Comments for I wish you'd made me angry earlier

Comment on Calvin Bridges, Automotive Pioneer by caseybergman

caseybergman — Sat, 15 Jun 2013 21:49:40 +0000

Thanks Margarida – I’m very much looking forward to seeing this film as well. The history of the early Drosophila researchers is something of a passion of mine, and to find a story like this is always very exciting. Glad you enjoyed it too!

Comment on Calvin Bridges, Automotive Pioneer by Margarida Cardoso Moreira

Margarida Cardoso Moreira — Sat, 15 Jun 2013 16:27:24 +0000

This is a really, really good story. Thank you for sharing it.

And thank you also for the heads up on the Fly Room movie. I hope it is as great as it could be.

Comment on From Electron to Retrotransposon: “-on” the Origin of a Common Suffix in Molecular Biology by Marc Perry

Marc Perry — Sun, 02 Jun 2013 07:15:41 +0000

A brilliant tour-de-force on the etymology of terms that a small number of us hold so near and dear. FYI: trans-splicing in nematodes (yes, thank you Seymour, trans as in the cis-trans test), lops off the 5′-UTR of the pre-mRNA, which is just upstream of the transcripts’ first exon. The discarded sequence has come to be called the “Outron” (admittedly among an extremely small group of people studying trans-splicing). This term was coined by Craig Hunter ~ 1990 when he was a grad student in Bill Wood’s lab. Tom Blumenthal (who was in the room at the time) adopted the term in his next publication.
While reading your post I was also reminded of a passage by the philosopher Richard Rorty: “The world does not speak, only we do.”

Comment on On The Neutral Sequence Fallacy by Reading list: unread | Annotary

Reading list: unread | Annotary — Fri, 31 May 2013 17:05:16 +0000

[…] Newest Oldest Title Publisher More from Daniel Standage: Miscellaneous Sort Share caseybergman.wordpress.com 1 minute […]

Comment on Twitter Tips for Scientific Journals by Interactions: May High Five | Altmetric.com

Interactions: May High Five | Altmetric.com — Thu, 30 May 2013 10:50:17 +0000

[…] attention paid to the paper appeared almost exclusively on social media (however, one blogger extended the advice for scientists detailed in the paper to journal staff), as one might have […]

Comment on Suggesting Reviewers in the Era of arXiv and Twitter by Twitter Tips for Scientific Journals | I wish you'd made me angry earlier

Twitter Tips for Scientific Journals | I wish you'd made me angry earlier — Thu, 23 May 2013 15:28:54 +0000

[…] to influence editorial or production processes, such as the acceptance/rejection of papers or choice of reviewers. Information on social media could be incorrect and by using unverified information from Twitter […]

Comment on Why Are There So Few Efforts to Text Mine the Open Access Subset of PubMed Central? by Launch of the PLOS Text Mining Collection | I wish you'd made me angry earlier

Wed, 17 Apr 2013 21:10:57 +0000

[...] 1. Dickman S (2003) Tough mining: the challenges of searching the scientific literature. PLoS biology 1: e48. doi:10.1371/journal.pbio.0000048. 2. Rebholz-Schuhmann D, Kirsch H, Couto F (2005) Facts from Text—Is Text Mining Ready to Deliver? PLoS Biol 3: e65. doi:10.1371/journal.pbio.0030065. 3. Cohen B, Hunter L (2008) Getting started in text mining. PLoS computational biology 4: e20. doi:10.1371/journal.pcbi.0040020. 4. Bourne PE, Fink JL, Gerstein M (2008) Open access: taking full advantage of the content. PLoS computational biology 4: e1000037+. doi:10.1371/journal.pcbi.1000037. 5. Rzhetsky A, Seringhaus M, Gerstein M (2009) Getting Started in Text Mining: Part Two. PLoS Comput Biol 5: e1000411. doi:10.1371/journal.pcbi.1000411. 6. Rodriguez-Esteban R (2009) Biomedical Text Mining and Its Applications. PLoS Comput Biol 5: e1000597. doi:10.1371/journal.pcbi.1000597. 7. Kim D, Yu H (2011) Figure text extraction in biomedical literature. PloS one 6: e15338. doi:10.1371/journal.pone.0015338. 8. Boyack K, Newman D, Duhon R, Klavans R, Patek M, et al. (2011) Clustering More than Two Million Biomedical Publications: Comparing the Accuracies of Nine Text-Based Similarity Approaches. PLoS ONE 6: e18029. doi:10.1371/journal.pone.0018029. 9. Kolluru B, Hawizy L, Murray-Rust P, Tsujii J, Ananiadou S (2011) Using workflows to explore and optimise named entity recognition for chemistry. PloS one 6: e20181. doi:10.1371/journal.pone.0020181. 10. Hayasaka S, Hugenschmidt C, Laurienti P (2011) A network of genes, genetic disorders, and brain areas. PloS one 6: e20907. doi:10.1371/journal.pone.0020907. 11. Roque F, Jensen P, Schmock H, Dalgaard M, Andreatta M, et al. (2011) Using electronic patient records to discover disease correlations and stratify patient cohorts. PLoS computational biology 7: e1002141. doi:10.1371/journal.pcbi.1002141. 12. Salathé M, Khandelwal S (2011) Assessing Vaccination Sentiments with Online Social Media: Implications for Infectious Disease Dynamics and Control. PLoS Comput Biol 7: e1002199. doi:10.1371/journal.pcbi.1002199. 13. Baran J, Gerner M, Haeussler M, Nenadic G, Bergman C (2011) pubmed2ensembl: a resource for mining the biological literature on genes. PloS one 6: e24716. doi:10.1371/journal.pone.0024716. 14. Fisher R, Knowlton N, Brainard R, Caley J (2011) Differences among major taxa in the extent of ecological knowledge across four major ecosystems. PloS one 6: e26556. doi:10.1371/journal.pone.0026556. 15. Hossain S, Gresock J, Edmonds Y, Helm R, Potts M, et al. (2012) Connecting the dots between PubMed abstracts. PloS one 7: e29509. doi:10.1371/journal.pone.0029509. 16. Ebrahimpour M, Putniņš TJ, Berryman MJ, Allison A, Ng BW-H, et al. (2013) Automated authorship attribution using advanced signal classification techniques. PLoS ONE 8: e54998. doi:10.1371/journal.pone.0054998. 17. Acerbi A, Lampos V, Garnett P, Bentley RA (2013) The Expression of Emotions in 20th Century Books. PLoS ONE 8: e59030. doi:10.1371/journal.pone.0059030. 18. Groza T, Hunter J, Zankl A (2013) Mining Skeletal Phenotype Descriptions from Scientific Literature. PLoS ONE 8: e55656. doi:10.1371/journal.pone.0055656. 19. Seltmann KC, Pénzes Z, Yoder MJ, Bertone MA, Deans AR (2013) Utilizing Descriptive Statements from the Biodiversity Heritage Library to Expand the Hymenoptera Anatomy Ontology. PLoS ONE 8: e55674. doi:10.1371/journal.pone.0055674. 20. Van Landeghem S, Bjorne J, Wei C-H, Hakala K, Pyysal S, et al. (2013) Large-Scale Event Extraction from Literature with Multi-Level Gene Normalization. PLOS ONE 8: e55814. doi:10.1371/journal.pone.0055814 21. Liu H, Hunter L, Keselj V, Verspoor K (2013) Approximate Subgraph Matching-based Literature Mining for Biomedical Events and Relations. PLoS ONE 8(4): e60954. doi:10.1371/journal.pone.0060954 22. Davis A, Weigers T, Johnson R, Lay J, Lennon-Hopkins K, et al. (2013) Text mining effectively scores and ranks the literature for improving chemical-gene-disease curation at the Comparative Toxicogenomics Database. PLOS ONE 8: e58201. doi:10.1371/journal.pone.0058201 23. Bergman CM (2012) Why Are There So Few Efforts to Text Mine the Open Access Subset of PubMed Central? http://caseybergman.wordpress.com/2012/03/02/why-are-there-so-few-efforts-to-text-mine-the-open-acce…. [...]

Comment on Announcing the PLoS Text Mining Collection by Launch of the PLOS Text Mining Collection | I wish you'd made me angry earlier

Wed, 17 Apr 2013 21:10:10 +0000

[...] PLOS Collection arose out of a twitter conversation with Theo Bloom last year, and has come together through the hard work of the authors of the papers in the [...]

Comment on On the Preservation of Published Bioinformatics Code on Github by Phillip Lord

Phillip Lord — Tue, 02 Apr 2013 09:02:26 +0000

DOIs are not unique. It is straight-forward to award multiple DOIs for the same object, and there is not restriction within the DOI system which prevents this. CrossRef DOIs do have a “we will fine you if you do this” post-hoc system for preventing this. But, then, Figshare is not using CrossRef DOIs. And even with CrossRef this requires an definition of equality between two papers. So, you can have multiple identifiers for a single entity.

Obtaining a unique ID in the other sense; yes, in some ways, this has an advantage, although you are dependant totally on figshare maintaining their DOIs. They don’t have to, and can break the link any time that they choose. Or, indeed they can point it at anything they like. You are not paying them, so, you have no control over this.

Finally, their supposed utility works on the basis that people actually use them. Given that it’s easier to cut and paste the URL from the title bar, why would they not do this?

Where I need a stable identifiers — for example for an ontology — then I use purls. These work perfectly well; here I avoid the last problem because ontology URls are not used in a browser.

Comment on On the Preservation of Published Bioinformatics Code on Github by Karthik Ram

Karthik Ram — Thu, 28 Mar 2013 18:50:55 +0000

Once it’s on Figshare, though, a git repository is a dead entity. Not clonably, forkable or accessable by git.In otherwords, you are archiving a different thing.

Yes, agreed. The only advantage here is for the CLOCKSS backup in case the original git repository disappears. If there is a viable and open source alternative to GitHub (I know of a few but haven’t tried them myself), it would be great if research libraries and journals forked copies after publication (with appropriate git tags) to their servers. Good point re: licensing.