Proposal to submit a manuscript on openTECR for the NAR Database Issue

[Robert Giessmann]

Dear Prof. Daniel J. Rigden,

We would like to propose the inclusion of our manuscript describing “openTECR”, the open Database on Thermodynamics of Enzyme-Catalyzed Reactions, in the upcoming database issue of NAR. You can find the abstract for this manuscript below, attached to the end of this email.

We have rigorously recurated the NIST Thermodynamics of Enzyme-Catalyzed Reactions database (TECRDB) in an unprecedented high quality. We improved the consistency of the data with the cited experimental literature, and developed an accessible and actively managed website for researchers to search and download experimental thermodynamic data.

This is a unique asset to the community because TECRDB is the largest database of experimental thermodynamic measurements, and is the basis of thermodynamic prediction tools such as eQuilibrator. However, NIST’s TECRDB provides only limited HTML-based access to the underlying data, which has led to various research teams independently web-scraping the database. Our openTECR database, in full cooperation with the developers of the original database, provides a standard for the community that can be useful to both experimentalists and computational researchers.

We also wish to highlight the fact that this effort has been undertaken by an international volunteer community and coordinated asynchronously over the past few years, representing a success story of scientific achievements through volunteer efforts.

Please let us know if we should proceed with submitting the manuscript.

With best regards,

Robert Giessmann, on behalf of the openTECR community

Title:

openTECR: A public catalog of experimental thermodynamic data of enzyme-catalyzed biochemical reactions

Abstract:

Enzyme-catalyzed metabolic reactions are ubiquitous in all domains of life, and the thermodynamics of these reactions is an essential aspect of understanding how they operate in a metabolic environment. However, published thermodynamic data for these biological reactions is sparse, heterogeneous, and often inaccessible. Robert Goldberg and colleagues published a collection of this data and the National Institute of Standards and Technology (NIST) developed a website to interface with this collection, termed TECRDB. But the database website is not developed further and its webpages have gradually corrupted and lost functionality and content over the years.

We therefore developed the “open database on Thermodynamics of Enzyme-Catalyzed Reactions” (openTECR) as a free and public resource for cataloging experimentally determined thermodynamic parameters. From a collection of over 1,000 publications, we curated a database with 5,565 data points, consisting of 773 enthalpy measurements and 4,792 measured equilibrium constants. In a first approach towards a continuously improving database, we re-curated the exact information given in the PDF version of TECRDB. We added links to the original source in the form of DOI and/or PMID and to the reaction in Rhea, where possible. This homogenized and accessible data will be invaluable for metabolic modeling and cheminformatics, among other fields. Our data set will further improve thermodynamic prediction tools such as eQuilibrator and dGpredictor and help pathway databases (e.g. Plant Reactome,  BioCyc, Reactome, etc.) to include additional information relevant to their users.

openTECR is the most comprehensive experimental database of thermodynamic metabolic data, adding 838 equilibrium constants and experimental conditions for an additional 239 enthalpy measurements relative to the best-known machine-readable data set. Our open source and open data initiative invites the community to contribute by submitting and curating new experimental data, as well as enhancing the user experience. The database is available at https://w3id.org/opentecr/tecrdb and can be downloaded as a single tabular file licensed under CC-0.

[Robert Giessmann]

Dear all,

As you can see, I submitted our proposal for inclusion of a manuscript to the executive editor of the NAR database issue.

Please be careful to not hit "reply all", including them with their email address narda...@gmail.com. ;) Thank you!

Best,

   Robert

[Daniel J. Rigden]

Dear Dr Geissmann

Thank you for your interest in the 2025NAR Database Issue.
Unfortunately, I will not be able to invite submission of your paper.

NAR annual Database Issue features well-designed Molecular Biology
databases intended for use by a wide variety of biologists, primarily
bench scientists looking for new convenient resources. We are mostly
interested in web-browsable databases that offer carefully curated
data that are not available elsewhere and which promise to be useful
to the wide readership of NAR.

Although I do appreciate the work that went into creation of your web
site and understand the value of your database for some users, I am
afraid that the online implementation is far too primitive to pass muster.

I understand the historical element here but here, for example

the first five columns are meaningless to the average browser (and

there's no tutorial, help, FAQ), there should be links out from the papers etc

And when you say the data are from over 1000 papers, that compares

unfavourably with the 1000 papers mentioned in the abstract of the now 

20-year old original paper. Of course, I understand the value of the data so

a more up-to-date database with a more comprehensive website could

be of future interest.

You might also want to try submitting to our sister journal "Database
(Oxford)" (http://database.oxfordjournals.org/) that is being produced
by the same team at the same publisher, Oxford University Press.
"Database (Oxford)" covers a variety of subjects related to biomedical
databases and is not limited to a single issue per year; its full content is now
included in PubMed and PubMed Central.

I am sorry not to be able to give you a more positive response.

Best wishes,
Daniel Rigden

--

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Prof. Daniel J. Rigden
Executive Editor, NAR Database Issue
University of Liverpool, UK
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[Robert Giessmann]

Dear Prof. Rigden,

Thank you very much for your very swift and detailed (and painfully correct...) assessment of our resource!

I acknowledge your decision to not invite submission this year.

If you allow, I would like to seize the opportunity to provide some more context about our work, with the intention to prepare some common ground regarding a possible re-submission for the 2026 issue.

You are very right that our online implementation is very primitive. The NIST database was primitive, too -- but of course this cannot be an excuse for our own implementation (screenshot of NIST's version at https://randr.nist.gov/ here:
)

We neglected the web implementation aspect shamefully, because we are a community of volunteers, who are mostly focused on the accuracy of the actual data, not too much on its representation. This felt natural to us, using this data ourselves in our work. We are by far no web designers, and did not have access to people with a more visual mindset so far. But you are right, for a public presentation the user experience should be much more intuitive and we should have invested more time into FAQ and help sections.

That is also why we wanted to reach out to the public with an article in NAR (which is the most respected publishing outlet on databases in our eyes): to invite further members to help us improve our resource. So far, we experienced that it is difficult to attract new people without being able to show any product or respectable publication about our work.

Regarding the 1000 papers, there is indeed room for more. We have already curated data from 15 additional papers (which, of course, is little compared to the immense amount of data already curated). To lay a foundation for additional curation, however, we wanted to focus first on the historical, already available data, and bring them in good shape. 

The data for the 1000 papers are actually only accessible from a set of 7 pdf files. The majority of the PDFs, however, are not searchable well because the text and tables within them are actually scanned images. The NIST database itself does not contain all data in the pdf files, partly probably due to human error, partly due to discontinued funding.

Taking your feedback into account, I feel our way forward is to improve our web presence over the upcoming year. We would be very happy to ask for an invitation regarding an improved version next year. Your feedback is very valuable in pointing out in which direction we have to head -- thank you so much!

A possible inclusion in NAR's Database Issue motivates us very much to continue our work. 

If you feel that our resource cannot possibly reach the relevance necessary for an inclusion in NAR's database issue, please let us know. To be very honest, a submission to "Database" feels for me like "we couldn't make it to the top" and "we didn't try hard enough", so your journal remains our top choice. But if you feel that our data is of too narrow relevance to ever get included in NAR's database issue, we could start a submission to Database soon.

Your feedback would be very much appreciated!

Thanks again for the time you invested already, and all the best,

    Robert

[Daniel J. Rigden]

Dear Dr Giessmann

I think the level of interest in (expressed as citation of) the original paper, while not outstanding, certainly suggests there's an interested body of users out there. And NAR will always be interested in databases that offer unique and fundamentally important information: I think you're in that category. However, as I say, the completeness of the information (here meaning pretty comprehensive mining of data generated since the original publication) is key so I'm afraid a re-presentation of largely the original data would not cut it. And a good web interface would be required - as for any database - before I could invite a submission.

In terms of journals, I would say Database is a decent option worth consideration, albeit without the cachet of NAR: you might well find they are open to a publication sooner that would help build a critical mass of people in your venture. It's relatively common for databases that publish in Database, where citation data demonstrate strong interest, to move to NAR with Update papers after a number (>=2) of years.

Good luck!

Daniel Rigden

[Robert Giessmann]

Dear Prof Ridgen,

Many thanks for your advice! That helps me to understand where we stand, indeed.

I guess we should take your advice and run with it, reaching out to you in a couple of years again. :)

Thank you so much for your candid assessment and your honesty!

Best,

   Robert