Predictive Workshop Worksheet

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Please find below worksheets that we have devised to aid our discussions on June 20. Because of other commitments by the participants, we are limited to one day in which we all convene. We wish to make the workshop as productive as possible and, in this context, ask you to take the time to work on the metabolic "puzzles" and questions regarding your logical processes below. We ask that you fax us your responses by June 15 to the Ellis Laboratory at (612) 625-1121. We will then organize the responses and share all the information with you for our discussions on June 20.

It is our goal to have a completely open process, without proprietary restraints, and this is reflected in choosing well-known compounds and our plan to publish significant findings, in paper- and web-format, that result from our discussions. We anticipate that everyone who contributes metabolic pathway and computational representation ideas that go into the publication will be included as a coauthor. Dr. Wackett has begun to write a draft manuscript that highlights what we feel are some of the key concepts and we would like to add additional points that arise at the workshop and then circulate that to all the co-authors for consideration, editing, etc. In discussions with Ken Timmis, it was suggested that this might reach a good target audience as a Feature Article in ASM News, that goes to all members of the American Society for Microbiology. We would like to get everyone's thoughts on these matters relating to publication and try to reach a consensus at the end of the Workshop.

As mentioned in the Introduction, we appreciate you taking the time to work on this project. With over ten million organic compounds known and solid biodegradation information available for perhaps 0.05% of them, our collective ignorance is great. It is in this context that we at Minnesota think a concerted effort by the workshop participants can really make an impact. We hope that we will all learn from each other as we collectively attain goals that would be beyond any one person.

We have provided example worksheets for Fentichlor and Saccharine.

The worksheets are:

We ask that those of you with more experience in the computational representation of reaction information, in addition to, or instead of, working through the worksheets, please look at the examples and describe your thoughts on how the expert reasoning expressed in them can be captured for use in a computerized predictive system. We have left space for this on the worksheet and example forms.

Worksheet Instructions

To facilitate the discussion at the Workshop, we request that everyone draw a set of possible bacterial biodegradation pathways for each of the listed compounds. Please continue the pathway until the metabolism of the compound or fragment becomes obvious (e.g., enters intermediary metabolism) or until no further reactions are likely or known. We understand that many of these compounds are not completely biodegradable via known biochemical reactions. Please feel free to stop a pathway when you consider that appropriate or be creative in devising new plausible bacterial enzymatic transformations. The compounds were selected because they: (1) are considered environmental pollutants, (2) present different organic functional groups for your consideration, (3) contain features that would allow an experimental test of our predictions. One of them, hydroxypivaldehyde, was contributed by an industrial member of the UM-BBD user e-mail list.

After drawing a pathway(s) for each compound, we ask that you reflect upon the mental process you went through by answering the set of questions below. The questions are:

  1. What was the first thing you focussed on to guide your development of a pathway(s)? Be specific please (most susceptible bond, least biodegradable part of the molecule, overall structure, visualizing an endpoint, i.e., metabolic intermediate, close to or in intermediary metabolism).
  2. How did you proceed after your initial focus point?
  3. How might this expert reasoning be captured for use in a computerized predictive system?
These questions are only meant to serve as a guide. When you are predicting metabolism, please record your own thought processes. There are probably many ways to arrive at developing a pathway. The best method may vary with the individual and their experience and it will likely vary for the same individual considering different compounds. At this point, we wish to consider as wide a range of mental processes as possible so let your creativity roam. If you are considering computational approaches, include any you have used and if possible give strengths and weaknesses of different approaches.

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