BHL and Key to Nature - use cases (G. Hagedorn)

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Gregor Hagedorn

Images for identification keys ecp-2006-edu-410019 Targeted Project 2007-2010 & BHL:

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

[object Object],[object Object],[object Object],[object Object]

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Work Packages: WP1 Project coordination and management WP2 Analysis of users' needs and demand WP4 Addressing access, searchability, use and re-use of secondary data and items WP11 Dissemination & exploitation of the e-contents and eLearning products WP5 Addressing, analysis and testing exchange and interoperability of identification data WP9 Educational contents reengineering WP6 Interfaces, usability and mobility WP7 Pedagogy and didactics WP8 User experience WP10 IPR issues WP3 Inventory of existing educational products WP12 Monitoring Evaluation and assessment

Media Identification tools may be on different media: ,[object Object],[object Object],[object Object],[object Object]

Tools used in the project FRIDA Diversity Descriptions DELTA Linnaeus II Xper²

FRIDA DiversityDescriptions Linnaeus II Xper² DELTA EDIT CDM IdentifyLife 3 I Lucid 2 & 3

Keys are tested by end-users School … and improved

Accessibility Functionality Usability “ Likeability”! “ Sociability”! “ Playability”!

[object Object],Key to Nature BHL use case

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Model for metadata aggregation XML / RDF ETI Univ. Triest JKI Indexing repository (FEDORA Commons, GSearch, SPARQL) CSIC RJB FLEX 3 Exchange repository (Push, Wiki) ? GBIF ? Standard Fedora Webservices NBII NHM PMSL Tartu Morphbank ?

Metadata on ,[object Object],[object Object],[object Object]

The Biodiversity Landscape BHL: (Mostly) old species descriptions, images, data and keys EoL: Mashup and pointers/citations of distributed content EoL-LiveDesk: Fill in information according to EoL needs EDIT Scratchpads: Create an “online-book” with closed authorship. Publication-like descriptions and keys? Wiki-based publication? With review? EDIT CDM System: platform for data management

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Introduction to FAIRDOM

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The objective of this webinar is to provide a brief overview of the Knowledge Organization Systems (KOS) and the tools used for managing them. The presentation will focus on the management of the multilingual Organic.Edunet ontology as a case study. In this context it will present aspects such as the collaborative work, multilinguality needs and update of the concepts using an online KOS management tool (MoKi).

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Presented at Digital Life 2018, Bergen, March 2018. In the Trust and Accountability session. In recent years we have seen a change in expectations for the management and availability of all the outcomes of research (models, data, SOPs, software etc) and for greater transparency and reproduciblity in the method of research. The “FAIR” (Findable, Accessible, Interoperable, Reusable) Guiding Principles for stewardship [1] have proved to be an effective rallying-cry for community groups and for policy makers. The FAIRDOM Initiative (FAIR Data Models Operations, http://www.fair-dom.org) supports Systems Biology research projects with their research data, methods and model management, with an emphasis on standards and sensitivity to asset sharing and credit anxiety. Our aim is a FAIR Research Commons that blends together the doing of research with the communication of research. The Platform has been installed by over 30 labs/projects and our public, centrally hosted FAIRDOMHub [2] supports the outcomes of 90+ projects. We are proud to support projects in Norway’s Digital Life programme. 2018 is our 10th anniversary. Over the past decade we learned a lot about trust between researchers, between researchers and platform developers and curators and between both these groups and funders. We have experienced the Tragedy of the Commons but also seen shifts in attitudes. In this talk we will use our experiences in FAIRDOM to explore the political, economic, social and technical, social practicalities of Trust. [1] Wilkinson et al (2016) The FAIR Guiding Principles for scientific data management and stewardship Scientific Data 3, doi:10.1038/sdata.2016.18 [2] Wolstencroft, et al (2016) FAIRDOMHub: a repository and collaboration environment for sharing systems biology research Nucleic Acids Research, 45(D1): D404-D407. DOI: 10.1093/nar/gkw1032

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Keynote presented at the workshop FAIRe Data Infrastructures, 15 October 2020 https://www.gmds.de/aktivitaeten/medizinische-informatik/projektgruppenseiten/faire-dateninfrastrukturen-fuer-die-biomedizinische-informatik/workshop-2020/ Remarkably it was only in 2016 that the ‘FAIR Guiding Principles for scientific data management and stewardship’ appeared in Scientific Data. The paper was intended to launch a dialogue within the research and policy communities: to start a journey to wider accessibility and reusability of data and prepare for automation-readiness by supporting findability, accessibility, interoperability and reusability for machines. Many of the authors (including myself) came from biomedical and associated communities. The paper succeeded in its aim, at least at the policy, enterprise and professional data infrastructure level. Whether FAIR has impacted the researcher at the bench or bedside is open to doubt. It certainly inspired a great deal of activity, many projects, a lot of positioning of interests and raised awareness. COVID has injected impetus and urgency to the FAIR cause (good) and also highlighted its politicisation (not so good). In this talk I’ll make some personal reflections on how we are faring with FAIR: as one of the original principles authors; as a participant in many current FAIR initiatives (particularly in the biomedical sector and for research objects other than data) and as a veteran of FAIR before we had the principles.

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This presentation introduces the main features of the Semantic MediaWiki (SMW) installation at http://terms.gbif.org, which was established by the ViBRANT[1] project and GBIF and is recommended by the Vocabulary Management Group (VoMaG) as a community platform for vocabulary development and maintenance. Dedicated ontology platforms are often geared towards trained knowledge engineers and are in danger of being impenetrable by domain experts. Furthermore, they often neglect the human readable definition for consumers of the terms, resulting in misapplication of terms. The platform at http://terms.gbif.org supports rich-media definitions of terms with the full functionality of a Wikipedia page, and extends this with basic SKOS (Simple Knowledge Organization System) and vocabulary management functionality. The focus is on improving the definition, understanding, annotation, discussion, translation, and long term stable maintenance of terms or concepts. The platform specifically supports the reuse of shared terms in overlapping vocabulary schemes or profiles. The intended use is to provide a base on which higher level ontologies that share the same terms can then be built. [1] http://vbrant.eu/ At the TDWG conference, the system was accepted as a core TDWG vocabulary management tool; it thus now runs under http://terms.tdwg.org See also http://www.slideshare.net/DagEndresen/tdwg-vomag-vocabulary-management-workflow-tdwg-2013-in-f

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As biological disciplines extend into the ‘big data’ world, they will need a names-based infrastructure to index and interconnect distributed data. The infrastructure must have access to all names of all organisms if it is to manage all information. There is no single compilation of all species nor of all names of organisms. Those who compile lists of species or names hold different views as to the intellectual property rights that apply to the lists. This creates uncertainty as to how names and compilations of names should be licensed, what conditions should apply to their re-use, and how to attribute the efforts of authors and others involved in making them available. The uncertainty, and in some cases protectionism, impedes the much-needed infrastructure that will enable sharing of biological data in the digital world. The laws in the United States of America and European Union are consistent with the position that scientific names of organisms and their compilation in checklists, classifications or taxonomic revisions are not subject to copyright. The spellings of names are facts and cannot be owned by individuals. Compilations of names, such as classifications or checklists, are presented in widely used layouts and are not creative in the sense of copyright law - even when considerable intellectual effort was needed to assemble them. A ‘blue list’ is presented that identifies familiar elements of checklists, classifications and monographs, and to which intellectual property rights do not apply. The absence of intellectual property rights stands in contrast to licensing statements associated with compilations that imply that rights apply. Many content providers desire credit for their efforts. In order to promote sharing, authors of taxonomic content, compilers, intermediaries, and aggregators should receive citable recognition for their contributions, with the greatest recognition being given to the originating authors.

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BHL and Key to Nature - use cases (G. Hagedorn)

1. Images for identification keys ecp-2006-edu-410019 Targeted Project 2007-2010 & BHL:

5. Work Packages: WP1 Project coordination and management WP2 Analysis of users' needs and demand WP4 Addressing access, searchability, use and re-use of secondary data and items WP11 Dissemination & exploitation of the e-contents and eLearning products WP5 Addressing, analysis and testing exchange and interoperability of identification data WP9 Educational contents reengineering WP6 Interfaces, usability and mobility WP7 Pedagogy and didactics WP8 User experience WP10 IPR issues WP3 Inventory of existing educational products WP12 Monitoring Evaluation and assessment

6. Identification tools

8. Tools used in the project FRIDA Diversity Descriptions DELTA Linnaeus II Xper²

9. FRIDA DiversityDescriptions Linnaeus II Xper² DELTA EDIT CDM IdentifyLife 3 I Lucid 2 & 3

10. Keys are tested by end-users School … and improved

11. Accessibility Functionality Usability “ Likeability”! “ Sociability”! “ Playability”!

12.

13.

14.

15. Key to Nature BHL use case

16. Model for metadata aggregation XML / RDF ETI Univ. Triest JKI Indexing repository (FEDORA Commons, GSearch, SPARQL) CSIC RJB FLEX 3 Exchange repository (Push, Wiki) ? GBIF ? Standard Fedora Webservices NBII NHM PMSL Tartu Morphbank ?

17.

18. Call for collaboration!

19. The Biodiversity Landscape BHL: (Mostly) old species descriptions, images, data and keys EoL: Mashup and pointers/citations of distributed content EoL-LiveDesk: Fill in information according to EoL needs EDIT Scratchpads: Create an “online-book” with closed authorship. Publication-like descriptions and keys? Wiki-based publication? With review? EDIT CDM System: platform for data management

20.

BHL and Key to Nature - use cases (G. Hagedorn)

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