk/uk-conference-bioinformatics-and-computational-biology-21
Susanna-Assunta Sansone is a data consultant and honorary academic editor who works on several projects related to making data FAIR (Findable, Accessible, Interoperable, Reusable). She is the associate director of Scientific Data, a peer-reviewed journal focused on publishing data descriptors to describe and provide access to scientifically valuable datasets. The goal of Scientific Data is to help promote open science and data reuse by publishing structured metadata and narratives about datasets alongside traditional research articles.
A 10 minute presentation given at the RDA UK meeting in London (Jan 2019). This presentation covers FAIRsharing work as part of the RDA/Force11 FAIRsharing WG.
Brief summary for the INCF Neuroscience Assembly (https://neuroinformatics.incf.org/2021/program-week-2) of the two sessions run at the RDA Plenary 17th, which FAIRsharing WG has contributed t.
This document summarizes Susanna-Assunta Sansone's presentation on FAIRsharing, a global resource for data repositories, standards, and policies that promotes FAIR data principles. FAIRsharing guides users to discover and select these resources and helps data producers make their resources more visible, widely adopted and cited. It contains over 3,500 indexed resources and has a dedicated collection of COVID-19 data sharing platforms and registries. The presentation discusses using FAIRsharing to map relationships between repositories in the collection and to external repositories and standards. It also notes the importance of stronger data policies from publishers to ensure access and reuse of COVID-19 research data.
My presentation at the http://neuroinformatics2017.org (Kuala Lumpur, Malaysia) on FAIR and FAIRsharing (previously BioSharing); metadata standards and their implementation by databases/repositories and adoption by journals' and funders' data policies.
This document summarizes the international FAIR movement, which developed principles to enhance the value of digital resources. The Findable, Accessible, Interoperable, Reusable (FAIR) principles were developed in 2014 and endorsed by researchers, funders, and other stakeholders in 2016. The principles aim to make data and other digital resources discoverable, accessible, interoperable, and reusable for both humans and machines. Implementing FAIR requires effort across technical, social, and cultural dimensions and long-term investment but helps ensure better science and more efficient research.
RDA Data Innovation Forum: FAIRsharing.org, an output of the joint RDA/Force ...Peter McQuilton
A 15 minute presentation at the RDA Data Innovation Forum in Brussels on the 20th January. This presentation covers the RDA/Force11 WG and FAIRsharing, mapping the landscape of data standards, databases and data policies.
CCCOER June 18 Webinar: OER & Supporting PlatformsUna Daly
Quill West, Open Educaiton Project Mgr, Pierce College District and CCCPER President, leads the discussion with Nicole Finkbeiner, Open Stax on how to evaluate OER partnerships through the lens of the CARE Framework.
EOSC-Life AGM 2022 Publishing FAIR RI data resources in EOSC.pdfAllyson Lister
FAIRsharing uses collections to create community-specific views of the resource descriptions we store and the relationships among them. This talk describes the work by EOSC-Life Work Package 1 to update and enrich the EOSC-Life collection, which groups together all resources created by EOSC-Life partners. Part of the EOSC-Life AGM 2022 (https://www.eosc-life.eu/news/3rd-agm/).
Managing Experimental Metadata using ISA data structures discusses using the ISA (Investigation/Study/Assay) format and tools to capture experimental workflows, make annotations explicit and discoverable, and structure descriptions for consistency and tracking. The ISA format supports data provenance tracking using a node/edge concept and tabular representation inspired by object models. It can be applied to experiments in various omics domains like microarrays, sequencing, flow cytometry, and mass spectrometry. The ISA tools provide a suite of modular, open source tools for creating, validating, loading, browsing, and analyzing ISA-formatted metadata and linking it to associated data files.
Philippe Rocca-Serra discusses streamlining the deposition of targeted metabolomics datasets to public repositories. He describes collaborating with Biocrates and EMBL-EBI Metabolights to develop a deposition pipeline. The pipeline involves exporting XML from Biocrates software, uploading to EMBL-EBI via Aspera, converting to ISA-Tab and MAF formats, and minting an accession number. Three datasets involving thousands of human plasma and urine samples are being handled through this pipeline. The take home message is that data custodians and suppliers can work together efficiently to avoid data loss and ensure visibility of datasets.
Modeling a Microbial Community and Biodiversity Assay with OBI and PCO OBO Fo...Philippe Rocca-Serra
This document discusses modeling microbial community biodiversity assays using ontologies from the OBO Foundry. It proposes representing targeted gene surveys using classes and relations from the Ontology for Biomedical Investigations (OBI) and Phenotypic Quality Ontology (PCO). This modular approach helps clarify experimental processes, facilitate standardized data collection, and reduce ambiguities compared to previous methods. Future work includes representing additional sample collection protocols and clarifying how results are reported.
Ontomaton: NCBO BioPortal Ontology lookups in Google Spreadsheets produced by ISATeam at University of Oxford e-Research Centre (Eamonn Maguire, Alejandra Gonzalez-Beltran, Philippe Rocca-Serra and Susanna Sansone) and NCBO (Trish Whetzel).
The work was presented during ICBO 2013 in Montreal by Trish Whetzel (Thanks Trish!)
This document provides an overview of BioSharing.org, a portal that monitors and curates standards, databases, and data policies to help inform and educate users. It summarizes key features including tracking over 225 content standards, 115 databases, and 554 data policies. The portal aims to help users understand how standards are used and make informed decisions on standards selection. It also links standards to training materials and allows custom collections and recommendations to be created.
RDA Webinar - BioSharing - mapping the landscape of data standards, repositor...Peter McQuilton
A 30 minute webinar presented on behalf of the RDA/Force11 BioSharing WG, covering our work to map data standards, databases, and data policies in the life, biomedical and environmental sciences.
NIH iDASH meeting on data sharing - BioSharing, ISA and Scientific DataSusanna-Assunta Sansone
1) The document discusses Susanna-Assunta Sansone's roles and work related to promoting FAIR data standards and practices.
2) It highlights some of her leadership positions with organizations like BioSharing that work to map and promote standards.
3) The document also discusses Scientific Data, a peer-reviewed journal launched by Nature Publishing Group to publish detailed descriptions of scientifically valuable datasets to facilitate reuse.
BioSharing, an ELIXIR Interoperability Platform resourcePeter McQuilton
A 20 minute presentation given at the 9th RDA Plenary in Barcelona as part of the BioSharing WG - ELIXIR Bridging Force IG session. This presentation covers the basics of what BioSharing is, who it's for, and how it captures and connects information on data standards, databases and data policies from the life, biomedical and environmental sciences.
The FAIR Cookbook poster, as presented at the ELIXIR-UK Node and the UK Conference of Bioinformatics and Computational Biology 2021: https://www.earlham.ac.uk/uk-conference-bioinformatics-and-computational-biology-21
Susanna-Assunta Sansone is a data consultant and honorary academic editor who works on several projects related to making data FAIR (Findable, Accessible, Interoperable, Reusable). She is the associate director of Scientific Data, a peer-reviewed journal focused on publishing data descriptors to describe and provide access to scientifically valuable datasets. The goal of Scientific Data is to help promote open science and data reuse by publishing structured metadata and narratives about datasets alongside traditional research articles.
A 10 minute presentation given at the RDA UK meeting in London (Jan 2019). This presentation covers FAIRsharing work as part of the RDA/Force11 FAIRsharing WG.
Brief summary for the INCF Neuroscience Assembly (https://neuroinformatics.incf.org/2021/program-week-2) of the two sessions run at the RDA Plenary 17th, which FAIRsharing WG has contributed t.
This document summarizes Susanna-Assunta Sansone's presentation on FAIRsharing, a global resource for data repositories, standards, and policies that promotes FAIR data principles. FAIRsharing guides users to discover and select these resources and helps data producers make their resources more visible, widely adopted and cited. It contains over 3,500 indexed resources and has a dedicated collection of COVID-19 data sharing platforms and registries. The presentation discusses using FAIRsharing to map relationships between repositories in the collection and to external repositories and standards. It also notes the importance of stronger data policies from publishers to ensure access and reuse of COVID-19 research data.
My presentation at the http://neuroinformatics2017.org (Kuala Lumpur, Malaysia) on FAIR and FAIRsharing (previously BioSharing); metadata standards and their implementation by databases/repositories and adoption by journals' and funders' data policies.
This document summarizes the international FAIR movement, which developed principles to enhance the value of digital resources. The Findable, Accessible, Interoperable, Reusable (FAIR) principles were developed in 2014 and endorsed by researchers, funders, and other stakeholders in 2016. The principles aim to make data and other digital resources discoverable, accessible, interoperable, and reusable for both humans and machines. Implementing FAIR requires effort across technical, social, and cultural dimensions and long-term investment but helps ensure better science and more efficient research.
RDA Data Innovation Forum: FAIRsharing.org, an output of the joint RDA/Force ...Peter McQuilton
A 15 minute presentation at the RDA Data Innovation Forum in Brussels on the 20th January. This presentation covers the RDA/Force11 WG and FAIRsharing, mapping the landscape of data standards, databases and data policies.
CCCOER June 18 Webinar: OER & Supporting PlatformsUna Daly
Quill West, Open Educaiton Project Mgr, Pierce College District and CCCPER President, leads the discussion with Nicole Finkbeiner, Open Stax on how to evaluate OER partnerships through the lens of the CARE Framework.
EOSC-Life AGM 2022 Publishing FAIR RI data resources in EOSC.pdfAllyson Lister
FAIRsharing uses collections to create community-specific views of the resource descriptions we store and the relationships among them. This talk describes the work by EOSC-Life Work Package 1 to update and enrich the EOSC-Life collection, which groups together all resources created by EOSC-Life partners. Part of the EOSC-Life AGM 2022 (https://www.eosc-life.eu/news/3rd-agm/).
Managing Experimental Metadata using ISA data structures discusses using the ISA (Investigation/Study/Assay) format and tools to capture experimental workflows, make annotations explicit and discoverable, and structure descriptions for consistency and tracking. The ISA format supports data provenance tracking using a node/edge concept and tabular representation inspired by object models. It can be applied to experiments in various omics domains like microarrays, sequencing, flow cytometry, and mass spectrometry. The ISA tools provide a suite of modular, open source tools for creating, validating, loading, browsing, and analyzing ISA-formatted metadata and linking it to associated data files.
Philippe Rocca-Serra discusses streamlining the deposition of targeted metabolomics datasets to public repositories. He describes collaborating with Biocrates and EMBL-EBI Metabolights to develop a deposition pipeline. The pipeline involves exporting XML from Biocrates software, uploading to EMBL-EBI via Aspera, converting to ISA-Tab and MAF formats, and minting an accession number. Three datasets involving thousands of human plasma and urine samples are being handled through this pipeline. The take home message is that data custodians and suppliers can work together efficiently to avoid data loss and ensure visibility of datasets.
Modeling a Microbial Community and Biodiversity Assay with OBI and PCO OBO Fo...Philippe Rocca-Serra
This document discusses modeling microbial community biodiversity assays using ontologies from the OBO Foundry. It proposes representing targeted gene surveys using classes and relations from the Ontology for Biomedical Investigations (OBI) and Phenotypic Quality Ontology (PCO). This modular approach helps clarify experimental processes, facilitate standardized data collection, and reduce ambiguities compared to previous methods. Future work includes representing additional sample collection protocols and clarifying how results are reported.
Ontomaton: NCBO BioPortal Ontology lookups in Google Spreadsheets produced by ISATeam at University of Oxford e-Research Centre (Eamonn Maguire, Alejandra Gonzalez-Beltran, Philippe Rocca-Serra and Susanna Sansone) and NCBO (Trish Whetzel).
The work was presented during ICBO 2013 in Montreal by Trish Whetzel (Thanks Trish!)
This document provides an overview of BioSharing.org, a portal that monitors and curates standards, databases, and data policies to help inform and educate users. It summarizes key features including tracking over 225 content standards, 115 databases, and 554 data policies. The portal aims to help users understand how standards are used and make informed decisions on standards selection. It also links standards to training materials and allows custom collections and recommendations to be created.
RDA Webinar - BioSharing - mapping the landscape of data standards, repositor...Peter McQuilton
A 30 minute webinar presented on behalf of the RDA/Force11 BioSharing WG, covering our work to map data standards, databases, and data policies in the life, biomedical and environmental sciences.
NIH iDASH meeting on data sharing - BioSharing, ISA and Scientific DataSusanna-Assunta Sansone
1) The document discusses Susanna-Assunta Sansone's roles and work related to promoting FAIR data standards and practices.
2) It highlights some of her leadership positions with organizations like BioSharing that work to map and promote standards.
3) The document also discusses Scientific Data, a peer-reviewed journal launched by Nature Publishing Group to publish detailed descriptions of scientifically valuable datasets to facilitate reuse.
This document discusses the BioSharing registry, which connects standards, databases, and policies in the life sciences. BioSharing provides a searchable portal for standards and databases, helping researchers choose the right options for publishing and funding requirements. It monitors the development of standards and their adoption. The registry links three sections on standards, databases, and policies to help answer common questions about which options to use. Users can search, filter, and refine results or create customized collections. BioSharing aims to support better informed decisions across the life sciences research community.
BioSharing Slides - Repository Fringe Edinburgh August 2015Peter McQuilton
The document describes a web-based portal that registers, links, and allows discovery of biological standards and databases. It monitors the development and evolution of standards and their use in databases and adoption in data policies. Its mission is to provide support and guidance to researchers, developers, curators, journal publishers, and funders on choosing the appropriate standards and databases by registering, linking, and making discoverable relevant biological standards and databases.
A 15 minutes presentation to the SCDS IUPAC Workshop in Amsterdam on the 16-17th July 2018. This presentation also introduces the current state of chemistry-related standards, databases and data policies in FAIRsharing (all included in a Collection in FAIRsharing), and an outline of the workshop conducted at the meeting.
This document describes a web-based registry that aims to provide guidance for researchers, developers, and curators on selecting content standards and databases. There are almost 600 content standards in the life sciences. The registry will allow users to search for, filter, submit, and view information on standards and databases. It will link standards to databases that implement them and provide visualizations of standard formats and terminologies. The goal is to help stakeholders make informed decisions by providing a curated, searchable registry of standards and database information. An advisory board and working group will oversee the registry's development and operations.
Overview to: BBSRC Oxford Doctoral Training Partnership - Dr Sansone - July 2014Susanna-Assunta Sansone
What to know when planning for your data management strategy and preparing a data management statement for a research proposal for BBSRC DTP first year students
FAIRsharing presentation at the Japan Science and Technology AgencyPeter McQuilton
A 30 minute seminar presented at the National Bioscience Database Center, part of the Japanese Science and Technology Agency, based in Tokyo, Japan. This presentation covers the FAIR Principles, the aims, methodology and use of FAIRsharing, related projects such as Bioschemas, and international initiatives such as ELIXIR and EOSC.
BioSharing - RDA Plenary 6 - Metadata Standards Catalog WG and BioSharing WG ...Peter McQuilton
An introduction to the metadata landscape in the life sciences. Covering metadata standards, the databases that implement them and the policies that endorse/recommend both standards and databases in the life sciences.
RDA Plenary 9 BioSharing WG output/recommendationPeter McQuilton
A 10 minute talk given at the RDA Plenary 9 meeting in Barcelona, April 2017. This talk covers the work performed over the past 18 months in the joint RDA/Force11 WG. This WG has two main outputs, a set of guidelines for how one can link data policies, databases and data standards (in the life sciences); and the BioSharing registry (building upon the prototype).
A 10 minute presentation for the virtual ELIXIR All Hands Meeting 2020 - FAIRification mini symposium. In this presentation I talk about some of the community work we do in FAIRsharing, from sharing our metadata with other resources to research on data policy repository criteria.
RDA BioSharing WG/ELIXIR Session Montreal 2017Peter McQuilton
A 15 minute presentation giving an introduction to FAIRsharing, an ELIXIR Interoperability Platform resource of curated and linked information on standards, databases and policies.
A 45min presentation given at the 'Getting published in Nature's Scientific Data journal', hosted by the University of Cambridge Research Data Management team (www.data.cam.ac.uk). Presented on Monday 11th January 2016.
FAIR StRePo - GO TRAIN Workshop, Hamburg, November 2019Peter McQuilton
A short 5 minute presentation on the GO FAIR StRePo Implementation Network. This presentation introduces FAIR StRePo, covering our work to map the landscape of standards, repositories and policies across the GO-FAIR network and particularly our work in GO-TRAIN, FAIRassist.org and terms4FAIRskills.
Overview of FAIRsharing in 5min; CODATA event on metadata, pre-RDA Plenary, Philadelphia 2019
https://conference.codata.org/Drexel_CODATA_2019/programme/
The document summarizes a workshop hosted by the NIH Associate Director for Data Science to discuss charting the future of data science at NIH. The workshop goals were to get input from all stakeholders, identify strategic directions, policies, and funding initiatives, and have participants leave as advocates and supporters. The agenda included providing background, open discussion, identifying topics for breakout groups, subgroup discussions, and reporting back. The document provides context on current NIH data science efforts and examples of collaborators in building a biomedical research digital enterprise.
Similar to BioSharing - mapping the landscape of Standards, Databases and Data policies in the life, biomedical and environmental sciences (20)
A 15 minute presentation covering the terms4FAIRskills project from conception in Jan 2019 until now. This presentation covers the methodology, model iteration and terminology building. Presented at RDA VP17 in the Professionalising Data Stewardship session.
This 15min presentation covers work from the FAIRsharing WG, including covering FAIRsharing.org, one of our RDA endorsed outputs, and our work with journal publishers and DataCite to define Repository Selection Criteria for journal and journal publisher data policies.
FAIRsharing - connecting standards, repositories and data policies across agr...Peter McQuilton
A 10 minute presentation on FAIRsharing, highlighting the manually curated metadata we provide on agri-related standards (ontologies, reporting guidelines, identifier schema, models and formats), databases (both knowledgebases and repositories) and data policies from funders and journal publishers. Presented at the RDA P14 meeting in Helsinki, Finland (October 2019).
FAIRsharing - manually curated metadata on standards, repositories and data p...Peter McQuilton
A 10 minute presentation on FAIRsharing, highlighting the manually curated metadata we provide on domain specific and cross-domain standards (ontologies, reporting guidelines, identifier schema, models and formats), databases (both knowledgebases and repositories) and data policies from funders and journal publishers. Presented at the RDA P14 meeting in Helsinki, Finland (October 2019).
Making Repositories FAIR (via metadata in FAIRsharing.orgPeter McQuilton
A 10 minute presentation on how we can make repositories FAIR, primarily through storing their metadata on FAIRsharing.org. Presented at the FAIRsFAIR FAIR Semantics & FAIR Repositories pre-RDA P14 meeting in Helsinki, Finland on the 22nd October 2019. FAIRsharing can be used to edit and store metadata on repositories from across the natural sciences, engineering sciences, social sciences and humanities. This metadata is marked-up in schema.org and bioschemas (where relevant) and is given a citable DOI. This metadata can be used to power DMP tools and wizards and can also be used to perform FAIR assessments, such as through the FAIR evaluator or FAIRshake.
A 10 minute presentation on the relationship between semantic terminologies and repositories. Presented at the FAIRsFAIR FAIR Semantics & FAIR Repositories pre-RDA P14 meeting in Helsinki, Finland on the 22nd October 2019. FAIRsharing can describe and display these relationships in a way that allows users to understand which standards are most adopted by the community and which terminologies are used by particular repositories across the natural sciences, engineering sciences, social sciences and humanities.
ELIXIR Standards and Formats: ISA Tools and FAIRsharingPeter McQuilton
This document summarizes Peter McQuilton's presentation on ELIXIR Standards and Formats, specifically the ISA Tools and FAIRsharing. It discusses how ISA (Investigation/Study/Assay) formats and tools help researchers describe experiments and share data according to community standards. It also describes FAIRsharing, a web portal that maps standards, databases, formats, and data policies to make them FAIR (Findable, Accessible, Interoperable, and Reusable). The presentation outlines how ISA and FAIRsharing connect to ELIXIR use cases and resources, and how the FAIRsharing team works with various groups and the community.
FAIR landscape in ELIXIR: FAIR metrics and other initiativesPeter McQuilton
A 15 minute talk presented at the ELIXIR Europe/ELIXIR UK SME Forum at Churchill College in Cambridge, UK in January 2018. This talk reviews the work our group does in relation to the FAIR principles as part of ELIXIR and beyond.
FAIRsharing Keynote - International Workshop on Sharing, Citation and Publica...Peter McQuilton
A 30 minute presentation on FAIRsharing given at the International Workshop on Sharing, Citation and Publication of
Scientific Data across Disciplines in Tachikawa, Tokyo, Japan on Tuesday 5th December, 2017
The BioSharing portal - linking journal and funder data policies to databases...Peter McQuilton
A 20 minute talk on the BioSharing portal, focusing on our work to link journal and funder data policies to the databases and data standards that they recommend/endorse. This was presented as part of a session on data policies in the life sciences with representation from JISC and Springer Nature.
The BioSharing portal - linking databases, data standards and policies in the...Peter McQuilton
A 15 minute presentation for the Interest Group on Agricultural Data (IGAD) RDA pre-meeting meeting. Presented in Barcelona (ES) on Monday 3rd April, 2017.
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...AbdullaAlAsif1
The pygmy halfbeak Dermogenys colletei, is known for its viviparous nature, this presents an intriguing case of relatively low fecundity, raising questions about potential compensatory reproductive strategies employed by this species. Our study delves into the examination of fecundity and the Gonadosomatic Index (GSI) in the Pygmy Halfbeak, D. colletei (Meisner, 2001), an intriguing viviparous fish indigenous to Sarawak, Borneo. We hypothesize that the Pygmy halfbeak, D. colletei, may exhibit unique reproductive adaptations to offset its low fecundity, thus enhancing its survival and fitness. To address this, we conducted a comprehensive study utilizing 28 mature female specimens of D. colletei, carefully measuring fecundity and GSI to shed light on the reproductive adaptations of this species. Our findings reveal that D. colletei indeed exhibits low fecundity, with a mean of 16.76 ± 2.01, and a mean GSI of 12.83 ± 1.27, providing crucial insights into the reproductive mechanisms at play in this species. These results underscore the existence of unique reproductive strategies in D. colletei, enabling its adaptation and persistence in Borneo's diverse aquatic ecosystems, and call for further ecological research to elucidate these mechanisms. This study lends to a better understanding of viviparous fish in Borneo and contributes to the broader field of aquatic ecology, enhancing our knowledge of species adaptations to unique ecological challenges.
When I was asked to give a companion lecture in support of ‘The Philosophy of Science’ (https://shorturl.at/4pUXz) I decided not to walk through the detail of the many methodologies in order of use. Instead, I chose to employ a long standing, and ongoing, scientific development as an exemplar. And so, I chose the ever evolving story of Thermodynamics as a scientific investigation at its best.
Conducted over a period of >200 years, Thermodynamics R&D, and application, benefitted from the highest levels of professionalism, collaboration, and technical thoroughness. New layers of application, methodology, and practice were made possible by the progressive advance of technology. In turn, this has seen measurement and modelling accuracy continually improved at a micro and macro level.
Perhaps most importantly, Thermodynamics rapidly became a primary tool in the advance of applied science/engineering/technology, spanning micro-tech, to aerospace and cosmology. I can think of no better a story to illustrate the breadth of scientific methodologies and applications at their best.
Travis Hills' Endeavors in Minnesota: Fostering Environmental and Economic Pr...Travis Hills MN
Travis Hills of Minnesota developed a method to convert waste into high-value dry fertilizer, significantly enriching soil quality. By providing farmers with a valuable resource derived from waste, Travis Hills helps enhance farm profitability while promoting environmental stewardship. Travis Hills' sustainable practices lead to cost savings and increased revenue for farmers by improving resource efficiency and reducing waste.
Nucleophilic Addition of carbonyl compounds.pptxSSR02
Nucleophilic addition is the most important reaction of carbonyls. Not just aldehydes and ketones, but also carboxylic acid derivatives in general.
Carbonyls undergo addition reactions with a large range of nucleophiles.
Comparing the relative basicity of the nucleophile and the product is extremely helpful in determining how reversible the addition reaction is. Reactions with Grignards and hydrides are irreversible. Reactions with weak bases like halides and carboxylates generally don’t happen.
Electronic effects (inductive effects, electron donation) have a large impact on reactivity.
Large groups adjacent to the carbonyl will slow the rate of reaction.
Neutral nucleophiles can also add to carbonyls, although their additions are generally slower and more reversible. Acid catalysis is sometimes employed to increase the rate of addition.
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...Ana Luísa Pinho
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required. Yet, to date, both structural atlases and parcellation-based activations do not fully account for cognitive function and still present several limitations. Further, they do not adapt overall to individual characteristics. In this talk, I will give an account of deep-behavioral phenotyping strategies, namely data-driven methods in large task-fMRI datasets, to optimize functional brain-data collection and improve inference of effects-of-interest related to mental processes. Key to this approach is the employment of fast multi-functional paradigms rich on features that can be well parametrized and, consequently, facilitate the creation of psycho-physiological constructs to be modelled with imaging data. Particular emphasis will be given to music stimuli when studying high-order cognitive mechanisms, due to their ecological nature and quality to enable complex behavior compounded by discrete entities. I will also discuss how deep-behavioral phenotyping and individualized models applied to neuroimaging data can better account for the subject-specific organization of domain-general cognitive systems in the human brain. Finally, the accumulation of functional brain signatures brings the possibility to clarify relationships among tasks and create a univocal link between brain systems and mental functions through: (1) the development of ontologies proposing an organization of cognitive processes; and (2) brain-network taxonomies describing functional specialization. To this end, tools to improve commensurability in cognitive science are necessary, such as public repositories, ontology-based platforms and automated meta-analysis tools. I will thus discuss some brain-atlasing resources currently under development, and their applicability in cognitive as well as clinical neuroscience.
Or: Beyond linear.
Abstract: Equivariant neural networks are neural networks that incorporate symmetries. The nonlinear activation functions in these networks result in interesting nonlinear equivariant maps between simple representations, and motivate the key player of this talk: piecewise linear representation theory.
Disclaimer: No one is perfect, so please mind that there might be mistakes and typos.
dtubbenhauer@gmail.com
Corrected slides: dtubbenhauer.com/talks.html
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
Current Ms word generated power point presentation covers major details about the micronuclei test. It's significance and assays to conduct it. It is used to detect the micronuclei formation inside the cells of nearly every multicellular organism. It's formation takes place during chromosomal sepration at metaphase.
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...Sérgio Sacani
Context. With a mass exceeding several 104 M⊙ and a rich and dense population of massive stars, supermassive young star clusters
represent the most massive star-forming environment that is dominated by the feedback from massive stars and gravitational interactions
among stars.
Aims. In this paper we present the Extended Westerlund 1 and 2 Open Clusters Survey (EWOCS) project, which aims to investigate
the influence of the starburst environment on the formation of stars and planets, and on the evolution of both low and high mass stars.
The primary targets of this project are Westerlund 1 and 2, the closest supermassive star clusters to the Sun.
Methods. The project is based primarily on recent observations conducted with the Chandra and JWST observatories. Specifically,
the Chandra survey of Westerlund 1 consists of 36 new ACIS-I observations, nearly co-pointed, for a total exposure time of 1 Msec.
Additionally, we included 8 archival Chandra/ACIS-S observations. This paper presents the resulting catalog of X-ray sources within
and around Westerlund 1. Sources were detected by combining various existing methods, and photon extraction and source validation
were carried out using the ACIS-Extract software.
Results. The EWOCS X-ray catalog comprises 5963 validated sources out of the 9420 initially provided to ACIS-Extract, reaching a
photon flux threshold of approximately 2 × 10−8 photons cm−2
s
−1
. The X-ray sources exhibit a highly concentrated spatial distribution,
with 1075 sources located within the central 1 arcmin. We have successfully detected X-ray emissions from 126 out of the 166 known
massive stars of the cluster, and we have collected over 71 000 photons from the magnetar CXO J164710.20-455217.
The binding of cosmological structures by massless topological defectsSérgio Sacani
Assuming spherical symmetry and weak field, it is shown that if one solves the Poisson equation or the Einstein field
equations sourced by a topological defect, i.e. a singularity of a very specific form, the result is a localized gravitational
field capable of driving flat rotation (i.e. Keplerian circular orbits at a constant speed for all radii) of test masses on a thin
spherical shell without any underlying mass. Moreover, a large-scale structure which exploits this solution by assembling
concentrically a number of such topological defects can establish a flat stellar or galactic rotation curve, and can also deflect
light in the same manner as an equipotential (isothermal) sphere. Thus, the need for dark matter or modified gravity theory is
mitigated, at least in part.
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...University of Maribor
Slides from talk:
Aleš Zamuda: Remote Sensing and Computational, Evolutionary, Supercomputing, and Intelligent Systems.
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Inter-Society Networking Panel GRSS/MTT-S/CIS Panel Session: Promoting Connection and Cooperation
https://www.etran.rs/2024/en/home-english/
ANAMOLOUS SECONDARY GROWTH IN DICOT ROOTS.pptxRASHMI M G
Abnormal or anomalous secondary growth in plants. It defines secondary growth as an increase in plant girth due to vascular cambium or cork cambium. Anomalous secondary growth does not follow the normal pattern of a single vascular cambium producing xylem internally and phloem externally.
Cytokines and their role in immune regulation.pptx
BioSharing - mapping the landscape of Standards, Databases and Data policies in the life, biomedical and environmental sciences
1. BioSharing.org
Mapping the landscape of Standards, Databases and
Data policies in the life, biomedical and
environmental sciences
Peter McQuilton
BioSharing Content Lead
@biosharing
2. Outline
• What is BioSharing?
• Ensuring FAIR-ness for standards, databases and
policies
• How do we describe and link records?
• Exploring the landscape of standards, databases
and data policies in the life sciences
3.
4. What is BioSharing?
A web-based, curated and searchable portal that monitors the development and
evolution of standards, their use in databases and the adoption of both in data
policies, to inform and educate the user community.
7. Guidelines = Minimum information
reporting requirements, checklists
o Report the same core, essential
information
o e.g. ARRIVE guidelines
Terminologies = Controlled
vocabularies, taxonomies,
thesauri, ontologies etc.
o Unambiguously refer to
an entity
o e.g. Gene Ontology
Models/Formats = Conceptual
model, conceptual schema,
exchange formats
o Allow data to flow from one
system to another
o e.g. FASTA
Enablers: to better describe, share
and query data
Formats Terminologies Guidelines
8. Data policies by
funders, journals and
other organizations
(>100)
Database, tools
and services
(>800)
Content standards
(>650)
Complex and evolving landscape
Formats Terminologies Guidelines
9. Model/format formalizing reporting guideline -->
<-- Reporting guideline used by model/format
Cross-linking standards to
standards and databases
10. Model/format formalizing reporting guideline -->
<-- Reporting guideline used by model/format
Cross-linking standards to
standards and databases
18. Ready for use, implementation, or recommendation
In development
Status uncertain
Deprecated as subsumed or superseded
Manually curated, approved by the community
Using indicators to describe the
‘status’ of a resource
22. BioSharing allows you to
• Track the provenance and evolution of a standard
or database
• See which standards a database uses
• Explore the resources appropriate to your domain,
species, technique etc.
• Map the resources available from a particular
funder, country or with a particular access license
• See which standards and databases a publisher,
funder or institution/organisation recommends
29. Collections group together
one or more types of
resource by domain,
project or organization.
Recommendations are a
core-set of resources that
are selected and
recommended by a funder
or journal data policy.
Grouping the data
30.
31.
32.
33. “BioSharing and its interactive browser will allow us to
discover which databases and standards are not currently
included in our author guidelines, enabling us to regularly
monitor and refine our policies as appropriate, in support of
our mission to help our authors enhance the reproducibility
of their work.” – Holly Murray, F1000Research
36. What we do
Inform – what’s out there, which databases use
which standards. Map the landscape.
Educate – what databases are recommended by your
funder, or journal of choice, which standards should
you be using, which standards and databases should
you recommend? Explore the landscape.
40. Thank – you!
• Add/link your standard to BioSharing
• Add/link your database
• Use us to inform your data policy (and add/link
your policy)
• Make a collection or recommendation for your
group/society
https://biosharing.org
@biosharing
peter.mcquilton@oerc.ox.ac.uk
@drosophilic