Tag Archives: DataONE

DataONE Funded by NSF for Another Round!

This is a week for important funding announcements! I already blogged about our new NSF funding for a Data-Level Metrics project with PLOS and DataONE, and on the heels of that, DataONE has announced their newest round of funding! I’ve borrowed heavily from their press release for this post. If you aren’t familiar with the work DataONE has been doing, go check out their website to learn more.

DataONE awarded $15 million from the NSF as part of an accomplishment based renewal.

DataONE: the Data Observation Network for Earth (www.dataone.org) is a distributed cyberinfrastructure that meets the needs of science and society for open, persistent, robust, and accessible Earth observational data. DataONE has dramatically increased the discoverability and accessibility of diverse yet interrelated Earth and environmental science data. In doing so, it has enhanced the efficiency of research and enabled scientists, policy makers and others to more easily address complex questions about our environment and our role within it.

DataONE Phase 1

Founded in 2009 by the NSF, DataONE was designed to provide both the tools and infrastructure for organizing and serving up vast amounts of scientific data, in addition to building an engaged community and developing openly available educational resources.

Accomplishments from the last five years include making over 260,000 publicly available data and metadata objects accessible through the DataONE search engine and building a growing network of 22 national and international data repositories. DataONE has published more than 74 papers, reached over 2,000 individuals via direct training events and workshops and connects with over 60,000 visitors annually via the website.

DataONE has developed an Investigator Toolkit that provides users with tools supporting activities across the full research data life cycle; a dynamic in-person and web-based education program comprising workshops, online best practices, curricula, training modules and other resources; and an engaged community of users via the DataONE Users Group and through collaboration with other national and international initiatives.

Plans for DataONE Phase 2

During the second phase, DataONE will target goals that enable scientific innovation and discovery while massively increasing the scope, interoperability, and accessibility of data. In particular DataONE will:

  • Significantly expand the volume and diversity of data available to researchers for large-scale scientific innovation;

  • Incorporate innovative features to dramatically improve data discovery and further support reproducible and open science; and

  • Establish an openly accessible online education series to support global participation and training in current techniques and perspectives.

DataONE will continue to engage, educate and grow the DataONE community, seek user input to ensure intuitive, user-friendly products and services, and work to ensure the long term sustainability of DataONE services so they continue to evolve and meet needs of researchers and other stakeholders for decades to come.

DataONE Phase 2 might not be quite as influential on graffiti culture as the 80s NY artist Phase 2. Click on the pic to learn more.

DataONE Phase 2 might not be quite as influential on graffiti culture as the 80s NY artist Phase 2. Click on the pic to learn more.

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DataUp is Merging with Dash!

Exciting news! We are merging the DataUp tool with our new data sharing platform, Dash.

About Dash

Dash is a University of California project to create a platform that allows researchers to easily describe, deposit and share their research data publicly. Currently the Dash platform is connected to the UC3 Merritt Digital Repository; however, we have plans to make the platform compatible with other repositories using protocols such as SWORD and OAI-PMH. The Dash project is open-source and we encourage community discussion and contribution to our GitHub site.

About the Merge

There is significant overlap in functionality for Dash and DataUp (see below), so we will merge these two projects to enable better support for our users. This merge is funded by an NSF grant (available on eScholarship) supplemental to the DataONE project.

The new service will be an instance of our Dash platform (to be available in late September), connected to the DataONE repository ONEShare. Previously the only way to deposit datasets into ONEShare was via the DataUp interface, thereby limiting deposits to spreadsheets. With the Dash platform, this restriction is removed and any dataset type can be deposited. Users will be able to log in with their Google ID (other options being explored). There are no restrictions on who can use the service, and therefore no restrictions on who can deposit datasets into ONEShare, and the service will remain free. The ONEShare repository will continue to be supported by the University of New Mexico in partnership with CDL/UC3. 

The NSF grant will continue to fund a developer to work with the UC3 team on implementing the DataONE-Dash service, including enabling login via Google and other identity providers, ensuring that metadata produced by Dash will meet the conditions of harvest by DataONE, and exploring the potential for implementing spreadsheet-specific functionality that existed in DataUp (e.g., the best practices check). 

Benefits of the Merge

  • We will be leveraging work that UC3 has already completed on Dash, which has fully-implemented functionality similar to DataUp (upload, describe, get identifier, and share data).
  • ONEShare will continue to exist and be a repository for long tail/orphan datasets.
  • Because Dash is an existing UC3 service, the project will move much more quickly than if we were to start from “scratch” on a new version of DataUp in a language that we can support.
  • Datasets will get DataCite digital object identifiers (DOIs) via EZID.
  • All data deposited via Dash into ONEShare will be discoverable via DataONE.

FAQ about the change

What will happen to DataUp as it currently exists?

The current version of DataUp will continue to exist until November 1, 2014, at which point we will discontinue the service and the dataup.org website will be redirected to the new service. The DataUp codebase will still be available via the project’s GitHub repository.

Why are you no longer supporting the current DataUp tool?

We have limited resources and can’t properly support DataUp as a service due to a lack of local experience with the C#/.NET framework and the Windows Azure platform.  Although DataUp and Dash were originally started as independent projects, over time their functionality converged significantly.  It is more efficient to continue forward with a single platform and we chose to use Dash as a more sustainable basis for this consolidated service.  Dash is implemented in the  Ruby on Rails framework that is used extensively by other CDL/UC3 service offerings.

What happens to data already submitted to ONEShare via DataUp?

All datasets now in ONEShare will be automatically available in the new Dash discovery environment alongside all newly contributed data.  All datasets also continue to be accessible directly via the Merritt interface at https://merritt.cdlib.org/m/oneshare_dataup.

Will the same functionality exist in Dash as in DataUp?

Users will be able to describe their datasets, get an identifier and citation for them, and share them publicly using the Dash tool. The initial implementation of DataONE-Dash will not have capabilities for parsing spreadsheets and reporting on best practices compliance. Also the user will not be able to describe column-level (i.e., attribute) metadata via the web interface. Our intention, however, is develop out these functions and other enhancements in the future. Stay tuned!

Still want help specifically with spreadsheets?

  • We have pulled together some best practices resources: Spreadsheet Help 
  • Check out the Morpho Tool from the KNB – free, open-source data management software you can download to create/edit/share spreadsheet metadata (both file- and column-level). Bonus – The KNB is part of the DataONE Network.

 

It's the dawn of a new day for DataUp! From Flickr by David Yu.

It’s the dawn of a new day for DataUp! From Flickr by David Yu.

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My picks for #AGU13

Nerds come in many flavors at the AGU meeting. From Flickr by Westfield, Ma

Nerds come in many flavors at the AGU meeting. From Flickr by Westfield, Ma

Next week, the city of San Francisco will be overrun with nerds. More specifically,more than 22,000 geophysicists, oceanographers, geologists, seismologists, meteorologists, and volcanologists will be descending upon the Bay Area to attend the 2013 American Geophysical Union Fall Meeting.

If you are among the thousands of attendees, you are probably (like me) overwhelmed by the plethora in sessions, speakers, posters, and mixers. In an effort to force myself to look at the schedule well in advance of the actual meeting, I’m sharing my picks for must-sees at the AGU meeting below.

Note! I’m co-chairing “Managing Ecological Data for Effective Use and Reuse” along with Amber Budden of DataONE and Karthik Ram of rOpenSci. Prepare for a great set of talks about DMPTool, rOpenSci, DataONE, and others.

Session Title

Abbr

Type

Day

Time

Translating Science into Action: Innovative Services for the Geo- and Environmental- Sciences in the Era of Big Data I GC11F Oral Mon 8:00 AM
Data Curation, Credibility, Preservation Implementation, and Data Rescue to Enable Multi-source Science I IN11D Oral Mon 8:00 AM
Data Curation, Credibility, Preservation Implementation, and Data Rescue to Enable Multi-source Science II IN12A Oral Mon 10:20 AM
Enabling Better Science Through Improving Science Software Development Culture I IN22A Oral Tue 10:20 AM
Collaborative Frameworks and Experiences in Earth and Space Science Posters IN23B Poster Tue 1:40 PM
Enabling Better Science Through Improving Science Software Development Culture II Posters IN23C Poster Tue 1:40 PM
Managing Ecological Data for Effective Use and Reuse I ED43E Oral Thu 1:40 PM
Open-Source Programming, Scripting, and Tools for the Hydrological Sciences II H51R Oral Fri 8:00 AM
Data Stewardship in Theory and in Practice I IN51D Oral Fri 8:00 AM
Managing Ecological Data for Effective Use and Reuse II Posters ED53B Poster Fri 1:40 PM

Download the full program as a PDF

Previous Data Pub blog post about AGU: Scientific Data at AGU 2011

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The Data Lineup for #ESA2013

Why am I excited about Minneapolis? Potential Prince sightings, of course!

Why am I excited about Minneapolis? Potential Prince sightings, of course! From http://www.emusic.com

In less than  week, the Ecological Society of America’s 2013 Meeting will commence in Minneapolis, MN. There will be zillions of talks and posters on topics ranging from microbes to biomes, along with special sessions on education, outreach, and citizen science. So why am I going?

For starters, I’m a marine ecologist by training, and this is an excuse to meet up with old friends. But of course the bigger draw is to educate my ecological colleagues about all things data: data management planning, open data, data stewardship, archiving and sharing data, et cetera et cetera. Here I provide a rundown of must-see talks, sessions, and workshops related to data. Many of these are tied to the DataONE group and the rOpenSci folks; see DataONE’s activities and rOpenSci’s activities. Follow the full ESA meeting on Twitter at #ESA2013. See you in Minneapolis!

Sunday August 4th

0800-1130 / WK8: Managing Ecological Data for Effective Use and Re-use: A Workshop for Early Career Scientists

For this 3.5 hour workshop, I’ll be part of a DataONE team that includes Amber Budden (DataONE Community Engagement Director), Bill Michener (DataONE PI), Viv Hutchison (USGS), and Tammy Beaty (ORNL). This will be a hands-on workshop for researchers interested in learning about how to better plan for, collect, describe, and preserve their datasets.

1200-1700 / WK15: Conducting Open Science Using R and DataONE: A Hands-on Primer (Open Format)

Matt Jones from NCEAS/DataONE will be assisted by Karthik Ram (UC Berkeley & rOpenSci), Carl Boettiger (UC Davis & rOpenSci), and Mark Schildhauer (NCEAS) to highlight the use of open software tools for conducting open science in ecology, focusing on the interplay between R and DataONE.

Monday August 5th

1015-1130 / SS2: Creating Effective Data Management Plans for Ecological Research

Amber, Bill and I join forces again to talk about how to create data management plans (like those now required by the NSF) using the free online DMPTool. This session is only 1.25 hours long, but we will allow ample time for questions and testing out the tool.

1130-1315 / WK27: Tools for Creating Ecological Metadata: Introduction to Morpho and DataUp

Matt Jones and I will be introducing two free, open-source software tools that can help ecologists describe their datasets with standard metadata. The Morpho tool can be used to locally manage data and upload it to data repositories. The DataUp tool helps researchers not only create metadata, but check for potential problems in their dataset that might inhibit reuse, and upload data to the ONEShare repository.

Tuesday August 6th

0800-1000 / IGN2: Sharing Makes Science Better

This two-hour session organized by Sandra Chung of NEON is composed of 5-minute long “ignite” talks, which guarantees you won’t nod off. The topics look pretty great, and the crackerjack list of presenters includes Ethan White, Ben Morris, Amber Budden, Matt Jones,  Ed Hart, Scott Chamberlain, and Chris Lortie.

1330-1700 / COS41: Education: Research And Assessment

In my presentation at 1410, “The fractured lab notebook: Undergraduates are not learning ecological data management at top US institutions”, I’ll give a brief talk on results from my recent open-access publication with Stephanie Hampton on data management education.

2000-2200 / SS19: Open Science and Ecology

Karthik Ram and I are getting together with Scott Chamberlain (Simon Fraser University & rOpenSci), Carl Boettiger, and Russell Neches (UC Davis) to lead a discussion about open science. Topics will include open data, open workflows and notebooks, open source software, and open hardware.

2000-2200 / SS15: DataNet: Demonstrations of Data Discovery, Access, and Sharing Tools

Amber Budden will demo and discuss DataONE alongside folks from other DataNet projects like the Data Conservancy, SEAD, and Terra Populus.

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DataUp is Live!

party girls

We are celebrating. From Boston Public Library via Flickr.

That’s right: DataUp is LIVE! I’m so excited I needed to type it twice.  So what does “DataUp is Live!” mean? Several things:

  • The DataUp website (dataup.cdlib.org) is up and running, and is chock full of information about the project, how to participate, and how to get the tool (in either web app or add-in form).
  • The DataUp web application is up and running (www.dataup.org). Anyone with internet access can start creating high-quality, archive-ready data! Would you rather use the tool within Excel? Download the add-in instead (available via the main site).
  • The DataUp code is available. DataUp is an open source project, and we strongly encourage community members to participate in the tool’s continued improvement. Check out the code on BitBucket.
  • The special repository for housing DataUp data, ONEShare, is up and running. This new repository is a special instance of the CDL’s Merritt Repository, and is connected to the DataONE project. ONEShare is the result of collaborations between CDL, University of New Mexico, and DataONE.  Read more in my blog post about ONEShare.
  • Please note that the current version of DataUp is Beta: this means it’s a work in progress. We apologize for any hiccups you may encounter; in particular, there is a known issue that currently prevents spreadsheets archived via DataUp from appearing in DataONE searches.

Today also marks the integration of the old DCXL/DataUp blog with the Data Pub Blog. You probably noticed that they are combined since the banner at the top says “Data Pub”. I will be posting here from now on, rather than at dataup.cdlib.org. The DataUp URL now hold the DataUp main website. Read more about these changes in my blog post about it.  The Data Pub Blog is intended to hold “Conversations About Data”. That means we will run the gamut of potential topics, including (but not limited to) data publication, data sharing, open data, metadata, digital archiving, etc. etc..  There are likely to be posts from others at CDL from time to time, which means you will have access to more than just my myopic views on all things data.

The DataUp project’s core team included yours truly, Patricia Cruse (UC3 Director), John Kunze (UC3 Associate Director), and Stephen Abrams (UC3 Associate Director). Of course, no project at CDL is an island. We had SO MUCH help from the great folks here:

  • DataUp Website: Eric Satzman, Abhishek Salve, Robin Davis-White, Rob Valentine, Felicia Poe
  • DataUp Communications: Ellen Meltzer (DataUp Press Release PDF)
  • DataUp development: Mark Reyes, David Loy, Scott Fisher, Marisa Strong
  • Machine configuration: Joseph Somontan
  • Administrative support: Beaumont Yung, Rondy Epting-Day, Stephanie Lew

Thanks to all of you!

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Counting Down Plus DataUp Webinar

celebration

Next week: The CDL DataUp team will be performing “Celebration” at a karaoke bar (undisclosed location).

We are nearing the (revised) launch date for DataUp: on Tuesday 2 October, one week from today, we plan on officially release the tool. This includes the DataUp website, the code, and the ability to download the add-in.  Of course, you never know what the next week will bring.  We aren’t promising these will be delivered on Tuesday, but we will do our very best!

Last week at the annual DataONE All Hands Meeting, I presented a demonstration of DataUp and showcased its capabilities for assisting in good data stewardship practices.  DataUp was met with much excitement, especially from the Citizen Science Working Group (technically called the PPSR group, which stands for Public Participation in Scientific Research). The PPSR folks were very excited about shaping DataUp to be something that will help their data contributors to submit high quality, well-documented data. This is one of the many extensions for which DataUp is ripe; others include its integration with repositories other than ONEShare.

If you would like a guided introduction and walk-through of the tool, mark your calendar for the DataUp webinar, scheduled for Wednesday 3 October.  You need to pre-register for the webinar to receive the connection information.  If you can’t make the webinar, don’t fret: we will record it and make it available afterward on the UC3 webinar page.

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Sustaining Data

Last week, folks from DataONE gathered in Berkeley to discuss sustainability (new to DataONE? Read my post about it). Of course, lots of people are talking about sustainability in Berkeley, but this discussion focused on sustaining scientific data and its support systems.  The truth is, no one wants to pay for data sustainability. Purchasing servers and software, and paying for IT personnel is not cheap. Given our current grim financial times, room in the budget is not likely to be made.  So who should pay?  Let’s first think about the different groups that might pay.

  1. Private foundations
  2. Public agencies (e.g., NSF, NIH)
  3. Institutions
  4. Professional societies and organizations
  5. Researchers

Although the NSF provides funds for organizations like DataONE to develop, they are not interested in funding “sustainability”. They are in the business of funding research, which means that come 2019 when NSF funding ends for DataONE, someone else is going to have to pick up the tab.

Any researcher (including myself) will tell you that the thought of paying for data archiving and personnel is not appealing.  Budgets are already tight in proposals (which have record low acceptance rates); combine that with the lack of clarity about data management and archiving costs, and researchers are not eager to take on sustainability.

Many researchers see data sustainability as the domain of their institutions: providing data management and archiving services in bulk to their faculty would allow institutions to both regulate how their researchers handle their data, and remove the guesswork and confusion for the researchers themselves.  However with budget crises plaguing higher education due to rising costs and decreasing revenue, this is not a cost that institutions are likely to take on in the near future.

Obviously I was going to reference Pink Floyd for this post on money… From Wikipedia.

Lack of funds for critical data infrastructure is a systematic problem, and DataUp is no exception. Although we have funds to promote DataUp and publish our findings in the course of the project, we do not have funds to continue development. There is also the question of storage for datasets. Storage is not free, and we have not yet solved the problem of who will pay in the long term for storing data ingested into the ONEShare repository via DataUp.

Now that I’ve completed this post, it seems rather bleak. I am confident, however, that we have the right people working on the problem of data sustainability. It is certainly a critical piece in the current landscape of digital data.

Love Pink Floyd AND The Flaming Lips? Check out the FL cover album for Dark Side of the Moon, including a spectacular version of “Money”.

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The Geek SXSW

Explosions

The Texan group Explosions in the Sky performed at SXSW. Another Texan native who wants to go? Me! Help by voting for my panel. From flickr by shotgunshy

Seeing the acronym SXSW is likely to elicit one of two responses: (1) Huh? or (2) OMGOMGOMG!! If you are in the former camp, rest easy: I will explain. SXSW is the abbreviation for South by Southwest, a big old festival/conference down in my home state of Texas. SXSW has been going strong in Austin since 1987 and gets bigger every year (60,000 registrants this year!).  Read more about it on Wikipedia, or check out SXSW’s stats pdf to be wowed and amazed at how huge this thing is. From the SXSW website:

The South by Southwest® (SXSW®) Conferences & Festivals (March 8-17, 2013) offer the unique convergence of original music, independent films, and emerging technologies. Fostering creative and professional growth alike, SXSW® is the premier destination for discovery.

 Most people who know about SXSW think it’s just about music, and perhaps know about the big film festival.  The arts is definitely a big part of the event: this year, 2,200 musical acts will appear during the main festival.  But there is also an interactive conference (SXSWi) that will takes place before the music week begins.  The geek version of SXSW is quite large: this year there will be an estimated 25,000 SXSWi participants.  If you haven’t heard of SXSWi, you’ve probable heard of a few of the innovations that have gained traction at this conference: Twitter or foursquare, anyone? Major interviews, announcements, and product introductions are made at SXSWi for all things geek including software, video games, and social media.

So why am I telling you this? Because I need your help to get to SXSWi! In typical innovative fashion, those who would like to present at SXSWi need to first make it through a rigorous selection process that includes votes from the public. I need your vote for my proposed panel! What am I proposing, you ask? Here is the description:

Funders, researchers, and public stakeholders increasingly see the need to better communicate and curate ever expanding bodies of research data. This panel will bring together stakeholders in scientific data community, including a researcher, a librarian, and a federated data repository director. Before the panel commences, we will describe the current landscape of scientific data and its management, including publication, citation, archiving, and sharing of data. The panel discussion will focus on identifying gaps and unmet needs in order to help chart a path for future policy, service, and infrastructure development. Questions will include:  How has the handling of scientific data changed in the last few years? What should researchers know about properly organizing, managing, and sharing their data? How can data centers, IT professionals, developers, librarians, and others help researchers with their data? Why should researchers consider sharing and/or publishing their data? How do researchers benefit from implementing data citation practices?

I’ve lined up four great speakers:

This promises to be a great group of folks who will undoubtedly provide for an entertaining and lively discussion; hopefully afterward we can celebrate our success over a few Shiner Bocks while jamming to some tunes at the SXSW festival.

Voting from the public accounts for about 30% of the decision-making process for SXSW panel programming, so we really want to make the part we can control count. Please vote by clicking the icon below and share with others!

Curious to hear what Explosions in the Sky sounds like? Here ya go. You’re welcome.

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DataUp at #ESA2012

I’m spending this week in Portland to attend the Ecological Society of America’s annual meeting.  If you are a long-timer of the blog, you might remember I was at ESA last year to collect requirements for DataUp (then DCXL) and reported on data sharing among ecologists.  Unfortunately I’m not presenting on DataUp specifically, but rather I’m here to tout the merits of DataONE. (This includes serving as one of the DataONE booth babes).  I’m anxious to showcase DataUp to the ESA crowd, but our public release isn’t until September… so I’m resisting the urge to show off the tool.  With DataONE going live a few weeks ago, there is plenty to talk about with ESA attendees.

That said, there are all kinds of great things to see at ESA this week. DataONE sponsored a workshop on data management this past Sunday where there were quite a few questions about DataUp.  I also participated in a session on data management planning yesterday, and will take part in a panel discussion today over lunch about the culture of data sharing in Ecology.  Rest assured that DataUp will be mentioned during that discussion!  Other must-sees at ESA: the session I organized with Josh Tewksbury and Steph Hampton on the future of ecology (Wednesday) and the workshop on using R to find ecological data (Thursday).

If you happen to be at ESA this year, stop by the DataONE booth and say hello.  You can use the new ONE-Mercury search engine to search DataONE repositories for data, chat with me about DataUp, and eat tasty chocolates.

Despite the NSF requirement for data management plans, I get the feeling that folks still haven’t gotten on board with learning about data management and sharing.  It will be fun to attend #ESA2013, showcase DataUp, and see how the culture has evolved.

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Looking for something? DataONE can help

ginsu knife

I’m not overselling it – DataONE is the Ginsu knife of data tools. From Flickr by inspector_81

At long last, DataONE has gone live.  For veterans of the DCXL/DataUp blog, you are probably well aware of the DataONE organization and project, but for newcomers I will provide a brief overview.  Fine print: this is NOT the official DataONE stance on DataONE.  This is merely my interpretation of it.

To explain DataONE, let’s have go through a little thought exercise. Let’s pretend I’m a researcher, starting a project on copepods in estuaries of the Pacific Northwest. I’m wondering who else has worked on them, what they have found, and whether I can use their data to help me parameterize my model.  Any researcher will tell you the best way to do this is to start searching for relevant journal articles.  I can then weave in and out of reference lists to hone in on the authors, topics, and species that might be of most use, continually refining my searches until I are satisfied.

Imagine I need the data from some of those articles I found.  I look for datasets on the authors’ websites, in the papers themselves, and online.  Some of the work was funded by NOAA, so I check there for data. I Google like crazy.  Alas, the data are nowhere to be found.

In real life, this is where I ended my search and started contacting authors directly.  Although I should have also checked data repositories, I didn’t. This was mostly because I wasn’t aware of them when I did this work back in 2008.  Sadly, many researchers are in a similar state of ignorance that I was.

The good news is that there are A LOT of data repositories out there (check out Databib.org for an intimidating list).  The bad news is it’s very difficult to know about and search all of the potential repositories with data you might want to use.

ENTER DataONE.

DataONE is all about linking together existing data repositories, allowing researchers to access, search, and discover all of the data through a single portal.  It’s basically cyber-glue for the different data centers out there. The idea is that you go to the DataONE search engine (ONEMercury) and hunt for data. It tells you where the data are housed, gives you lots of metadata, and gives you access to data when the authors have allowed this.

But wait, there’s MORE!

DataONE is also all about providing tools for researchers to find, use, organize, and manage their data throughout the research life cycle.  This is where DataUp connects with DataONE: DataUp will be part of the Investigator Toolkit, which also includes nifty things like the DMPTool, ONE-R (an R package for DataONE), and ONE-Drive (a Dropbox-esque way to look at data in DataONE, in production).

The exciting news this week is that DataONE’s search and discovery tool has gone live (check out the NSF press release or the DataONE press release).  You can now start looking for data that might be housed in any participating repository.  There are only a few data repositories (called member nodes in DataONE speak) currently on board, but the number is expected to increase exponentially over the coming years.

More questions about DataONE? I can help, or at least direct you to the person that can. Alternatively start poking around the DataONE website and ONEMercury, and give feedback so we can make it better.

 

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