National Academies Press: OpenBook

Designing the Microbial Research Commons: Proceedings of an International Symposium (2011)

Chapter: 22. Accessing Microbiological Data: A User's Perspective

« Previous: 20. Microbial Commons: Governing Complex Knowledge Assets
Suggested Citation:"22. Accessing Microbiological Data: A User's Perspective." National Research Council. 2011. Designing the Microbial Research Commons: Proceedings of an International Symposium. Washington, DC: The National Academies Press. doi: 10.17226/13245.
×

22. Accessing Microbiological Data: A User’s Perspective
– Mark Segal
49

Environmental Protection Agency

My purpose today is to demonstrate that there is a potential user community for the microbial research commons that goes beyond researchers—that there is a cohort of us who are primarily users, not suppliers of data. At the same time, however, some of our needs may be the same as, or similar to, the needs of researchers.

I will begin by giving you some examples of people, like myself, who are included in that cohort. I am a scientist doing science, but within government. I work within a regulatory organization, and I am part of a scientific support group for the people who actually do the regulation writing. There are other scientists who are not also primarily researchers yet are potential users of the kinds of data and information that the commons can make more accessible. Some governments or parts of governments hire scientists to provide analyses, rather than employ them directly. These scientists may provide similar functions to mine while under contract. Besides analysts who support governmental actions, there are scientists responsible for funding research who could benefit from improved data access. Outside government, there are a number of other analysts, including those at commercial think tanks and non-governmental organization staff or NGOs who may benefit from use of consolidated microbiological information. Finally, those employed by various media to report on science issues may find it necessary to get deep into the details of given projects in order to present the results in an accurate manner to the public.

Box 22–1 illustrates the range of data types that make microbiologists remarkable in the diversity of information they must utilize.

Box 22-1

Range of Data and Information Types Routinely Used by Microbiologists

– Text

– Numerical

– Binary

– Graphical

• Images

– Macroscopic (e.g., colony morphology)

– Microscopic (e.g., cell structure)

• Charts and graphs

• Diagrams and Cartoons

• Molecular structures

– Sequence

At some point in our careers we use just about everything that is on this list, so the commons will have to deal with as wide a range of data as is ever encountered in science.

_____________

49 Presentation slides available at: http://sites.nationalacademies.org/xpedio/idcplg?IdcService=GET_FILE&dDocName=PGA_053678&RevisionSelectionMethod=Latest.

Suggested Citation:"22. Accessing Microbiological Data: A User's Perspective." National Research Council. 2011. Designing the Microbial Research Commons: Proceedings of an International Symposium. Washington, DC: The National Academies Press. doi: 10.17226/13245.
×

I am going to use myself as an example to illustrate where the microbial commons can be useful. Box 22–2 lists some areas of microbiology in which people in the categories previously described could be interested.

BOX 22–2
Areas of Interest in Microbiology

• Public health and pandemics

    – Analysis of outbreaks

    – Evaluation of drugs and vaccines

• Food security

    – Evaluation of products of food biotechnology

    – Diagnostics

    – Antiterrorism

• Bioremediation

    – Evaluation of microorganisms used for cleanup

• Biofuel and bioproducts

    – Evaluation of microorganisms used to make biocatalysts, enzymes

    – Evaluation of microorganisms used to make fuels

    – Evaluation of microorganisms used to make chemical substances

Specifically, bioremediation and biofuels or bioproducts are products and processes in which I am closely involved. In particular, the items in these categories are examples of products or services provided by microorganisms that are subject to oversight by my organization. You can see that there is a wide range of potential commercial uses for which microbiological data made accessible through a commons could be used. I want to discuss the kinds of data and information that we have to deal with on a routine basis that could be made more accessible to us if the commons did exist and was in operation.

One of the things that we constantly have to deal with is knowing exactly which organism is being worked with when a submitter provides us with information on an organism. Has the submitter obtained an accurate species identification using the tools available to him? More often than not, commercial organisms belong to that collection of open-genome organisms in which there is a broad range of entities falling within a genus or within a species, with lots of apparent gene exchange and a consequently diverse gene pool. These taxa would appear to have tiny core genomes compared to many genomes in genera that are less diverse. They often have lots of mobile genetic elements. Because of this diversity and especially if determinants used for identification reside on these elements, trying to identify the species of such an organism is a challenge. But, since much of the pan-genome gene pool is sharable, this can at least tell us the range of potential functions that may be expressed, regardless of the species name applied to the strain. Knowledge of the content of this gene pool is something we can work from. We understand about the utility of metadata—how it enables us to know where an organism came from, trace it back to its origins, and figure out what it did, or at least what its precursor did, in the natural environment. Because we deal with health and safety, environmental effects, and those kinds of things, there are different types of information that are useful to us: Where is the organism from? Was it part of an outbreak? Is it is known to be relatively safe when it or its precursors are used commercially? What else could the organism be used for besides what we are being told it might be used for?

We get our data from a variety of sources: the open literature, grey literature, company files, public data banks, and other Web resources. We are interested in various

Suggested Citation:"22. Accessing Microbiological Data: A User's Perspective." National Research Council. 2011. Designing the Microbial Research Commons: Proceedings of an International Symposium. Washington, DC: The National Academies Press. doi: 10.17226/13245.
×

issues concerning the sources of microbiological data. The participation of private-sector parties in a consortium raises issues, such as having data held confidentially. Classified data also would not be included within the commons. Nevertheless, we need to be able to integrate those data with what we can get from public sources.

Concerning the open literature, subscription costs may limit the number of subscriptions to journals and other sources that potential users can readily obtain. As journal costs to libraries increase, this circumstance may become critical for many parties. Language can be an issue. Some of the older articles are in languages that we may not be able to translate. Recently, I had to deal with an article in Portuguese. Fortunately, I had enough French to enable me to understand the key issues I was looking for. If the article were in some language that is outside the set of language skills possessed by our group of scientists, we would have to send it off for translation. That takes time we often cannot afford.

Grey literature poses problems, particularly in finding it. It often is not catalogued. Yet it may contain valuable information. When present on the Web, it often resides on obscure sites. The fact is, we ourselves generate grey literature. The assessments of our group become grey literature. Some portions are made public, but much of it is confidential because it may contain proprietary data and information. Only a few are permitted to see it. It is not easy for others to find our reports. So, anything that makes it easier for us to make our work available and to find work that is similar to ours elsewhere is going to help us.

We need to use databanks, but we know they may not be complete. We also know there may be accuracy issues. Many databanks need to be better curated than they are. Also, who is doing the annotations? Who is printing the information? How old is it? Sometimes we have the skill to recognize the errors, and sometimes not. In some cases, we heard the data were stove-piped, which can be a problem since the data are not connected with potentially related data, leading to a limited perspective. My group integrates a lot of different types of information, and so we tend to go across disciplines a lot. Getting past those barriers is critical. There were earlier examples in this symposium in which people are trying to break down these barriers. We encourage that, but wish there was more of it.

How can we, the data users, benefit from the commons? Overall, having access to researchers and other data users is certainly going to help us. If we were able to have one-stop shopping—having portals that allow us to move back and forth among the range of data sources that we routinely use—that would be great.

We use many different digital information resources. Many of them are linked or are becoming linked, but sometimes the linkages are very awkward. It would help us tremendously if there were a way to navigate through the maze of data sources that are now out there, so that we could deal with them more easily than is possible now.

In what ways can we exert some influence on improving the situation? Can we do a better job, for instance, of getting our grey literature posted and accessible on the Web so that you can locate it? Can we find a way to limit the amount of data that is treated as confidential? We are trying to facilitate information sharing, as appropriate, so that our analyses can be made more transparent and so that the way in which we do our work can be better understood by others. Some of this is changing, but hopefully we can do more.

Suggested Citation:"22. Accessing Microbiological Data: A User's Perspective." National Research Council. 2011. Designing the Microbial Research Commons: Proceedings of an International Symposium. Washington, DC: The National Academies Press. doi: 10.17226/13245.
×

This page intentionally left blank.

Suggested Citation:"22. Accessing Microbiological Data: A User's Perspective." National Research Council. 2011. Designing the Microbial Research Commons: Proceedings of an International Symposium. Washington, DC: The National Academies Press. doi: 10.17226/13245.
×
Page 161
Suggested Citation:"22. Accessing Microbiological Data: A User's Perspective." National Research Council. 2011. Designing the Microbial Research Commons: Proceedings of an International Symposium. Washington, DC: The National Academies Press. doi: 10.17226/13245.
×
Page 162
Suggested Citation:"22. Accessing Microbiological Data: A User's Perspective." National Research Council. 2011. Designing the Microbial Research Commons: Proceedings of an International Symposium. Washington, DC: The National Academies Press. doi: 10.17226/13245.
×
Page 163
Suggested Citation:"22. Accessing Microbiological Data: A User's Perspective." National Research Council. 2011. Designing the Microbial Research Commons: Proceedings of an International Symposium. Washington, DC: The National Academies Press. doi: 10.17226/13245.
×
Page 164
Next: 23. The Microbial Commons: Journals and Professional Societies »
Designing the Microbial Research Commons: Proceedings of an International Symposium Get This Book
×
Buy Paperback | $55.00 Buy Ebook | $43.99
MyNAP members save 10% online.
Login or Register to save!
Download Free PDF

Recent decades have witnessed an ever-increasing range and volume of digital data. All elements of the pillars of science--whether observation, experiment, or theory and modeling--are being transformed by the continuous cycle of generation, dissemination, and use of factual information. This is even more so in terms of the re-using and re-purposing of digital scientific data beyond the original intent of the data collectors, often with dramatic results.

We all know about the potential benefits and impacts of digital data, but we are also aware of the barriers, the challenges in maximizing the access, and use of such data. There is thus a need to think about how a data infrastructure can enhance capabilities for finding, using, and integrating information to accelerate discovery and innovation. How can we best implement an accessible, interoperable digital environment so that the data can be repeatedly used by a wide variety of users in different settings and with different applications?

With this objective: to use the microbial communities and microbial data, literature, and the research materials themselves as a test case, the Board on Research Data and Information held an International Symposium on Designing the Microbial Research Commons at the National Academy of Sciences in Washington, DC on 8-9 October 2009. The symposium addressed topics such as models to lower the transaction costs and support access to and use of microbiological materials and digital resources from the perspective of publicly funded research, public-private interactions, and developing country concerns. The overall goal of the symposium was to stimulate more research and implementation of improved legal and institutional models for publicly funded research in microbiology.

  1. ×

    Welcome to OpenBook!

    You're looking at OpenBook, NAP.edu's online reading room since 1999. Based on feedback from you, our users, we've made some improvements that make it easier than ever to read thousands of publications on our website.

    Do you want to take a quick tour of the OpenBook's features?

    No Thanks Take a Tour »
  2. ×

    Show this book's table of contents, where you can jump to any chapter by name.

    « Back Next »
  3. ×

    ...or use these buttons to go back to the previous chapter or skip to the next one.

    « Back Next »
  4. ×

    Jump up to the previous page or down to the next one. Also, you can type in a page number and press Enter to go directly to that page in the book.

    « Back Next »
  5. ×

    Switch between the Original Pages, where you can read the report as it appeared in print, and Text Pages for the web version, where you can highlight and search the text.

    « Back Next »
  6. ×

    To search the entire text of this book, type in your search term here and press Enter.

    « Back Next »
  7. ×

    Share a link to this book page on your preferred social network or via email.

    « Back Next »
  8. ×

    View our suggested citation for this chapter.

    « Back Next »
  9. ×

    Ready to take your reading offline? Click here to buy this book in print or download it as a free PDF, if available.

    « Back Next »
Stay Connected!