August 2017 - tdwg - lists.tdwg.org

Public review - metadata for HTS libraries based on the GGBN Data Standard - deadline 22. September 2017
by Dröge, Gabriele 23 Aug '17

23 Aug '17

Dear colleagues, Last year the Global Genome Biodiversity Network (GGBN, http://www.ggbn.org ) has published the GGBN Data Standard, which covers terms related to DNA and tissue samples (https://terms.tdwg.org/wiki/GGBN_Data_Standard, Droege et al. 2016 (https://library.ggbn.org/share/s/E3qbuKsJSwaI67IWItXCKw)). Many of you were part of the public revision process. In addition to genomic DNA the development and use of high-throughput next generation sequencing (HTS) have outstripped current plans of SYNTHESYS (http://www.synthesys.info) and GGBN to join natural history (NH) collection data with DNA and tissue collection data. HTS libraries can be considered a preparation of the genetic material of an organism(s), the actual physical molecular representation of a collection/specimen. These libraries come with specific adaptors that limit their transferability to other sequencing systems. They are prepared at great expense, but usually are only used for a single project, whilst a great deal of additional useful information may be available within these libraries. To increase the potential of the HTS libraries to be used for multiple projects they would need to be discoverable and metadata information made available. HTS library searches require the metadata to be queried on specific standardized keywords (by e.g. organism, HTS method etc.). HTS library parameters already in the GGBN Data Standard have been reviewed and augmented in order to incorporate library metadata of existing as well as future techniques. This is being realized by preparation of use-cases incorporating a range of different HTS techniques (e.g. whole genome shotgun sequencing, RADseq sequencing, single molecule MinIon sequencing). The result is a set of terms dedicated to library preparation including the pipeline parameters. Use cases are available in the GGBN Sandbox and will kept stable for at least three years. (http://wiki.ggbn.org/ggbn/Use_Cases_HTS_library_samples) Now we are kindly seeking your help with reviewing the terms and also ask for your general feedback on this initiative. GGBN does not want to reinvent the wheel, but work together with other organisations and initiatives, such as MIxS, GBIF, BOLD, INSDC. The template with the proposed HTS terms can be found in our Document Library (https://library.ggbn.org/share/s/dbHuLYuGQOiv5v8avKhhPw) for your review. We would appreciate if you could send the filled out excel sheet back before 22. September 2017 to support(a)ggbn.org<mailto:support@ggbn.org>. We are planning to present the results at TDWG 2017. This email text can also be found in our wiki: http://wiki.ggbn.org/ggbn/HTS_Public_Consultation Please feel free to forward this email to interested colleagues. With Warm Regards, Gabi Droege Technical Manager, Global Genome Biodiversity Network Botanic Garden and Botanical Museum Berlin-Dahlem Berlin, Germany And Katie Barker Program Manager, Global Genome Initiative and Global Genome Biodiversity Network National Museum of Natural History Smithsonian Institution [cid:image002.png@01D0C941.7EB85050]

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automated response
by Christy Semmens 21 Aug '17

21 Aug '17

Thank you for your message. I am out of the country leading a REEF Field Survey Trip to the Sea of Cortez. I will not have any internet access until August 26. I will respond to your message as soon as possible after that. If you need immediate assistance, please contact one of my colleagues at REEF (see http://www.REEF.org/about/staff). And don't hesitate to send me a follow-up email after my return. Thank you. Christy Pattengill-Semmens, REEF Director of Science

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DC-2017 Workshop - Metadata 2020: Accelerating Scholarly Discovery
by DCMI Announce 20 Aug '17

20 Aug '17

********PLEASE EXCUSE THE CROSS-POSTING******** *Metadata 2020: Accelerating Scholarly Discovery* * Half Day Workshop at DC-2017, Washington, DC, 26-29 October 2017* *==================================================* *:: Workshop Facilitators:* *Clare Dean*, *Community Outreach Manager, Metadata 2020* *Chuck Kosher*, *Director of Technology, Crossref* *Patricia Feeney*, *Product Support Manager, Crossref* *:: Time:* 8:30-12:30 DST *:: Date:* Saturday, 28 October 2017 *:: Session Homepage: * http://dcevents.dublincore.org/IntConf/index/pages/view/sp17-2020 *:: Registration:* http://dcevents.dublincore.org/IntConf/index/pages/view/reg17 *Early registration ends 15 September 2017. **Register now and save! * *Full conference and day rates are available.* *==================================================* SESSION DESCRIPTION: All of those who are involved in scholarly communications have the same end goal: to conduct, facilitate and/or communicate research, and have that research be discoverable. Whether they’re funders, authors, preprint servers, publishers, libraries, repositories; or the numerous tools seeking to add value through search, discovery, annotation, or analyses; so many of these organizations contribute along the way but often important details get mistyped, misrepresented, or missed out entirely. We all face the same problem—how to include as much useful information as possible. This includes basic information but also license information, funding/grant data, ORCID iDs, organization IDs, clinical trial data, and—along the way—corrections and retractions. How can we manage the efficient entry and use of clean and complete metadata, in a way that can grow and permeate through other systems usable by all in the scholarly communications chain? We envision a future with better metadata, not only increasing discoverability of content, but also benefiting reputation management, attribution, discoverability, efficiency, data reproducibility and reusability, in addition to future services that don’t yet exist! A group of organizations (including Crossref, DataCite, ORCID, OpenAIRE, California Digital Library, Wikimedia, OCLC among others) have come together to rally the community around this critical issue in scholarly communications: sharing richer metadata. Metadata 2020 is a collaboration that advocates richer, connected and reusable metadata for all research outputs with the understanding that: - Richer metadata fuels discoverability and innovation; - Connected metadata bridges the gaps between systems and communities; - Reusable metadata eliminates duplication of effort. We seek input from librarians, publishers, aggregators, service providers, funders, data repositories and researchers, to share user stories and insights about the journey that metadata takes, and to help prioritize goals and tactics for Metadata 2020. Metadata 2020 is a campaign that is bigger than just one organization or sector, but a collective responsibility shared by us all. This workshop invites contributions from specialists in the librarian community to help advance the library element of a metadata maturity model. This element will contribute to a larger maturity model in service of the wider scholarly communications community. WORKSHOP FACILITATORS: *Clare Dean*, *Community Outreach Manager, Metadata 2020* Clare Dean is the Community Outreach Manager for the advocacy campaign Metadata 2020, founded by a number of organizations including Crossref, DataCite, and ORCID. She is a publishing consultant for publishers and service providers with over 12 years experience in the scholarly publishing industry. *Chuck Kosher*, *Director of Technology, Crossre*f Chuck Koscher has been the Director of Technology for Crossref since 2002. His primary responsibility has been the development and operation of Crossref’s core services and technical infrastructure. As a senior staff member, he also contributes to the definition of Crossref’s mission and the expansion of its services such as the launch of Funding Data (formerly known as FundRef). His role includes management of technical support and back-end business operations. Chuck and his team interface directly with publisher members in dealing with issues affected by new or evolving industry practices such as those involving non-journal content like books, standards and databases. Chuck has been active within the industry having served 9 years on the NISO board of directors, and a participant in initiatives such as the NISO/NFAIS Best practice in Journal Publishing and NISO’s Supplemental Material Working Group. Prior to Crossref Chuck has over 20 years in software engineering experience primarily in the aerospace industry. *Patricia Feeney*, *Product Support Manager, Crossref* Patricia Feeney oversees Product Support and has been at Crossref for 10 years. She's also worked in publishing and as a systems librarian and cataloger and knows a lot about metadata. *For additional information about the workshop and to register, visit the conference website at http://dcevents.dublincore.org/index.php/IntConf/dc-2017 <http://dcevents.dublincore.org/index.php/IntConf/dc-2017>.*

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DC-2017 Special Session: Linked Data for Production (LD4P)
by DCMI Announce 12 Aug '17

12 Aug '17

********PLEASE EXCUSE THE CROSS-POSTING******** *Linked Data for Production (LD4P): Technical services workflow evolution through Tracer Bullets* *Special Session at DC-2017, Washington, D.C., 26-29 October 2017* ======================================= *:: Stanford University Presenters: * *Arcadia Falcone*, *Metadata Coordinator* *Josh Greben*, *Systems Programmer/Analyst* *Nancy Lorimer*, *Head, Metadata Department* * Christina Harlow*, *Digital Repository, Data Operations* * Philip Schreur*, *Associate University Librarian for Technical and Access Services* *:: Time:* 1:30-3:00 DST *:: Date:* Thursday, 26 October 2017 *:: Session Homepage:* http://dcevents.dublincore.org/IntConf/index/pages/view/sp17-ld4p *:: Registration:* http://dcevents.dublincore.org/IntConf/index/pages/view/reg17 ======================================= SESSION DESCRIPTION: Linked Data for Production (LD4P) is a Mellon-supported collaboration between six institutions (Columbia, Cornell, Harvard, Library of Congress, Princeton, and Stanford) to begin the transition of technical services production workflows to ones based in Linked Open Data (LOD). This first phase of the transition focuses on the development of the ability to produce metadata as LOD communally, the enhancement of the BIBFRAME ontology to encompass the multiple resource formats that academic libraries must process, and the engagement of the broader academic library community to ensure a sustainable and extensible environment. As its name implies, LD4P is focused on the immediate needs of metadata production such as ontology coverage and workflow transition. The focus of LD4P is on the identification, evaluation and adaption of existing viable tools to immediate production needs. A related project, LD4L-Labs, focuses on solutions that can be implemented in production at research libraries within the next three to five years. Their efforts focus on the enhancement and development of existing or new linked data creation and editing tools, exploration of linked data relationships, analysis of the graph to directly improve discovery, BIBFRAME ontology development, piloting efforts in URI persistence, and metadata conversion tool development needed by LD4P and the broader library community. As part of LD4P, Stanford is leading the development of a Performed Music Ontology and is converting four key technical services production pathways from MARC-based to RDF-based in a project called the Tracer Bullets. In this panel, we will discuss our work on these projects, highlighting achievements and difficulties of current efforts, as well as plans for future work. In this panel, we plan to discuss our work on these projects, highlighting achievements and difficulties of current efforts, as well as plans for future work. On the Performed Music Ontology, we will discuss our work on extending BIBFRAME 2 with community input to better support description of music artifacts. With regards to the “Tracer Bullets”, we will go through the progress on our four designated end-to- end pathways: vendor-supplied copy-cataloging (Tracer Bullet 1); original cataloging (Tracer Bullet 2); deposit of a single item to the Digital Repository (Tracer Bullet 3); and ingestion of a collection into the Digital Repository (Tracer Bullet 4). We have examined each of these pathways, from acquisition to discovery. Based on that analysis, we are converting all key elements in those workflows to a process rooted in linked data, balanced with the current needs and resources of the systems interacting with those pathways. Our emphasis is on the completeness of the pathway, and we plan for the workflows themselves to be expanded in the future to account for additional complexities and fully leveraging the capabilities of the RDF data models once our initial pathway has been established. For these tracer bullet pathways, Stanford is developing parallel processing streams. Resources flowing through these pathways will be processed in the traditional way with MARC or MODS-based metadata. A parallel, linked data workflow will be created for LD4P and duplicative metadata created. This metadata currently feeds into a parallel discovery environment so that we mimic the entire processing workflow. The metadata can also be sent to various library vendors and programs so that they can begin to adjust their businesses to incorporate linked data. Although this solution requires duplicative effort, it will allow Stanford to experiment with an alternative pathway without being dependent on the results for discovery. It also has the benefit of testing the new pathway with actual library resources and staff so that a true measure of effort and cost to implement the new paradigm can be evaluated. LD4P has completed the first year of its two-year grant and has made substantial process on the Tracer Bullets. In our panel presentation, we’d like to focus on five main areas: PANEL PRESENTATIONS: *Introduction: General information on the goals of LD4P and its context in the current library technical services paradigm* Philip Schreur, *Associate University Librarian for Technical and Access Services* *Workflow analysis for Tracer Bullets 1 & 2 including the testing of Tracer Bullet 1 with actual library data* Arcadia Falcone, *Metadata Coordinator* *MARC Data Enhancement and Conversion: Suggestions for enhancements to MARC data to make their conversion to RDF cleaner and our testing of MARC to BIBFRAME 2.0 conversion* Josh Greben, *Systems Programmer/Analyst* Nancy Lorimer, *Head, Metadata Department* *Tooling: Experimentation with current tools available to support Tracer Bullets 1 & 2 along with their enhancement and new tool development* Josh Greben, *Systems Programmer/Analyst* Nancy Lorimer, *Head, Metadata Department* *Digital Repository: Initial exploration of Tracer Bullets 3 & 4 and their implications for the Stanford Digital Repository* Christina Harlow, Digital Repository, Data Operations

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DC-2017 Full Day Session - Taming the Graph: Profiles over Linked Data
by DCMI Announce 09 Aug '17

09 Aug '17

********PLEASE EXCUSE THE CROSS-POSTING******** *Taming the Graph: Profiles over Linked Data* *Full day session at DC-2017, Washington, D.C., **26-28 **October 2017* * Day registration rates available* *===============================================* *:: Presenters: * *Tom Baker*, *DCMI* *Karen Coyle*, *Consultant* *Stefanie Rühle*, *SUB Goettingen* *Kirk Hess*, *Library of Congress* *Mariana Malta*, *Polytechnic of Oporto* *Eric Prud'hommeaux*, *World Wide Web (W3C)* *Gregg Kellogg*, *Semantic Media Consultant* *Paul Walk*, University of *Edinburgh* *:: Time:* 8:30am - 5:30pm EDT *:: Date:* Friday, 27 October 2017 *:: Session Homepage:* http://dcevents.dublincore.org/IntConf/index/pages/view/sp17-taming *:: Registration:* http://dcevents.dublincore.org/IntConf/index/pages/view/reg17 *===============================================* *SESSION DESCRIPTION:* The idea of application profile was proposed at a Dublin Core workshop in 2000 as a way to customize metadata for specific application domains, mixing-and-matching multiple metadata vocabularies as needed, and to share these customizations within communities of practice. This day-long event will start with a look back at how the discourse around profiles has evolved since 2000, then it will examine new technologies that can help us tame the boundless sea of Linked Data with controlled metadata. This event is sponsored by the DCMI, which participates in W3C efforts to develop standards relevant to profiles and seeks direction for its future work, and by LD4, a coordinated program to advance the use and utility of linked data in research and cultural heritage organizations, especially libraries. *We ask the following questions:* - Can Linked Data conceptualization and design be enhanced with metadata profiles? - How can profiles provide different views: data validation vs discovery, strict vs tolerant? - How can we express profiles for processing by machines? - How can we publish profiles for human consumption? *PRESENTERS:* *Morning Session 1: The Role of Profiles (90 min)* *"Application Profiles" since DC-2000* Tom Baker, DCMI * Pieces of the profile puzzle* Karen Coyle, Consultant *Profiles and Data Quality* Stefanie Rühle, SUB Goettingen * Morning Session 2: Developing and Using Profiles (90 min)* *Requirements for BIBFRAME profiles* Kirk Hess, Library of Congress *Structured methods for developing profiles* Mariana Malta, Polytechnic of Oporto *Agile, data-driven methods for developing profiles* Eric Prud'hommeaux, World Wide Web (W3C) *Discussion* *Afternoon Session 1: Expressing and Profiling Data (90 min)* *JSON-LD: The data syntax and its uses* Gregg Kellogg, *Semantic Media Consultant* *ShEx: the Shapes Expression Language* Eric Prud'hommeaux, World Wide Web (W3C) *Afternoon Session 2: Sharing profiles (90 min)* *Documenting profiles and vocabularies on the Web* Paul Walk, Edinburgh University * Maintaining RDF vocabularies in spreadsheets* Gregg Kellogg, *Semantic Media Consultant* *Answering the questions posed* Conference participants are free to attend any or all sessions or parts of sessions. The event assumes familiarity with the basic concepts of RDF and Linked Data. Participants will get more out of Afternoon Session 1 if they prepare beforehand by reading (or watching videos) about JSON-LD [1] and by perusing the ShEx Primer [2]. [1] https://json-ld.org/learn.html [2] http://shex.io/shex-primer

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