Insect goo aids biodiversity research Apologies to Jonathan Eisen (see Badomics in the journal), but today in GigaScience we publish a new “squishomics” approach for assessing and understanding biodiversity, using the slightly wacky sounding method of combining DNA-soup made from crushed-up insects and the latest sequencing technology.
The new look Biodiversity Heritage Library includes articles extracted from BioStor, which is a step forwards in making the "legacy" biodiversity literature more accessible. But we still have some way to go. In particular the articles lack the obvious decoration of a modern article, the DOI.
The worm that turned (epigenetics) GigaDB, GigaScience ’s associated database, has had a number of new datasets just added, many for data types previously not hosted. Today marks the publication of new research in our sister BMC journal Genome Biology shaking up the epigenetics field by shattering the assumption that DNA methylation is absent in nematodes.
Quick note that as much as I like that the Biodiversity Heritage Library is using DOIs, they are generating them for publications that already have them (or are acquiring them from other sources). For example, here are the two DOIs for the same article (formatted using the DOI Citation Formatter), one from BHL and one from the Smithsonian:The BHL DOI resolves to a page in BHL, the other DOI resolves to the a page in the Smithsonian Digital
Quick thoughts on the recent announcement by figshare and F1000 about the new journals being launched on the F1000 Research site. The articles being published have data sets embedded as figshare widgets in the body of the text, instead of being, say, a static table. For example, the article:has a widget that looks like this:You can interact with this widget to view the data.
Quick note that Morgan Jackson (@BioInFocus) has written nice blog post Citations, Social Media & Science inspired by the fact that the following paper:Kwong, S., Srivathsan, A., & Meier, R. (2012). An update on DNA barcoding: low species coverage and numerous unidentified sequences. Cladistics, no–no. doi:10.1111/j.1096-0031.2012.00408.xcites my "Dark taxa" in the body of the text but not in the list of literature cited.
A correspondence we have contributed to has just been published in the BMC Research Notes “Data standardization, sharing and publication series” on the adventures in data-citation and data-release practices surrounding the Sorghum genome that is available in our GigaDB database and that was published last year in Genome Biology . We use Sorghum as an example to highlight the issues surrounding data release and use strong words,
Based on recent discussions my sense is that our community will continue to thrash the issue of identifiers to death, repeating many of the debates that have gone on (and will go on) in other areas. To be trite, it seems to me we have three criteria: cheap , resolvable , and persistent . We get to pick two. Cheap and resolvable means URLs, which everybody is nervous about because they break.
Another incremental step has been achieved for the adoption of the practice of data citation; this week, Nature Biotechnology has included one of our dataset DOIs in their references for the first time.