A few days ago I got a message that made a big impact on my publication record in PubMed Central. My number of publications there went up by 85 in one fell swoop (see below for the list ...). Did I publish 85 new papers yesterday? No. But a journal in which I have been a co-author on many papers recently finally showed up in Pubmed Central. The journal is called Standards in Genomic Sciences
. The journal's scope is:
The goal of SIGS is to serve as an open-access, standards-supportive publication for rapid dissemination of concise genome and metagenome reports that comply with the emerging MIGS/MIMS standards, detailed standard operating procedures, meeting reports, reviews and commentaries, data policies, white papers and other gray literature that is relevant to genome sciences but currently absent from the scholarly literature.
Lots of jargon, I know. But you can ignore that. The reason I am writing here is that this journal is a place to publish what could be called "genome sequencing data reports." These reports are a way for data producers to describe, in a formal manner, their sequencing project - and to share - in a formal manner - not only the data but also metadata about the organism(s) sequenced and the methods used. As sequencing gets cheaper and easier, we need places for people to publish these types of "data papers" to both produce a citable unit with a DOI relating to the data, and to also share the details of the data production in a way that a simple Genbank entry does not.
One aspect of the papers in this "SIGS" journal is that they are being done in a way that is compliant with sets of standards for sharing metadata
about the organism and the project. I confess, when I first heard about these standards developments, I was bored almost to tears. But now I realize that this is a very important aspect of getting the most out of genome data. If people who sequence a genome not only release the sequence data, but also a table of information about the project, such as information about the organism (e.g., aerobic vs anaerobic, location of isolation) and about the data production (e.g., sequencing methods used) then people will be able to do high throughput analyses of these features. Then we will not just be looking at sequence but also connecting these sequences to organismal features. Right now that is very hard to do since genome data is rarely accompanied by machine usable information about the organism that has been sequenced.
Anyway - long story short - there will be a paper published in this journal for each genome being produced as part of the "Genomic Encyclopedia of Bacteria and Archaea
" project that I have been coordinating at the DOE Joint Genome Institute
in collaboration with the DSMZ
Today I am writing to recognize the people connected to this movement - the people who created the standards, the people who created and run the journal, and the people writing papers for this journal. All of them are to be commended for their vision and their dedication to openness. Thus I am giving George Garrity the EIC of SIGS
my "Open Access Pioneer Award
" for creating SIGS, making it an open access journal, for keeping it running and for getting its papers into Pubmed Central and soon Pubmed. Many others should be recognized too for their contribution to SIGS (see the whole list of founding members here
). I also should recognize Nikos Kyrpides
from the DOE JGI who helped coordinate the writing and submission of these papers along with Hans Peter Klenk
from the DSMZ. Without them, these papers would never have gotten out there. Plus I think some credit goes to Michigan State University and the Department of Energy which apparently are sponsors of SIGS