Letter to Editors
Discussion on the list resulted in a draft of a letter to editors and/or publishers asking for collaboration in providing a complete and accurate annotation of all the molecular species and gened discussed in each published paper. The most recent version of this letter and a list of signatures is provided below. MSWord version of the letter can be downloaded from here . The letter refers to the original initiative of TAIR that resulted in a collaboration with Plant Physiology. It is intended to demonstrate a community-wide support when contacting other journals.
We, the undersigned members of the community of biological database curators and developers, invite you to join a collaboration to improve access to and organization of biological data.
The huge volume of biological data would be nearly impenetrable without organization and synthesis. Biological databases, such as those we represent, provide an essential service by organizing, archiving, and unifying these data. With a few exceptions, this organization is achieved through manual curation of the published literature. That is, we read each paper, filter through its contents, and record the pertinent information.
Although different databases extract different information, we all rely on clear and unambiguous identification of the genes, macromolecules, metabolites, and chemicals under study. Unfortunately, we regularly encounter papers with missing or ambiguous information (1,2, 3), which slows or prevents curation, and reduces our ability to cover the breadth of known biology.
We therefore suggest a collaboration with your journal, to incorporate the direct submission of gene/biomolecule names, identifiers, and source organisms into your editorial review process for research articles. At http://imex.mbi.ucla.edu/MIMIX/Annotate.cgi , we provide an example web form that could be added to an online submission & review process. This form is similar to one already in use through a collaboration between the journal Plant Physiology and the database TAIR (4). We feel that requiring this information strikes a good balance between improving the accuracy and completeness of curated data and minimizing the burden on authors and editors.
While such a system will benefit us, it will also benefit (journal/publisher), your authors, and the scientific community. Clear identification of biological components will ensure that your authors and publications can be cited in our databases, thereby increasing their visibility. We will also be able to curate more articles more quickly, allowing our databases to provide a more complete picture of biology for the scientific community at large. In addition, readers of the articles will directly benefit from knowing, unambiguously, what biological components are being studied.
We look forward to working with you to make this vision a reality.
(1) Bartsch, S. et al. 2008. Three thioredoxin targets in the inner envelope membrane of chloroplasts function in protein import and chlorophyll metabolism. PNAS 105(12):4933-8. This paper reports studies on plant thioredoxins, but identifies neither the source organism(s) nor the identities of the specific thioredoxin proteins studied. A cited paper (Balmer, Y. et al. 2003. Proteomics gives insight into the regulatory function of chloroplast thioredoxins. PNAS 100(1):370-5.) is equally uninformative.
(2) Gestaut, DR. et al. 2008. Phosphoregulation and depolymerization-driven movement of the Dam1 complex do not require ring formation. Nat Cell Biol. 10(4):407-14. There is no report of the source organism for the Dam1 complex under study. There is also no reported ORF identifier, accession number, or other unambiguous or organism-specific identifier. While the proteins shown in Figure 1a have the same names as the Saccharomyces cerevisiae Dam1 complex, there is a related Schizosaccharomyces pombe protein also called Dam1. Although the bibliography cites papers on S. cerevisiae Dam1, and there are keywords in Medline for "Saccharomyces cerevisiae" and "Saccharomyces cerevisiae Proteins," the microtubules purified for the reported assays are from cow.
(3) Cerpa, W. et al. 2008. Wnt-7a modulates the synaptic vesicle cycle and synaptic transmission in hippocampal neurons. J Biol Chem. 283(9):5918-27. There is no mention of the species of the cDNAs used in the paper. A note in the paper refers to the Wnt-7a construct as a gift from another scientist, a search of whom led to the following paper: Lucas, F.R. and Salinas, P.C. 1997. WNT-7a induces axonal remodeling and increases synapsin I levels in cerebellar neurons. Dev Biol. 192(1):31-44. This second paper has no mention of species and no reference for the Wnt-7a cDNA, nor does it report the cloning of the Wnt-7a cDNA.
(4) See Plant Physiology 146:1022-1023 (2008) for a description of this collaboration. The web form can be viewed at http://www.aspb.org/publications/tairsubmission.cfm.