Dear Haloferax researcher,

My name is Ron Caspi, and I am the curator of the MetaCyc database (metacyc.org). My colleague Wai Kit Ong and I are about to propose a new archaeal resource to the National Science Foundation (NSF), and we would like to ask for your support in the form of a letter of collaboration if you find the proposed resource useful.

I have known Friedhelm Pfeiffer for many years through my work as a member of the Enzyme Commission (EC), and when I contacted him about the project, he told me about the Haloferax community mailing list. Friedhelm has introduced me to Thorsten and as both of them are supportive of the project, it was decided to give me the opportunity to contact you via the mailing list, for which I am very grateful.

Despite being a significant and extremely important part of the microbial ecosystem in almost all environments, resources for archaeal research are limited. As far as we know, there are currently no resources dedicated to archaeal metabolism. Some databases are available, but they are based on the initial genome annotation, and thus contain many errors and omissions and often miss data that journal articles reported years ago. We intend to submit to NSF a proposal for the development of a one-stop encyclopedic resource for the archaeal domain that is complete with a mature set of bioinformatics tools to help guide exploration and analysis of the available organisms. We propose to generate and manually curate 53 high-quality Pathway/Genome Databases (PGDBs) that will include representative species of all main archaeal phylogenetic groups as well as the better-studied archaeal species. The new archaeal PGDBs will be hosted at the BioCyc<https://biocyc.org/> Portal. Each PGDB will integrate the genomic information of a single organism (e.g., genome sequence, transcription units, encoded proteins) with the inferred metabolic network (e.g., chemical reactions, transport reactions, metabolic pathways). The curation process will include manual curation of the available published literature, resulting in textbook-style summaries for studied enzymes and pathways. By hosting the databases at the BioCyc Portal, users will be able to take advantage of the numerous existing visualization and analysis tools available at the site (e.g., omics data analysis and comparative analyses).

We will also build manually curated genome-scale metabolic network models for those organisms with sufficient experimental data to support it, to enable a systems-level study of the organism’s metabolism. For those archaea with insufficient experimental data, we will generate reports summarizing their predicted biosynthetic capabilities and suggest possible essential growth media components.

In addition to the impact of this project on archaeal research, we hope that archaeal researchers who teach will adapt the resource as an educational tool. The new archaeal databases and metabolic models will provide a solid foundation for the development of teaching curricula, enabling the students to discover the unique metabolism of archaeal species in an exploratory manner. An example for such use can be seen at the E. coli student portal<http://ecolistudentportal.org/>, which takes advantage of our E. coli database, EcoCyc.

Would you be willing to help us by answering questions about your field of expertise in case we encounter them during curation of that database? Our curators are experienced PhD level scientists, so we promise that the questions will be few and not frequent. If relevant, would you be willing to review entries that were written specifically about proteins that you have studied?

If you agree, we kindly ask you to write a letter of collaboration that we could include in our proposal, in which you confirm that you are willing to provide expert advice. NSF has strict rules for such letters, so the text must be as follows:

To the National Science Foundation (NSF)

If the proposal submitted by Drs. Ron Caspi and Wai Kit Ong (SRI International, Menlo Park, CA) entitled “High Quality Pathway/Genome Databases and Metabolic Models for Archaea”, is selected for funding by the NSF, it is my intent to collaborate as detailed in the Project Description or the Facilities, Equipment and Other Resources section of the proposal.

Accordingly, we will state in the proposal that you have agreed to provide expert advice during curation. We would be extremely grateful if you could email such a letter, printed on your institution’s letterhead, to [log in to unmask]<mailto:[log in to unmask]>, by the 30th of September.

We hope that you will be willing to give us your support and look forward to working together to establish what we believe would be a very valuable resource to the archaeal community.

Best regards,
Ron Caspi and Wai Kit Ong

Bioinformatics Research Group
SRI International
333 Ravenswood Ave, Menlo Park 94025
USA

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