Marrying models and data: Adventures in Modeling, Data Wrangling and Software Design
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Description of the process of populating the GISR database. Includes information data sharing, data discovery, data citation and integration strategies. This talk was given in session SCI-030 Monday, November 4, 2013 at CERF2013 in San Diego, CA, USA.
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Marrying models and data: Adventures in Modeling, Data Wrangling and Software Design
- 1. Marrying Models and Data: Adventures in Modeling, Data Wrangling and Software Design Anne E. Thessen, Elizabeth North, Sean McGinnis and Ian Mitchell
- 3. LTRANS • Lagrangian Transport Model • Open Source • http://northweb.hpl.umc es.edu/LTRANS.htm • Used to predict transport of particles, subsurface hydrocarbons, and surface oil slicks (in development)
- 4. GISR Deepwater Horizon Database Number of Data Points • Over 7 million georeferenced data points • Over 9 GB • Over 2000 analytes and parameters
- 5. Database Contents • Oceanographic Data – – – – Salinity Temperature Oxygen More • Chemistry Data – – – – Hydrocarbons Heavy metals Nutrients More
- 6. Database Contents • Oceanographic Data – – – – Salinity Temperature Oxygen More • Chemistry Data – – – – Hydrocarbons Heavy metals Nutrients More • • • • Air Water Tissue Sediment/Soil
- 7. Example Plots for One Analyte Naphthalene, August 1-15, 2010 mg l-1
- 8. Heterogeneity • Heterogeneity – Terms – Units – Format – Structure Benzoic Acid Carboxybenzene E210 Benzoic Acid Dracylic Acid C7H6O2 2,016 1,848
- 9. Heterogeneity • Heterogeneity n-Decane – Terms – Units – Format – Structure 103 parts per trillion ppbv 66 μg/g ng/g ppt mg/kg μg/kg ppb
- 10. Metadata • Metadata – Missing – Not computable Name Unit Location 0.23 Attribution Time
- 11. Metadata • Metadata – Missing – Not computable Name Unit Method Location 0.23 Attribution Uncertainty Time
- 12. The Great Data Hunt • Discovery – Project directory – Funding agency records – Literature – Internet search Total Data Sets Discovered n = 140
- 13. The Great Data Hunt • Discovery – Project directory – Funding agency records – Literature – Internet search We identified 90 relevant data sets Relevant
- 14. The Great Data Hunt • Discovery • Access – Online – Ask directly – Literature Relevant
- 15. The Great Data Hunt • Discovery • Access – Online – Ask directly – Literature We received responses to 59% of our inquires and obtained 34% of the identified data sets Relevant
- 16. The Great Data Hunt – Online – Ask directly – Literature We received responses to 59% of our inquires and obtained 34% of the identified data sets Frequency • Discovery • Access 41% of those responses were received within 24 hours and 29% were received within the first week Days to Response
- 17. The Great Data Hunt – Online – Ask directly – Literature 0-20 email exchanges per data set We received responses to 59% of our inquires and obtained 34% of the identified data sets Frequency • Discovery • Access 41% of those responses were received within 24 hours and 29% were received within the first week Number of Emails
- 18. The Great Data Hunt • Discovery • Access • Citation – Literature – Existing requirements – Generate new
- 19. Why didn’t people share? • • • • • Paper not published yet – 35% Passed the buck – 20% Too busy – 10% Medical problems – 10% Poor quality – 10%
- 20. Why should anyone share? • Mandated • Increased citation and visibility • Early access to GISR database • New insights
- 21. Future Work • • • • • Incorporate data as available Incorporate user feedback Web Access Users’ Guide Manuscripts
- 22. Thank You to Data Providers • • • • • • • • • • • • • • • • • • • • NOAA/NOS Office of Response and Restoration Commonwealth Scientific and Industrial Research Organization Environmental Protection Commission of Hillsborough County National Estuarine Research Reserves Sarah Allan Kim Anderson Jamie Pierson Nan Walker Ed Overton Richard Aronson Ryan Moody Charlotte Brunner William Patterson Kyeong Park Kendra Daly Liz Kujawinski Jana Goldman Jay Lunden Samuel Georgian Leslie Wade • • • • • • • • • • • • • • • • • • • • • • • Joe Montoya Terry Hazen Mandy Joye Richard Camilli Chris Reddy John Kessler David Valentine Tom Soniat Matt Tarr Tom Bianchi Tom Miller Elise Gornish Terry Wade Steven Lohrenz Dick Snyder Paul Montagna Patrick Bieber Wei Wu Mitchell Roffer Dongjoo Joung Mark Williams Don Blake Jordan Pino • • • • • • • • • • • • • • • • • • • • • • • John Valentine Jeffrey Baguely Gary Ervin Erik Cordes Michaeol Perdue Bill Stickle Andrew Zimmerman Andrew Whitehead Alice Ortmann Alan Shiller Laodong Guo A. Ravishankara Ken Aikin Tom Ryerson Prabhakar Clement Christine Ennis Eric Williams Ed Sherwood Julie Bosch Wade Jeffrey Chet Pilley Just Cebrian Ambrose Bordelon
- 23. Questions?
Hinweis der Redaktion
- Hello, my name is Anne Thessen and I’m going to speak to you about some model development that we’ve been doing. First I would like to acknowledge my coauthors, Elizabeth North, Sean McGinnis and Ian Mitchell. We are part of the Gulf Integrated Spill Research Consortium. Our work was funded by the Gulf of Mexico Research Initiative. We received institutional support from Arizona State University and the University of Maryland Center for Environmental Science. I recently started my own business called The Data Detektiv that does this type of data work. If you like what you see and have need of this sort of expertise in your project please see me after the talk or swing by my exhibitor booth.
- On April 20, 2010 the Deepwater Horizon oil rig exploded in the Gulf of Mexico. The broken well flowed for 87 days before being capped and released an estimated 4.9 million barrels of crude. One of the more unique aspects of this particular spill was that oil was being released under 1600 m of water. The surface slick appeared on Apr 22, 2010. This is a satellite image of the surface slick near the Mississippi River delta from NASA’s Terra satellite on May 24. The slick directly impacted about 180,000 sq km and by early June, oil had washed up on 200 km of coastline. Understanding how oil is transported in the Gulf of Mexico is key to being able to launch an effective spill response.
- The goal of our project is to modify an existing Lagrangian transport model, called LTRANS, that has been used to predict transport of other types of particles, so that it can be effectively used to predict where oil will go in the event of a Gulf of Mexico spill. In this panel we see snapshot of particle distributions from a model run that simulates subsurface hydrocarbons. We want to know if the particles are in the right place and if we can estimate degradation rates from the data.
- To determine the efficacy of the model, we are comparing the output to field data collected after the Deepwater Horizon explosion. To accomplish this, we are compiling a database of oceanographic and hydrocarbon field measurements called the GISR Deepwater Horizon database. It can be queried to get the output we need for comparison. It is over 9 GB in size and contains over 7 million georeferenced data points gathered from published and unpublished sources, government databases, volunteer networks and individual researchers.
- The data base contains multiple types of oceanographic and chemistry data. Here are some examples.
- The database contains data from air, water, tissue and sediment or soil.
- This is an example of the type of coverage we have in the database for a single analyte, Naphthalene.This panel is a top view showing the spatial coverage of Naphthalene samples. The red indicates Naphthalene was detected while the open circles indicate that Naphthalene was tested for, but not detected. This panel shows the depth distribution while the color indicates concentration in micrograms per liter. The green square on both panels is where the oil was released. We have over 10,000 Naphthalene measurements in the database. Assembling a database of this nature was a huge challenge. We had to develop some interesting algorithms and methods to find, access and integrate all of the data. I’m going to describe that process and, if we have time, show some LTRANS output and field data comparison visualizations.
- The first challenge was heterogeneity between data sets, which was quite broad. We needed to bring everything together into a single database and then be able to effectively query that database. Every provider had their own favorite terms and units and we normalized them algorithmically. Terms were normalized using a Google Fusion Table that lists a “preferred name” and all of the homonyms for that name. An algorithm can read the term used in the original data set, find it in the Fusion Table and then tag the database entry with the “preferred name”. That way when the database is queried for a particular analyte, we don’t have missed data because one homonym is used instead of another. For example, benzoic acid has five homonyms in the table. We had over 2,000 terms before reconciliation and 1,848 terms after reconciliation. We expect this number to decrease further once the Fusion table is complete.
- The units are handled in the same way, except there is a transformation step, wherein some math is done to convert the value to the “preferred unit”. This allows us to normalize terms and units without changing the original data set. For example, n-Decane was represented by 6 different units. The number of different units in the database was almost decreased by half after reconciliation. Formats varied from Access databases and shape files to pdf tables. All data sets, except for the databases, were normalized to our schema and then imported into an SQL database. The databases were transformed to SQL and then joined. Sometimes this had to be done manually. Sometimes we were able to write scripts to help.
- The second challenge was metadata (or lack thereof). Metadata was often missing, in a separate location or in a separate format from the actual data. At a minimum, for the database to work, we needed to know the basics of what, where and when.
- Ideally, we were able to get more information, like about methods and uncertainty. Compiling the metadata was an exercise in detective work. Even simple information like coordinates and dates were sometimes buried. Metadata about methods were often found in narrative form in published literature. Sometimes metadata were in companion files, such as xml. Sometimes I would just have to contact the data provider directly. This was often a very time consuming process because they frequently had to hunt for the data or direct me to someone else like a student or a technician.
- Third, locating and accessing data was also a big challenge. The first step is knowing what data sets to ask for and who to ask. A significant number of data sets were not in a repository or part of the published literature - and we knew that this would be the case. The question is, how do you learn of a data set’s existence if it hasn’t been published or deposited? We did a couple of things. One of the Gulf coast SeaGrants has a project directory for the Deepwater Horizon spill. The directory was not comprehensive and depended on folks self reporting their projects, but it was a start. We also looked for awarded projects through funding agency web sites to find folks who were likely to have data. Of course there was a literature search and a basic internet search for folks claiming to do research on the spill. That gave us a list of contacts. We ended up making contact with 140 projects. We approached each contact via email to find out if they had data and if it was relevant.
- Many of these contacts revealed that their data sets were not relevant to our model development. For example, measurements of hydrocarbons in fish tissues were not going to help with our model, so we did not pursue those data sets. Sometimes two different contacts were working on the same data set, so what we thought were two data sets were really only one. At the end of the process we identified 90 relevant data sets.
- Once the data sets were discovered, they had to be accessed. Some were freely available and were simply downloaded. Some data sets were in repositories that may or may not involve working with the data manager to gain access. Others were published as a table in supplementary material. Most data sets involved communicating with the provider to get the complete data set and the metadata. There were a few instances where the provider instructed us to take the data from the figure, but we tried to avoid doing that.
- Out of those 90 relevant data sets, we received responses to 59% of our inquiries and were able to obtain 34% of the data sets. The bottom chart is a breakdown of the 90 data sets. The dark orange represents the data sets we asked for - and received a response and the data. The dark purple are the data sets that were freely available online, so no response was necessary. The light orange represents the data sets that were denied us. The light purple represents the inquires that went completely unanswered. You can look at this another way. The orange represents inquiries that got a response and the purple represents the inquiries that did not get a response. The dark colors represent the inquiries that resulted in data while the light colors represent inquiries that did not result in data. This is quite good compared to sharing in some communities which can be as low as 10%.
- Most of the responses we received were quite timely. 41% were received within the first 24 hours and 29% were received within 2-7 days.
- This process can be quite labor intensive. Some data sets required up to 20 email exchanges to get all of the data and metadata situated. The average was 7.6 emails.
- An important part of reusing other people’s data is citing them appropriately. Data set citation is still a relatively new concept, but its starting to gain momentum. We worked with each of the data providers to find out how they wanted to be cited. Typically, if the data had a publication, the provider wanted the publication to be cited. Not all data sets had a publication. Data sets in repositories often had a citation already developed and provided by the repository. There were plenty of data sets that were unpublished and not in a repository. For these data sets we worked with the provider to generate a citation. This involved encouraging the provider to deposit in FigShare, which is a free place to deposit data and receive a citable, unique identifier for your data. If the data set was already online, like on a personal web site, the access URL was given in the citation. We also plan to develop a citation for the database as a whole with all of the providers as authors. In the future, when a user executes a query, they will also be presented with a list of citations for the data sets that appear in the query results. So they can cite the database as a whole or the individual data sets they actually use. We hope, through tools like ImpactStory, that providers can start getting credit for the data sets they generate and share.
- We were actively denied data by 24% of the 90 contacts made. The other 40% did not respond to our requests at all. We know nothing about the data set or why it wasn’t shared. For those 24% that did give us a reason we see that “paper not published yet” was the primary reason. All of these folks expressed willingness to share after publication. So the sharing rate will increase dramatically once all these papers come out. 20% directed me to another person who did not respond at all. Only 10% told me they were too busy. Another 10% said the data or the samples got messed up in some way and was not useful. Interestingly, medical problems were also cited as a reason for not sharing. There were actually two contacts that died unexpectedly during this period. I also want to say, as an aside, that we know there are large data sets that are not available to us because of legal reasons. They were part of the Natural Resources Damage Assessment. These data sets were not included in any of these statistics. This does not add up to 100. The last 15% was a combination of random, one-off reasons or folks being hesitant and not really giving a reason.
- A big impediment to data sharing is the lack of incentives for data providers. Why should anyone share? Funding agencies and publishers may mandate sharing. Sharing can increase citation rates and visibility within the community. In our case, we gave early access to the contributors. By sharing, we can develop more comprehensive, large-scale datasets that will allow us to address new challenges. Understanding the fate and transport of oil in the Gulf of Mexico is one of those challenges. Having an integrated database of the sort that we are building is the first step in improving the response to- and remediation of- oil spills. The panel shows an example of the LTRANS output compared to the field data in the database for Naphthalene. The red circles indicate field data where the analyte was detected. The open circles indicate field data where a measurement was taken and the analyte was not detected. The blue points are where LTRANS predicts that the analyte should be. This is an example of what can be achieved when data are shared and integrated.
- We have accomplished a lot, but we still have much to do to fulfill our goals. There will be a lot of additional data released over the next year that will be added to the database. We will be giving web access to the contributors and plan to incorporate their feedback to improve usability before opening to a wider audience. We are currently drafting and refining a users’ guide. There will be manuscripts published on the process of gathering data that I just described and a more technical paper on the database itself.
- Here is a list of all the data providers.As you can see, we have many. It takes a village to build a database.
- With that, I can take questions now or if you want to speak in more detail about this project or The Data Detektiv you can find me during breaks and poster sessionsat exhibitor booth #29.