Questions to explore in breakouts- Google Doc
https://docs.google.com/spreadsheets/d/1tXbXg3wH1CVEReySAaGPut8sX1vuZ352KNrEU29OnMQ/edit#gid=0&fvid=1495463877
Structure - subject to suggestions and change
9:00-9:15 Introduction, goals, Barcelona recap – Ian Fore, Rafael Jimenez
How we will gather the output from the workshop
9:15-10:00am Introduction of each tool/approach
Six minute lightning talks – moderated by Lisa Mahoney
HubZero/nanoHUB/NCIPHUB – Michael Zentner
CEDAR - Mark Musen
bioCADDIE User Interface – Jeff Grethe
bioCADDIE Metadata Model – Susanna Sansone
Schema.org – Natasha Noy
BioSchemas – Rafael Jimenez
Content Management - Ian Fore
10am-12pm 4 x 30 min quarters in groups
12pm-12:30pm Discussion and Reporting
Summary
How do different tools to discover research data compare when used by real users with real use cases? Driven by the need in the biomedical community to find data this hands on workshop will explore that question. We will look at the NIH funded bioCADDIE index, Elixir/Excelerate projects, other indexes of biomedical data and generic search engines. While the subject matter is driven by biomedical research exploring tools like nanoHUB show how other fields address the issues. Bring your laptop and examples ready to share. Explore other’s examples and learn something yourself. No Powerpoint - just a working session on searching. We will aim to gather the learning from the workshop to inform NIH’s Big Data to Knowledge program, Elixir’s Excelerate and other resource indexing projects.
Think of this as a hackathon without the hacking. The characteristic of a hackathon we would like to preserve is as a hands-on activity where participants work side by side on a common problem, sharing their knowledge and learning from one another. We won’t build new tools in this workshop, but we will aim to learn more from one another about how we search for data and what different tools can do... so a searchathon. Maybe you have a better name for it - let us know that too.
Nor are we confined to tools specific to biology, science or research. How far can we get using the search engines that scientists use day to day? If those engines only takes us part of the way then what’s the gap?The following are examples of the kinds of tools it would be useful to explore.
Specialized indexes or catalogs that serve a particular domain well.
Bodies of datasets marked up with metadata/microformats which mean that Google, Bing and other search engines are now useful tools to reach into research ot other scholarly domains?
Tools that allow metadata mark-up by data producers and integrate with search engines to make that data findable.
The workshop will be organized with a lightning-style introduction to a number of relevant tools. Then we’ll break into groups to share and compare approaches. We’ll wrap up with a brief recap of the main things learnt. After the meeting we’ll share a summary to identify findings useful to the EU Elixir and NIH BD2K indexing projects.
Additional details of each tool are listed here.
9:00-9:15 Introduction (Michel Dumontier)
9:15-9:45 Francesco Osborne - Two roads to Semantic Publishing
9:45-10:15 Alex Garcia - A Semantic Print for Experimental Protocols
10:15-10:45 coffee break
10:45-11:15 Anita Bandrowski - Semantic publishing based in scientific ground truth; the RRID use case.
11:15-11:45 Peter Murray-Rust - Semantifying Scholarly publications using ContentMine and Wikidata
11:45-12:15 Panel discussion on the challenges and future of Semantic Publishing (moderated by Michel Dumontier)
12:15-12:30 Wrap up session (Michel Dumontier)
You are also encouraged to participate in the evening 'curate-a-thon.'
SHARE’s data set of research and scholarly activities throughout their lifecycle is free, openly licensed, and built with open source technology developed at the Center for Open Science (COS). Launched in beta in April 2015 the data set has grown to over 4 million records and 80+ providers, including CrossRef, PubMedCentral, DataOne, library institutional repositories and more. This infrastructure will contribute to a “network of knowledge” that links research objects (e.g., workflows, publications, funding information, data sets) that will enable better stewardship of this work, verification of claims, meta-scholarship, and the discoverability and reuse of these research objects.
SHARE is committed to openness, transparency, inclusive collaboration, and international interoperability. To make the most use of the data SHARE is aggregating, community involvement and contribution is essential to enhance the highly variable metadata associated with scholarly and research activity, to link objects together as part of the same activity, and in the process to promote innovative scholarship and a range of outputs beyond traditional publications.
This half day workshop will focus on (1) SHARE metadata curation and enhancement needs and priorities as they relate to the FAIR data principles, and (2) Force11 community needs for the SHARE data set. This is a hands-on workshop and attendees are encouraged to bring laptops to follow along.
Place contemporary research into historical context! OHSU Historical Collections & Archives (HC&A) will share selections from OHSU's collections of rare books, manuscripts, archives and artifacts from the history of the health sciences.
Visit the HC&A table at the tram reception to explore the rich history of research in Oregon, view rare books from the history of genetics, and check out our public health legacy data digitization project.
SHARE’s data set of research and scholarly activities throughout their lifecycle is free, openly licensed, and built with open source technology developed at the Center for Open Science (COS). Launched in beta in April 2015 the data set has grown to over 4 million records and 80+ providers, including CrossRef, PubMedCentral, DataOne, library institutional repositories and more. This infrastructure will contribute to a “network of knowledge” that links research objects (e.g., workflows, publications, funding information, data sets) that will enable better stewardship of this work, verification of claims, meta-scholarship, and the discoverability and reuse of these research objects.
SHARE is committed to openness, transparency, inclusive collaboration, and international interoperability. To make the most use of the data SHARE is aggregating, community involvement and contribution is essential to enhance the highly variable metadata associated with scholarly and research activity, to link objects together as part of the same activity, and in the process to promote innovative scholarship and a range of outputs beyond traditional publications.
Join us for curate-a-thon that will give participants the opportunity to directly contribute to enriching the SHARE dataset and implement many of the metadata priorities discussed in the first half of the day. Participants will learn how to access data using API’s, integrate information and datasets using IPython/Jupyter and other tools, and create links between related digital objects.
The Virus Pathogen Resource (ViPR) team recently released a new data portal for direct access to Zika virus-related data, including the consistent calculation of mature peptide sequences for all GenBank records - http://www.viprbrc.org/brc/home.spg?decorator=flavi_zika.
This session will work with this or similar data, such as:
