Please give feedback on the manuscript proposal abstract

[Robert Giessmann]

Dear all,

As you probably know, we want to submit an abstract on the re-curation work done at the beginning of this year.

We need to send a pre-submission inquiry to NAR by July 1st -- and this text reads currently as follows:

openTECR: laying the foundation for Open Thermodynamics of Enzyme-Catalyzed Reactions

Thermodynamics data is one key to understanding metabolism. However, data on the thermodynamics of biologically relevant molecules is sparse and hard to locate. NIST provides a set of reviews on this topic, but abandoned their online database, which led us to this work.

From a set of >1000 publications, we curated a database consisting of 5565 data points, of which 773 concern enthalpy measurements and 4792 concern equilibrium constants. We cleaned the database from inconsistencies and duplicates and augmented our dataset with links (DOI and PMID) to the respective primary literature. This data will be invaluable for metabolic modeling and cheminformatics among other fields, and will be integral to thermodynamic prediction tools such as eQuilibrator and dGpredictor. 

There is no other database with such a high number of data points about experimental measurements of thermodynamic data about metabolites. In comparison to the most well-known previously available machine readable data set, our database adds an additional 838 equilibrium constants and experimental conditions for an additional 239 enthalpy measurements.

Our open-source effort invites community contributions by submitting and curating new experimental data and further developing the user experience. The database is currently available on the web at https://w3id.org/opentecr/tecrdb and can optionally be downloaded as a single tabular file.

Do you see problems with the text? It is available for commenting / editing here: https://docs.google.com/document/d/15pbGxppRh6AglC9c1Fw0ri4xdSv8KfIhsuTB3VHHp3Q/edit 

In the Google Docs you also find the currently planned storyline for the paper itself. If you have time to give feedback on that, this is also very much appreciated :)

Thanks and best,

   Robert

[Maren Philipps]

Hi Robert,

thanks for sharing! I do not see an issue with the text. I left some
feedback in the Google Doc but it's very subjective; feel free to consider
it or just dimiss as you see fit.

Best, Maren


On Do, 13 Jun 2024 10:48:32 +0200

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[Naithani, Sushma]

Hi Robert,

I have added a few suggestions in the Google doc on abstract and in the overall draft-structure and headings.

Typically, the NAR database papers do not have M&M or Results, Discussion headings.

It may help to look into couple of papers published last year by NAR database issue.

Here is link for one that we published

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10767815/

Best wishes

Sushma

Sushma Naithani (she/her), Ph.D.

Associate Professor (Sr. Res.), Plant Genomics and Bioinformatics

Lead Biocuration Scientist for Plant Reactome Knowledgebase

4619 Cordley Hall, 

Dept. of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331

Phone: +1-541-737-8022 I E-mail: sushma....@oregonstate.edu   

webpage: https://agsci.oregonstate.edu/users/sushma-naithani 

PubMed I  Google Scholar I ORCID

---

From: Robert Giessmann <rgies...@gmail.com>
Sent: Thursday, June 13, 2024 1:48 AM
To: openTECR: Open Database of Thermodynamics of Enzyme-Catalyzed Reactions <open...@googlegroups.com>
Subject: Please give feedback on the manuscript proposal abstract

 

[This email originated from outside of OSU. Use caution with links and attachments.]

[Melanie Stefan]

Great work thank you Robert and team! I have added a few suggestions on the google doc, but it looks quite good to me!

Melanie

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Professur für Physiologie 
Medical School Berlin
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[Robert Giessmann]

Dear all,

I am somewhat overwhelmed by the loads of feedback you provided. We can for sure send out the proposal text to the NAR office.

About the full submission, I want to raise the flag already: I don't think I can manage this. My schedule is pretty full till then, my family and I have vacations planned during July, and I need to keep an eye on my health and energy to be able to serve this community in the long run, too. I also want to respect all your feedback, and there is lots of it. :)

At the present point, I would suggest that we send out the proposal to see if our resource would get included at all. If anyone of you would like to and is able to finish the manuscript, that would be great, but otherwise I think a more realistic time is something like the end of September. 

I feel that otherwise I cannot do justice to the topic and our effort.

Sorry that I let you down now, but I think that this is the smarter approach for the long run. I hope you understand. Let me know what you think!

Best,

   Robert

[A. Freiburger]

Hello Robert!

Thank you for your candid assessment!   I merged the abstract suggestions and drafted a message to the NAR DI editor in the Google Docs.    I may be able to draft the manuscript, but I agree that we should send the proposed topic to the editor before we begin writing the manuscript.    Can you review the latest draft?   I can provide additional edits as are needed, since I have some time over the next weeks and months until September. 

Thank you for all of your service to the community :)

    Andrew